Starting phenix.real_space_refine on Sun Sep 13 09:51:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vyb_21457/09_2026/6vyb_21457.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vyb_21457/09_2026/6vyb_21457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vyb_21457/09_2026/6vyb_21457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vyb_21457/09_2026/6vyb_21457.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vyb_21457/09_2026/6vyb_21457.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vyb_21457/09_2026/6vyb_21457.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vyb_21457/09_2026/6vyb_21457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vyb_21457/09_2026/6vyb_21457.cif" } resolution = 3.2 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= -0.001 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 14245 2.51 5 N 3677 2.21 5 O 4347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22365 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7393 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 47, 'TRANS': 918} Chain breaks: 12 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 216 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 6865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6865 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 46, 'TRANS': 902} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 7281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 7281 Classifications: {'peptide': 960} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 47, 'TRANS': 912} Chain breaks: 11 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 278 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 7, 'ASP:plan': 13, 'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 143 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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 chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 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 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 chiralities: 2 Chain: "L" 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 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 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 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 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 chiralities: 10 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 6.07, per 1000 atoms: 0.27 Number of scatterers: 22365 At special positions: 0 Unit cell: (126, 131.25, 182.7, 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 96 16.00 O 4347 8.00 N 3677 7.00 C 14245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.22 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 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=1.67 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=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.20 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=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1316 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1314 " - " ASN B1074 " " NAG B1319 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1315 " - " ASN C1074 " " NAG C1320 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1098 " " NAG O 1 " - " ASN C1134 " Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.2 seconds 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5404 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 43 sheets defined 26.5% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.573A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.396A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.660A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 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 760 through 783 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.852A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.140A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.253A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.662A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.148A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.946A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.893A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.080A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.501A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 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 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.804A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.197A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.997A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.552A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.937A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.287A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.302A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.170A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.444A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (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 654 through 655 removed outlier: 5.956A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.824A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.427A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.427A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.419A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.602A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.153A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.527A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.307A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.765A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.234A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.913A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.359A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.359A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.321A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.602A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.195A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.551A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.410A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.733A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.130A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.130A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.337A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.108A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.819A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.985A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.344A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.733A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1018 hydrogen bonds defined for protein. 2823 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: 5.71 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6444 1.33 - 1.47: 6606 1.47 - 1.61: 9648 1.61 - 1.75: 4 1.75 - 1.89: 117 Bond restraints: 22819 Sorted by residual: bond pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 1.516 1.348 0.168 2.50e-02 1.60e+03 4.52e+01 bond pdb=" NE ARG C 454 " pdb=" CZ ARG C 454 " ideal model delta sigma weight residual 1.326 1.381 -0.055 1.10e-02 8.26e+03 2.51e+01 bond pdb=" CB LEU B 242 " pdb=" CG LEU B 242 " ideal model delta sigma weight residual 1.530 1.614 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" CB HIS A1048 " pdb=" CG HIS A1048 " ideal model delta sigma weight residual 1.497 1.443 0.054 1.40e-02 5.10e+03 1.50e+01 bond pdb=" C CYS C 743 " pdb=" O CYS C 743 " ideal model delta sigma weight residual 1.235 1.283 -0.048 1.26e-02 6.30e+03 1.44e+01 ... (remaining 22814 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 30627 4.09 - 8.18: 469 8.18 - 12.27: 9 12.27 - 16.36: 1 16.36 - 20.44: 5 Bond angle restraints: 31111 Sorted by residual: angle pdb=" N ALA B1070 " pdb=" CA ALA B1070 " pdb=" C ALA B1070 " ideal model delta sigma weight residual 113.18 133.62 -20.44 1.33e+00 5.65e-01 2.36e+02 angle pdb=" N ALA C1070 " pdb=" CA ALA C1070 " pdb=" C ALA C1070 " ideal model delta sigma weight residual 112.72 130.02 -17.30 1.28e+00 6.10e-01 1.83e+02 angle pdb=" N GLN B1071 " pdb=" CA GLN B1071 " pdb=" C GLN B1071 " ideal model delta sigma weight residual 109.40 91.69 17.71 1.63e+00 3.76e-01 1.18e+02 angle pdb=" N GLN C1071 " pdb=" CA GLN C1071 " pdb=" C GLN C1071 " ideal model delta sigma weight residual 109.40 92.78 16.62 1.63e+00 3.76e-01 1.04e+02 angle pdb=" N THR B 124 " pdb=" CA THR B 124 " pdb=" C THR B 124 " ideal model delta sigma weight residual 113.28 125.33 -12.05 1.22e+00 6.72e-01 9.75e+01 ... (remaining 31106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 12542 17.97 - 35.95: 389 35.95 - 53.92: 80 53.92 - 71.89: 38 71.89 - 89.87: 20 Dihedral angle restraints: 13069 sinusoidal: 4722 harmonic: 8347 Sorted by residual: 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 -174.22 88.22 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 176.71 -83.71 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 174.10 -81.10 1 1.00e+01 1.00e-02 8.11e+01 ... (remaining 13066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 3791 0.315 - 0.629: 30 0.629 - 0.944: 0 0.944 - 1.258: 0 1.258 - 1.573: 1 Chirality restraints: 3822 Sorted by residual: chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-01 2.50e+01 6.18e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.73e+00 chirality pdb=" CA ALA B1070 " pdb=" N ALA B1070 " pdb=" C ALA B1070 " pdb=" CB ALA B1070 " both_signs ideal model delta sigma weight residual False 2.48 2.06 0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 3819 not shown) Planarity restraints: 3983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.057 2.00e-02 2.50e+03 5.77e-02 4.16e+01 pdb=" CG ASN A 331 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG A1306 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " 0.050 2.00e-02 2.50e+03 5.05e-02 3.19e+01 pdb=" CG ASN B 343 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " -0.077 2.00e-02 2.50e+03 pdb=" C1 NAG B1306 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.041 2.00e-02 2.50e+03 4.41e-02 2.43e+01 pdb=" CG ASN A 709 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.070 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " -0.054 2.00e-02 2.50e+03 ... (remaining 3980 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6121 2.82 - 3.34: 20155 3.34 - 3.86: 36890 3.86 - 4.38: 43741 4.38 - 4.90: 72533 Nonbonded interactions: 179440 Sorted by model distance: nonbonded pdb=" N ALA A 520 " pdb=" O ALA A 520 " model vdw 2.299 2.496 nonbonded pdb=" N GLN B1071 " pdb=" O GLN B1071 " model vdw 2.349 2.496 nonbonded pdb=" N GLN C1071 " pdb=" O GLN C1071 " model vdw 2.351 2.496 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.407 3.120 nonbonded pdb=" NZ LYS A 811 " pdb=" OD2 ASP A 820 " model vdw 2.424 3.120 ... (remaining 179435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 345 or (resid 346 through 360 and (name N or na \ me CA or name C or name O or name CB )) or resid 361 or (resid 362 through 378 a \ nd (name N or name CA or name C or name O or name CB )) or resid 379 or (resid 3 \ 80 and (name N or name CA or name C or name O or name CB )) or resid 381 or (res \ id 382 through 383 and (name N or name CA or name C or name O or name CB )) or r \ esid 384 or (resid 385 through 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or (resid 392 through 403 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 404 through 411 and (name N or name CA or \ name C or name O or name CB )) or resid 412 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 or (resi \ d 417 through 425 and (name N or name CA or name C or name O or name CB )) or re \ sid 426 through 427 or (resid 428 through 430 and (name N or name CA or name C o \ r name O or name CB )) or resid 431 through 432 or (resid 433 through 442 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 450 through 451 and \ (name N or name CA or name C or name O or name CB )) or (resid 453 and (name N \ or name CA or name C or name O or name CB )) or resid 463 or (resid 464 through \ 466 and (name N or name CA or name C or name O or name CB )) or resid 491 or (re \ sid 492 through 495 and (name N or name CA or name C or name O or name CB )) or \ resid 496 or (resid 497 through 498 and (name N or name CA or name C or name O o \ r name CB )) or resid 499 or (resid 500 through 503 and (name N or name CA or na \ me C or name O or name CB )) or (resid 504 through 506 and (name N or name CA or \ name C or name O or name CB )) or resid 507 or (resid 508 through 515 and (name \ N or name CA or name C or name O or name CB )) or (resid 522 through 524 and (n \ ame N or name CA or name C or name O or name CB )) or resid 525 through 528 or ( \ resid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 \ through 553 or (resid 554 and (name N or name CA or name C or name O or name CB \ )) or resid 555 through 793 or (resid 794 and (name N or name CA or name C or na \ me O or name CB )) or resid 795 or (resid 796 and (name N or name CA or name C o \ r name O or name CB )) or resid 797 through 810 or (resid 811 and (name N or nam \ e CA or name C or name O or name CB )) or resid 813 through 827 or resid 856 thr \ ough 866 or (resid 867 through 868 and (name N or name CA or name C or name O or \ name CB )) or resid 869 through 939 or (resid 940 and (name N or name CA or nam \ e C or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N o \ r name CA or name C or name O or name CB )) or resid 986 through 987 or (resid 9 \ 88 through 989 and (name N or name CA or name C or name O or name CB )) or resid \ 990 through 1141 or (resid 1142 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or \ name CA or name C or name O or name CB )) or resid 1147 through 1316)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 442 or resid 450 through 451 or resid 453 or resid 46 \ 3 through 501 or resid 503 through 567 or (resid 568 and (name N or name CA or n \ ame C or name O or name CB )) or resid 569 through 570 or (resid 571 and (name N \ or name CA or name C or name O or name CB )) or resid 572 through 581 or (resid \ 582 through 583 and (name N or name CA or name C or name O or name CB )) or res \ id 584 through 585 or (resid 586 and (name N or name CA or name C or name O or n \ ame CB )) or resid 587 through 613 or (resid 614 and (name N or name CA or name \ C or name O or name CB )) or resid 615 through 618 or (resid 619 and (name N or \ name CA or name C or name O or name CB )) or resid 620 through 676 or resid 690 \ through 744 or (resid 745 and (name N or name CA or name C or name O or name CB \ )) or resid 746 through 810 or (resid 811 and (name N or name CA or name C or na \ me O or name CB )) or resid 813 through 827 or resid 856 through 866 or (resid 8 \ 67 through 868 and (name N or name CA or name C or name O or name CB )) or resid \ 869 through 920 or (resid 921 and (name N or name CA or name C or name O or nam \ e CB )) or resid 922 through 939 or (resid 940 and (name N or name CA or name C \ or name O or name CB )) or resid 941 through 984 or (resid 985 and (name N or na \ me CA or name C or name O or name CB )) or resid 986 through 987 or (resid 988 t \ hrough 989 and (name N or name CA or name C or name O or name CB )) or resid 990 \ through 1072 or (resid 1073 and (name N or name CA or name C or name O or name \ CB )) or resid 1074 through 1117 or (resid 1118 and (name N or name CA or name C \ or name O or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 \ and (name N or name CA or name C or name O or name CB )) or resid 1147 through 1 \ 310)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 344 or (resid 345 through 360 and (name N or name CA or name C or name O o \ r name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or na \ me C or name O or name CB )) or resid 379 or (resid 380 and (name N or name CA o \ r name C or name O or name CB )) or resid 381 or (resid 382 through 383 and (nam \ e N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 thro \ ugh 390 and (name N or name CA or name C or name O or name CB )) or resid 391 or \ (resid 392 through 403 and (name N or name CA or name C or name O or name CB )) \ or (resid 404 through 411 and (name N or name CA or name C or name O or name CB \ )) or resid 412 through 413 or (resid 414 through 415 and (name N or name CA or \ name C or name O or name CB )) or (resid 416 through 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 or (resid 427 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 through 442 and (name N or name CA or name C or name O or name CB )) o \ r (resid 448 through 449 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 451 and (name N or name CA or name C or name O or name CB )) or resi \ d 463 or (resid 464 through 466 and (name N or name CA or name C or name O or na \ me CB )) or resid 491 or (resid 492 through 495 and (name N or name CA or name C \ or name O or name CB )) or resid 496 or (resid 497 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 through 500 or (resid 501 \ and (name N or name CA or name C or name O or name CB )) or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (n \ ame N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 th \ rough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 25 through 527 or (resid 528 through 529 and (name N or name CA or name C or nam \ e O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA \ or name C or name O or name CB )) or resid 555 through 567 or (resid 568 and (na \ me N or name CA or name C or name O or name CB )) or resid 569 through 570 or (r \ esid 571 and (name N or name CA or name C or name O or name CB )) or resid 572 t \ hrough 581 or (resid 582 through 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or n \ ame C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 645 or (resid \ 646 through 647 and (name N or name CA or name C or name O or name CB )) or res \ id 648 through 793 or (resid 794 and (name N or name CA or name C or name O or n \ ame CB )) or resid 795 or (resid 796 and (name N or name CA or name C or name O \ or name CB )) or resid 797 through 920 or (resid 921 and (name N or name CA or n \ ame C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (r \ esid 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 \ through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or name C \ or name O or name CB )) or resid 1147 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.090 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.015 0.362 22914 Z= 0.821 Angle : 1.410 36.449 31360 Z= 0.941 Chirality : 0.097 1.573 3822 Planarity : 0.005 0.024 3936 Dihedral : 10.403 89.868 7557 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.43 % Favored : 97.50 % Rotamer: Outliers : 0.13 % Allowed : 0.44 % Favored : 99.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 2797 helix: 0.08 (0.17), residues: 714 sheet: 1.14 (0.20), residues: 570 loop : 0.28 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 454 TYR 0.039 0.005 TYR A 266 PHE 0.021 0.004 PHE B 201 TRP 0.026 0.006 TRP A 353 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.01473 / 0.79 (22819) covalent geometry : angle 1.37769 / 0.94 (31111) SS BOND : bond 0.07411 / 3.27 ( 36) SS BOND : angle 3.26242 / 2.05 ( 72) hydrogen bonds : bond 0.16846 / 11.18 ( 1002) hydrogen bonds : angle 8.08929 / 5.58 ( 2823) link_BETA1-4 : bond 0.06486 / 4.02 ( 12) link_BETA1-4 : angle 3.30627 / 2.07 ( 36) link_NAG-ASN : bond 0.06888 / 4.39 ( 47) link_NAG-ASN : angle 3.92926 / 2.30 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 344 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 753 LEU cc_start: 0.8434 (tp) cc_final: 0.8223 (tp) REVERT: B 935 GLN cc_start: 0.7224 (mt0) cc_final: 0.6853 (mt0) REVERT: C 453 TYR cc_start: 0.5675 (p90) cc_final: 0.5415 (p90) outliers start: 3 outliers final: 1 residues processed: 347 average time/residue: 0.1629 time to fit residues: 86.6351 Evaluate side-chains 118 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN A 913 GLN A 935 GLN A1010 GLN A1119 ASN B 703 ASN B 774 GLN B 804 GLN B 935 GLN B1071 GLN C 954 GLN C 955 ASN C1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.131904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097322 restraints weight = 37740.301| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.05 r_work: 0.3311 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22914 Z= 0.149 Angle : 0.638 12.188 31360 Z= 0.333 Chirality : 0.045 0.329 3822 Planarity : 0.004 0.029 3936 Dihedral : 4.577 47.291 3027 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.07 % Favored : 98.89 % Rotamer: Outliers : 1.51 % Allowed : 4.83 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.15), residues: 2797 helix: 1.77 (0.20), residues: 681 sheet: 0.89 (0.18), residues: 668 loop : 0.17 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 273 TYR 0.022 0.002 TYR A1067 PHE 0.019 0.002 PHE A 377 TRP 0.017 0.001 TRP A 104 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (22819) covalent geometry : angle 0.60679 / 0.33 (31111) SS BOND : bond 0.00306 / 0.19 ( 36) SS BOND : angle 1.39571 / 0.87 ( 72) hydrogen bonds : bond 0.05310 / 3.41 ( 1002) hydrogen bonds : angle 6.21949 / 4.34 ( 2823) link_BETA1-4 : bond 0.00617 / 0.40 ( 12) link_BETA1-4 : angle 1.68545 / 1.09 ( 36) link_NAG-ASN : bond 0.00606 / 0.40 ( 47) link_NAG-ASN : angle 2.77079 / 1.65 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.9020 (p) cc_final: 0.8724 (t) REVERT: A 287 ASP cc_start: 0.7925 (t0) cc_final: 0.7606 (m-30) REVERT: A 564 GLN cc_start: 0.6786 (tm-30) cc_final: 0.6426 (tm-30) REVERT: A 740 MET cc_start: 0.8170 (tpt) cc_final: 0.7942 (tpp) REVERT: A 955 ASN cc_start: 0.8521 (m-40) cc_final: 0.8281 (m-40) REVERT: C 453 TYR cc_start: 0.5175 (p90) cc_final: 0.4666 (p90) REVERT: C 571 ASP cc_start: 0.8373 (t0) cc_final: 0.7993 (t0) REVERT: C 581 THR cc_start: 0.8000 (m) cc_final: 0.7677 (p) REVERT: C 804 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8111 (mt0) REVERT: C 950 ASP cc_start: 0.8388 (t70) cc_final: 0.8119 (t0) outliers start: 34 outliers final: 23 residues processed: 185 average time/residue: 0.1283 time to fit residues: 40.1364 Evaluate side-chains 137 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 887 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 144 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 955 ASN A1048 HIS ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B1048 HIS C 804 GLN C 913 GLN C 935 GLN C1048 HIS ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.125250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.090652 restraints weight = 38395.660| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.03 r_work: 0.3209 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 22914 Z= 0.277 Angle : 0.665 11.733 31360 Z= 0.346 Chirality : 0.047 0.209 3822 Planarity : 0.004 0.060 3936 Dihedral : 4.622 37.960 3027 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.86 % Allowed : 6.16 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 2797 helix: 1.62 (0.20), residues: 692 sheet: 0.28 (0.17), residues: 717 loop : -0.07 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1019 TYR 0.021 0.002 TYR A 265 PHE 0.020 0.002 PHE B 906 TRP 0.016 0.002 TRP A 104 HIS 0.007 0.002 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.28 (22819) covalent geometry : angle 0.63491 / 0.34 (31111) SS BOND : bond 0.00327 / 0.21 ( 36) SS BOND : angle 2.42697 / 1.28 ( 72) hydrogen bonds : bond 0.05239 / 3.36 ( 1002) hydrogen bonds : angle 5.94292 / 4.13 ( 2823) link_BETA1-4 : bond 0.00488 / 0.31 ( 12) link_BETA1-4 : angle 1.29796 / 0.85 ( 36) link_NAG-ASN : bond 0.00855 / 0.59 ( 47) link_NAG-ASN : angle 2.42640 / 1.48 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.9033 (p) cc_final: 0.8827 (t) REVERT: A 523 THR cc_start: 0.8002 (m) cc_final: 0.7564 (p) REVERT: A 564 GLN cc_start: 0.7061 (tm-30) cc_final: 0.6706 (tm-30) REVERT: A 740 MET cc_start: 0.8449 (tpt) cc_final: 0.8234 (tpp) REVERT: A 856 ASN cc_start: 0.8119 (m-40) cc_final: 0.7790 (m-40) REVERT: A 950 ASP cc_start: 0.8348 (t70) cc_final: 0.7883 (t0) REVERT: C 453 TYR cc_start: 0.5223 (p90) cc_final: 0.4743 (p90) REVERT: C 571 ASP cc_start: 0.8397 (t0) cc_final: 0.7888 (t0) REVERT: C 950 ASP cc_start: 0.8431 (t70) cc_final: 0.8196 (t0) outliers start: 42 outliers final: 30 residues processed: 160 average time/residue: 0.1383 time to fit residues: 36.6390 Evaluate side-chains 137 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 941 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 3 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 263 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 131 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 256 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 171 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 913 GLN B 804 GLN C 901 GLN C 955 ASN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.126989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.092439 restraints weight = 38051.574| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.02 r_work: 0.3237 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22914 Z= 0.159 Angle : 0.549 10.165 31360 Z= 0.284 Chirality : 0.045 0.403 3822 Planarity : 0.004 0.047 3936 Dihedral : 4.306 36.159 3027 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.82 % Allowed : 6.51 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.15), residues: 2797 helix: 1.97 (0.20), residues: 680 sheet: 0.08 (0.17), residues: 729 loop : -0.13 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 346 TYR 0.020 0.001 TYR A1067 PHE 0.016 0.001 PHE A 565 TRP 0.021 0.001 TRP A 104 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (22819) covalent geometry : angle 0.52511 / 0.28 (31111) SS BOND : bond 0.00354 / 0.23 ( 36) SS BOND : angle 1.57930 / 0.89 ( 72) hydrogen bonds : bond 0.04346 / 2.80 ( 1002) hydrogen bonds : angle 5.61773 / 3.90 ( 2823) link_BETA1-4 : bond 0.00484 / 0.31 ( 12) link_BETA1-4 : angle 1.13404 / 0.76 ( 36) link_NAG-ASN : bond 0.00624 / 0.42 ( 47) link_NAG-ASN : angle 2.13250 / 1.29 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8970 (p) cc_final: 0.8765 (t) REVERT: A 269 TYR cc_start: 0.7905 (m-10) cc_final: 0.7601 (m-10) REVERT: A 564 GLN cc_start: 0.7079 (tm-30) cc_final: 0.6684 (tm-30) REVERT: A 950 ASP cc_start: 0.8215 (t70) cc_final: 0.7779 (t0) REVERT: A 1019 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7615 (ttp80) REVERT: B 241 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7283 (pt) REVERT: B 950 ASP cc_start: 0.8251 (t0) cc_final: 0.8027 (t0) REVERT: C 453 TYR cc_start: 0.5169 (p90) cc_final: 0.4799 (p90) REVERT: C 571 ASP cc_start: 0.8431 (t0) cc_final: 0.7883 (t0) REVERT: C 950 ASP cc_start: 0.8325 (t70) cc_final: 0.8060 (t0) outliers start: 41 outliers final: 25 residues processed: 157 average time/residue: 0.1289 time to fit residues: 33.7856 Evaluate side-chains 131 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 887 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 40 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 149 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 284 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 GLN C 955 ASN C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.126172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091535 restraints weight = 37896.253| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.02 r_work: 0.3223 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22914 Z= 0.164 Angle : 0.540 11.497 31360 Z= 0.280 Chirality : 0.044 0.328 3822 Planarity : 0.004 0.043 3936 Dihedral : 4.171 33.806 3027 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.73 % Allowed : 7.53 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 2797 helix: 2.07 (0.21), residues: 677 sheet: -0.06 (0.17), residues: 715 loop : -0.23 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.019 0.001 TYR A1067 PHE 0.014 0.001 PHE A 565 TRP 0.024 0.001 TRP A 104 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (22819) covalent geometry : angle 0.51820 / 0.27 (31111) SS BOND : bond 0.00314 / 0.20 ( 36) SS BOND : angle 1.48086 / 0.82 ( 72) hydrogen bonds : bond 0.04264 / 2.74 ( 1002) hydrogen bonds : angle 5.47894 / 3.79 ( 2823) link_BETA1-4 : bond 0.00418 / 0.25 ( 12) link_BETA1-4 : angle 1.07238 / 0.70 ( 36) link_NAG-ASN : bond 0.00449 / 0.29 ( 47) link_NAG-ASN : angle 2.06992 / 1.24 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8972 (p) cc_final: 0.8758 (t) REVERT: A 269 TYR cc_start: 0.7907 (m-10) cc_final: 0.7572 (m-10) REVERT: A 564 GLN cc_start: 0.7079 (tm-30) cc_final: 0.6677 (tm-30) REVERT: A 950 ASP cc_start: 0.8158 (t70) cc_final: 0.7738 (t0) REVERT: A 1019 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7665 (ttp80) REVERT: B 133 PHE cc_start: 0.5848 (m-80) cc_final: 0.5017 (t80) REVERT: B 950 ASP cc_start: 0.8272 (t0) cc_final: 0.8047 (t0) REVERT: C 269 TYR cc_start: 0.8537 (m-80) cc_final: 0.7857 (m-10) REVERT: C 453 TYR cc_start: 0.5096 (p90) cc_final: 0.4699 (p90) REVERT: C 571 ASP cc_start: 0.8351 (t0) cc_final: 0.7789 (t0) REVERT: C 740 MET cc_start: 0.8321 (tpt) cc_final: 0.8005 (tmm) REVERT: C 950 ASP cc_start: 0.8287 (t70) cc_final: 0.8015 (t0) outliers start: 39 outliers final: 29 residues processed: 141 average time/residue: 0.1380 time to fit residues: 32.5053 Evaluate side-chains 130 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 887 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 89 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 158 optimal weight: 0.0040 chunk 134 optimal weight: 9.9990 chunk 252 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.125530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.091000 restraints weight = 38165.783| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.02 r_work: 0.3214 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22914 Z= 0.172 Angle : 0.539 11.964 31360 Z= 0.276 Chirality : 0.044 0.332 3822 Planarity : 0.004 0.060 3936 Dihedral : 4.119 30.396 3027 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.90 % Allowed : 7.88 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.15), residues: 2797 helix: 2.05 (0.21), residues: 680 sheet: -0.09 (0.18), residues: 703 loop : -0.23 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 214 TYR 0.019 0.001 TYR A1067 PHE 0.014 0.001 PHE B1052 TRP 0.025 0.001 TRP A 104 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (22819) covalent geometry : angle 0.51682 / 0.27 (31111) SS BOND : bond 0.00254 / 0.17 ( 36) SS BOND : angle 1.65047 / 1.01 ( 72) hydrogen bonds : bond 0.04197 / 2.70 ( 1002) hydrogen bonds : angle 5.37799 / 3.73 ( 2823) link_BETA1-4 : bond 0.00398 / 0.26 ( 12) link_BETA1-4 : angle 1.03921 / 0.68 ( 36) link_NAG-ASN : bond 0.00447 / 0.29 ( 47) link_NAG-ASN : angle 2.03086 / 1.21 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.8961 (p) cc_final: 0.8750 (t) REVERT: A 269 TYR cc_start: 0.7925 (m-10) cc_final: 0.7557 (m-10) REVERT: A 564 GLN cc_start: 0.7095 (tm-30) cc_final: 0.6684 (tm-30) REVERT: A 751 ASN cc_start: 0.8619 (m-40) cc_final: 0.8364 (m110) REVERT: A 950 ASP cc_start: 0.8111 (t70) cc_final: 0.7689 (t0) REVERT: B 133 PHE cc_start: 0.5869 (m-80) cc_final: 0.5552 (m-10) REVERT: B 950 ASP cc_start: 0.8260 (t0) cc_final: 0.7991 (t0) REVERT: C 269 TYR cc_start: 0.8549 (m-80) cc_final: 0.7847 (m-10) REVERT: C 453 TYR cc_start: 0.5039 (p90) cc_final: 0.4686 (p90) REVERT: C 571 ASP cc_start: 0.8237 (t0) cc_final: 0.7642 (t0) REVERT: C 740 MET cc_start: 0.8562 (tpt) cc_final: 0.8186 (tmm) REVERT: C 950 ASP cc_start: 0.8287 (t70) cc_final: 0.8012 (t0) outliers start: 43 outliers final: 34 residues processed: 146 average time/residue: 0.1306 time to fit residues: 32.5461 Evaluate side-chains 138 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 887 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 72 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 283 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 138 optimal weight: 0.0050 chunk 273 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.126697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.092308 restraints weight = 38031.372| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.01 r_work: 0.3235 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22914 Z= 0.126 Angle : 0.505 11.909 31360 Z= 0.258 Chirality : 0.044 0.321 3822 Planarity : 0.004 0.041 3936 Dihedral : 3.938 26.872 3027 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.59 % Allowed : 8.41 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2797 helix: 2.12 (0.21), residues: 686 sheet: -0.05 (0.18), residues: 703 loop : -0.21 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 214 TYR 0.020 0.001 TYR B 170 PHE 0.014 0.001 PHE A 377 TRP 0.021 0.001 TRP A 104 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (22819) covalent geometry : angle 0.48490 / 0.25 (31111) SS BOND : bond 0.00280 / 0.18 ( 36) SS BOND : angle 1.16261 / 0.72 ( 72) hydrogen bonds : bond 0.03869 / 2.48 ( 1002) hydrogen bonds : angle 5.24004 / 3.63 ( 2823) link_BETA1-4 : bond 0.00355 / 0.24 ( 12) link_BETA1-4 : angle 0.99509 / 0.65 ( 36) link_NAG-ASN : bond 0.00428 / 0.28 ( 47) link_NAG-ASN : angle 1.94748 / 1.15 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 GLN cc_start: 0.7133 (tm-30) cc_final: 0.6725 (tm-30) REVERT: A 751 ASN cc_start: 0.8629 (m-40) cc_final: 0.8377 (m110) REVERT: B 133 PHE cc_start: 0.5955 (m-80) cc_final: 0.5664 (m-10) REVERT: B 241 LEU cc_start: 0.7735 (pt) cc_final: 0.7420 (pp) REVERT: B 586 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: B 950 ASP cc_start: 0.8185 (t0) cc_final: 0.7914 (t0) REVERT: C 269 TYR cc_start: 0.8544 (m-80) cc_final: 0.7898 (m-10) REVERT: C 453 TYR cc_start: 0.5017 (p90) cc_final: 0.4666 (p90) REVERT: C 571 ASP cc_start: 0.8213 (t0) cc_final: 0.7795 (t0) REVERT: C 950 ASP cc_start: 0.8223 (t70) cc_final: 0.7965 (t0) outliers start: 36 outliers final: 26 residues processed: 139 average time/residue: 0.1388 time to fit residues: 31.6488 Evaluate side-chains 131 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 223 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 93 optimal weight: 0.0670 chunk 84 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 267 optimal weight: 0.0980 chunk 163 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.126879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092462 restraints weight = 37921.547| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.02 r_work: 0.3238 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22914 Z= 0.122 Angle : 0.497 11.857 31360 Z= 0.254 Chirality : 0.043 0.323 3822 Planarity : 0.004 0.046 3936 Dihedral : 3.865 26.543 3027 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.82 % Allowed : 8.72 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2797 helix: 2.19 (0.21), residues: 682 sheet: -0.02 (0.18), residues: 708 loop : -0.19 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 214 TYR 0.019 0.001 TYR A1067 PHE 0.013 0.001 PHE A 377 TRP 0.019 0.001 TRP A 104 HIS 0.011 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (22819) covalent geometry : angle 0.47787 / 0.25 (31111) SS BOND : bond 0.00274 / 0.18 ( 36) SS BOND : angle 1.13518 / 0.70 ( 72) hydrogen bonds : bond 0.03781 / 2.43 ( 1002) hydrogen bonds : angle 5.13439 / 3.56 ( 2823) link_BETA1-4 : bond 0.00383 / 0.24 ( 12) link_BETA1-4 : angle 0.98834 / 0.65 ( 36) link_NAG-ASN : bond 0.00423 / 0.27 ( 47) link_NAG-ASN : angle 1.89988 / 1.12 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8379 (m-80) cc_final: 0.7476 (m-80) REVERT: A 564 GLN cc_start: 0.7166 (tm-30) cc_final: 0.6760 (tm-30) REVERT: B 133 PHE cc_start: 0.6169 (m-80) cc_final: 0.5909 (m-10) REVERT: B 586 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: B 950 ASP cc_start: 0.8206 (t0) cc_final: 0.7906 (t0) REVERT: C 214 ARG cc_start: 0.5927 (mmp80) cc_final: 0.5406 (ppt170) REVERT: C 453 TYR cc_start: 0.5038 (p90) cc_final: 0.4700 (p90) REVERT: C 571 ASP cc_start: 0.8246 (t0) cc_final: 0.7733 (t0) REVERT: C 950 ASP cc_start: 0.8216 (t70) cc_final: 0.7959 (t0) outliers start: 41 outliers final: 30 residues processed: 139 average time/residue: 0.1336 time to fit residues: 31.4317 Evaluate side-chains 135 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 93 optimal weight: 0.8980 chunk 266 optimal weight: 0.8980 chunk 260 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 246 optimal weight: 0.8980 chunk 206 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 907 ASN C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.126641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.092245 restraints weight = 38168.030| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.02 r_work: 0.3233 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22914 Z= 0.133 Angle : 0.506 11.731 31360 Z= 0.259 Chirality : 0.044 0.324 3822 Planarity : 0.004 0.041 3936 Dihedral : 3.920 31.864 3027 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.55 % Allowed : 9.08 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.73 % 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: 0.60 (0.16), residues: 2797 helix: 2.14 (0.21), residues: 688 sheet: -0.01 (0.18), residues: 705 loop : -0.20 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 214 TYR 0.019 0.001 TYR A1067 PHE 0.015 0.001 PHE B 338 TRP 0.017 0.001 TRP A 104 HIS 0.011 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (22819) covalent geometry : angle 0.48483 / 0.25 (31111) SS BOND : bond 0.00263 / 0.17 ( 36) SS BOND : angle 1.54772 / 0.99 ( 72) hydrogen bonds : bond 0.03803 / 2.45 ( 1002) hydrogen bonds : angle 5.12341 / 3.56 ( 2823) link_BETA1-4 : bond 0.00368 / 0.23 ( 12) link_BETA1-4 : angle 0.98652 / 0.64 ( 36) link_NAG-ASN : bond 0.00414 / 0.27 ( 47) link_NAG-ASN : angle 1.88830 / 1.12 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8388 (m-80) cc_final: 0.7498 (m-80) REVERT: A 564 GLN cc_start: 0.7190 (tm-30) cc_final: 0.6784 (tm-30) REVERT: A 740 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7726 (tpp) REVERT: B 133 PHE cc_start: 0.6209 (m-80) cc_final: 0.5929 (m-10) REVERT: B 586 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: B 950 ASP cc_start: 0.8210 (t0) cc_final: 0.7928 (t0) REVERT: C 453 TYR cc_start: 0.5019 (p90) cc_final: 0.4551 (p90) REVERT: C 571 ASP cc_start: 0.8246 (t0) cc_final: 0.7730 (t0) REVERT: C 950 ASP cc_start: 0.8219 (t70) cc_final: 0.7961 (t0) outliers start: 35 outliers final: 28 residues processed: 130 average time/residue: 0.1329 time to fit residues: 29.3042 Evaluate side-chains 130 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 175 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 220 optimal weight: 4.9990 chunk 253 optimal weight: 0.9980 chunk 211 optimal weight: 0.1980 chunk 166 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN B 907 ASN C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.125042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090467 restraints weight = 38308.469| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.02 r_work: 0.3204 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22914 Z= 0.173 Angle : 0.533 11.548 31360 Z= 0.272 Chirality : 0.044 0.321 3822 Planarity : 0.004 0.042 3936 Dihedral : 4.029 26.818 3027 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.55 % Allowed : 9.12 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.16), residues: 2797 helix: 2.06 (0.21), residues: 687 sheet: -0.09 (0.18), residues: 699 loop : -0.26 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 214 TYR 0.019 0.001 TYR A1067 PHE 0.014 0.001 PHE A 377 TRP 0.015 0.001 TRP A 104 HIS 0.009 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (22819) covalent geometry : angle 0.51271 / 0.27 (31111) SS BOND : bond 0.00280 / 0.18 ( 36) SS BOND : angle 1.44905 / 0.91 ( 72) hydrogen bonds : bond 0.04107 / 2.64 ( 1002) hydrogen bonds : angle 5.22368 / 3.63 ( 2823) link_BETA1-4 : bond 0.00384 / 0.25 ( 12) link_BETA1-4 : angle 1.02533 / 0.67 ( 36) link_NAG-ASN : bond 0.00413 / 0.26 ( 47) link_NAG-ASN : angle 1.94383 / 1.17 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5594 Ramachandran restraints generated. 2797 Oldfield, 0 Emsley, 2797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8417 (m-80) cc_final: 0.7572 (m-80) REVERT: A 751 ASN cc_start: 0.8652 (m-40) cc_final: 0.8385 (m110) REVERT: B 133 PHE cc_start: 0.6015 (m-80) cc_final: 0.5779 (m-10) REVERT: B 586 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7900 (m-30) REVERT: B 950 ASP cc_start: 0.8190 (t0) cc_final: 0.7933 (t0) REVERT: C 453 TYR cc_start: 0.4970 (p90) cc_final: 0.4453 (p90) REVERT: C 571 ASP cc_start: 0.8241 (t0) cc_final: 0.7721 (t0) REVERT: C 950 ASP cc_start: 0.8256 (t70) cc_final: 0.7986 (t0) outliers start: 35 outliers final: 27 residues processed: 126 average time/residue: 0.1234 time to fit residues: 27.4914 Evaluate side-chains 123 residues out of total 2523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 959 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 259 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 907 ASN C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.125836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.092453 restraints weight = 37236.311| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.91 r_work: 0.3206 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22914 Z= 0.126 Angle : 0.504 11.229 31360 Z= 0.258 Chirality : 0.044 0.318 3822 Planarity : 0.004 0.039 3936 Dihedral : 3.963 27.768 3027 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.51 % Allowed : 9.26 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.51 (0.16), residues: 2797 helix: 2.11 (0.21), residues: 686 sheet: -0.08 (0.18), residues: 701 loop : -0.27 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 214 TYR 0.019 0.001 TYR A1067 PHE 0.013 0.001 PHE B 168 TRP 0.018 0.001 TRP A 104 HIS 0.009 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (22819) covalent geometry : angle 0.48355 / 0.25 (31111) SS BOND : bond 0.00236 / 0.15 ( 36) SS BOND : angle 1.39030 / 0.86 ( 72) hydrogen bonds : bond 0.03806 / 2.45 ( 1002) hydrogen bonds : angle 5.14482 / 3.57 ( 2823) link_BETA1-4 : bond 0.00396 / 0.25 ( 12) link_BETA1-4 : angle 0.99921 / 0.65 ( 36) link_NAG-ASN : bond 0.00402 / 0.26 ( 47) link_NAG-ASN : angle 1.94049 / 1.16 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4741.73 seconds wall clock time: 82 minutes 29.93 seconds (4949.93 seconds total)