Starting phenix.real_space_refine on Thu Mar 5 18:53:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wpt_21865/03_2026/6wpt_21865.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wpt_21865/03_2026/6wpt_21865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wpt_21865/03_2026/6wpt_21865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wpt_21865/03_2026/6wpt_21865.map" model { file = "/net/cci-nas-00/data/ceres_data/6wpt_21865/03_2026/6wpt_21865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wpt_21865/03_2026/6wpt_21865.cif" } resolution = 3.7 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= 0.004 sd= 0.048 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 107 5.16 5 C 15472 2.51 5 N 4080 2.21 5 O 4667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 151 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24326 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 7049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 945, 7049 Classifications: {'peptide': 945} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 44, 'TRANS': 900} Chain breaks: 13 Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 446 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 22, 'GLU:plan': 21, 'PHE:plan': 7, 'GLN:plan1': 7, 'ASN:plan1': 4, 'ARG:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 259 Chain: "B" Number of atoms: 6561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 937, 6561 Classifications: {'peptide': 937} Incomplete info: {'truncation_to_alanine': 213} Link IDs: {'PTRANS': 45, 'TRANS': 891} Chain breaks: 13 Unresolved non-hydrogen bonds: 787 Unresolved non-hydrogen angles: 1014 Unresolved non-hydrogen dihedrals: 647 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'ASP:plan': 27, 'ASN:plan1': 22, 'ARG:plan': 11, 'GLU:plan': 17, 'PHE:plan': 14, 'GLN:plan1': 8, 'TYR:plan': 15, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 509 Chain: "C" Number of atoms: 6997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 952, 6997 Classifications: {'peptide': 952} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 46, 'TRANS': 905} Chain breaks: 12 Unresolved non-hydrogen bonds: 458 Unresolved non-hydrogen angles: 584 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ASP:plan': 21, 'ASN:plan1': 11, 'GLU:plan': 13, 'GLN:plan1': 6, 'PHE:plan': 7, 'TYR:plan': 6, 'ARG:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 291 Chain: "H" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 876 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "L" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 590 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 2 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 783 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "E" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 580 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.90, per 1000 atoms: 0.24 Number of scatterers: 24326 At special positions: 0 Unit cell: (139.65, 138.6, 179.55, 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 107 16.00 O 4667 8.00 N 4080 7.00 C 15472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.08 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=2.12 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=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=2.01 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.04 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=2.03 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=2.18 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.07 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " BETA1-6 " NAG J 1 " - " FUC J 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 6 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1314 " - " ASN A1074 " " NAG A1317 " - " ASN A1134 " " 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 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1314 " - " ASN C1074 " " NAG C1319 " - " ASN C 165 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " " NAG S 1 " - " ASN C 343 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.0 seconds 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6104 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 55 sheets defined 23.5% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.791A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.508A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.749A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 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: 4.977A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.199A 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: 3.651A 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 884 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.906A 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: 5.099A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 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: 4.371A 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 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.503A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) 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: 4.731A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.772A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.742A pdb=" N SER D 31 " --> pdb=" O PRO D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.867A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.035A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.070A 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: 7.690A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.918A 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: 4.006A 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: 6.768A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.087A 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: 6.267A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.163A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.163A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.397A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.950A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.596A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.525A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.525A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 removed outlier: 3.551A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.545A 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: 7.738A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.084A 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: 3.520A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.910A 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: 5.336A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.415A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.907A 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: 6.270A 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: 5.995A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.576A 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: 6.496A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.628A 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: 6.496A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.749A 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: 7.844A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.509A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.330A 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: 5.385A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.291A 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: 3.716A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.977A 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: 7.181A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.367A 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: 7.181A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.618A 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: 6.366A pdb=" N TYR C 660 " --> pdb=" O SER C 698 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.641A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.787A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.121A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.324A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.548A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.107A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.107A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.520A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.520A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 11 removed outlier: 7.122A pdb=" N GLU D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 10 through 11 removed outlier: 7.122A pdb=" N GLU D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASN D 116 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AG1, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.597A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) 1172 hydrogen bonds defined for protein. 3153 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: 6.04 Time building geometry restraints manager: 2.95 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: 6533 1.33 - 1.47: 7772 1.47 - 1.61: 10369 1.61 - 1.75: 6 1.75 - 1.89: 134 Bond restraints: 24814 Sorted by residual: bond pdb=" NE ARG C 454 " pdb=" CZ ARG C 454 " ideal model delta sigma weight residual 1.326 1.380 -0.054 1.10e-02 8.26e+03 2.43e+01 bond pdb=" CB ILE B 210 " pdb=" CG1 ILE B 210 " ideal model delta sigma weight residual 1.530 1.626 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" CB LEU C 212 " pdb=" CG LEU C 212 " ideal model delta sigma weight residual 1.530 1.616 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" CB ILE A 68 " pdb=" CG1 ILE A 68 " ideal model delta sigma weight residual 1.530 1.616 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.615 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 24809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 28028 1.65 - 3.31: 4919 3.31 - 4.96: 683 4.96 - 6.62: 234 6.62 - 8.27: 40 Bond angle restraints: 33904 Sorted by residual: angle pdb=" C THR C 599 " pdb=" N PRO C 600 " pdb=" CA PRO C 600 " ideal model delta sigma weight residual 119.56 127.03 -7.47 1.02e+00 9.61e-01 5.37e+01 angle pdb=" C PRO C 792 " pdb=" N PRO C 793 " pdb=" CA PRO C 793 " ideal model delta sigma weight residual 119.56 126.91 -7.35 1.02e+00 9.61e-01 5.20e+01 angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.56 126.77 -7.21 1.01e+00 9.80e-01 5.09e+01 angle pdb=" C PRO A 862 " pdb=" N PRO A 863 " pdb=" CA PRO A 863 " ideal model delta sigma weight residual 120.03 127.05 -7.02 9.90e-01 1.02e+00 5.03e+01 angle pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.87 127.22 -7.35 1.04e+00 9.25e-01 4.99e+01 ... (remaining 33899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 15014 21.47 - 42.95: 294 42.95 - 64.42: 69 64.42 - 85.90: 36 85.90 - 107.37: 12 Dihedral angle restraints: 15425 sinusoidal: 5969 harmonic: 9456 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 93.00 171.61 -78.61 1 1.00e+01 1.00e-02 7.70e+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 93.00 169.91 -76.91 1 1.00e+01 1.00e-02 7.43e+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 93.00 161.68 -68.68 1 1.00e+01 1.00e-02 6.11e+01 ... (remaining 15422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3058 0.089 - 0.177: 818 0.177 - 0.266: 250 0.266 - 0.354: 51 0.354 - 0.443: 7 Chirality restraints: 4184 Sorted by residual: chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.37e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.36e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.19e+01 ... (remaining 4181 not shown) Planarity restraints: 4351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.037 2.00e-02 2.50e+03 3.73e-02 1.74e+01 pdb=" CG ASN B 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.056 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 266 " 0.044 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR A 266 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 266 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 266 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 266 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 266 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 266 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 266 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 200 " -0.040 2.00e-02 2.50e+03 2.21e-02 9.78e+00 pdb=" CG TYR A 200 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 200 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 200 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 200 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 200 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 200 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 200 " -0.036 2.00e-02 2.50e+03 ... (remaining 4348 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 12 2.52 - 3.12: 17482 3.12 - 3.71: 35194 3.71 - 4.31: 53789 4.31 - 4.90: 85514 Nonbonded interactions: 191991 Sorted by model distance: nonbonded pdb=" CD2 PHE B 817 " pdb=" NE2 GLN B 935 " model vdw 1.930 3.420 nonbonded pdb=" CD2 PHE C 817 " pdb=" NE2 GLN C 935 " model vdw 2.027 3.420 nonbonded pdb=" NZ LYS C1028 " pdb=" O PHE C1042 " model vdw 2.410 3.120 nonbonded pdb=" CE2 PHE B 817 " pdb=" NE2 GLN B 935 " model vdw 2.413 3.420 nonbonded pdb=" N ALA C 520 " pdb=" O ALA C 520 " model vdw 2.441 2.496 ... (remaining 191986 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 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 44 or (resid 45 through 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 50 or (res \ id 51 and (name N or name CA or name C or name O or name CB )) or resid 52 or (r \ esid 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thr \ ough 59 or (resid 60 and (name N or name CA or name C or name O or name CB )) or \ resid 61 through 66 or resid 82 through 94 or (resid 95 through 102 and (name N \ or name CA or name C or name O or name CB )) or resid 103 through 104 or (resid \ 105 and (name N or name CA or name C or name O or name CB )) or resid 106 throu \ gh 107 or (resid 108 through 118 and (name N or name CA or name C or name O or n \ ame CB )) or resid 119 through 120 or (resid 121 and (name N or name CA or name \ C or name O or name CB )) or resid 122 through 123 or (resid 124 through 130 and \ (name N or name CA or name C or name O or name CB )) or resid 131 through 139 o \ r (resid 140 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 through 169 or (resid 170 through 172 and (name N or name CA or name C or nam \ e O or name CB )) or resid 188 through 189 or (resid 190 through 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 203 and (name N or name CA or name C or name O or name CB )) or res \ id 204 through 209 or (resid 210 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 216 and (name N or name CA or name C or name O or name CB )) \ or resid 217 through 223 or (resid 224 and (name N or name CA or name C or name \ O or name CB )) or resid 225 through 226 or (resid 227 through 229 and (name N \ or name CA or name C or name O or name CB )) or resid 230 or (resid 231 and (nam \ e N or name CA or name C or name O or name CB )) or resid 232 through 235 or (re \ sid 236 through 237 and (name N or name CA or name C or name O or name CB )) or \ resid 238 or (resid 239 through 264 and (name N or name CA or name C or name O o \ r name CB )) or resid 265 through 273 or (resid 274 and (name N or name CA or na \ me C or name O or name CB )) or resid 275 through 279 or (resid 280 through 281 \ and (name N or name CA or name C or name O or name CB )) or resid 282 through 28 \ 3 or (resid 284 and (name N or name CA or name C or name O or name CB )) or resi \ d 285 through 286 or (resid 287 through 288 and (name N or name CA or name C or \ name O or name CB )) or resid 289 through 316 or (resid 317 and (name N or name \ CA or name C or name O or name CB )) or resid 318 through 323 or (resid 324 and \ (name N or name CA or name C or name O or name CB )) or resid 325 through 332 or \ (resid 333 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 4 through 344 or (resid 345 through 360 and (name N or name CA or name C or name \ O or name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA o \ r name C or name O or name CB )) or resid 379 or (resid 380 and (name N or name \ CA or name C or name O or name CB )) or resid 381 or (resid 382 through 383 and \ (name N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 \ through 390 and (name N or name CA or name C or name O or name CB )) or resid 39 \ 1 or (resid 392 through 403 and (name N or name CA or name C or name O or name C \ B )) or (resid 404 through 411 and (name N or name CA or name C or name O or nam \ e CB )) or resid 412 through 413 or (resid 414 through 415 and (name N or name C \ A or name C or name O or name CB )) or (resid 416 through 425 and (name N or nam \ e CA or name C or name O or name CB )) or resid 426 through 427 or (resid 428 th \ rough 430 and (name 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 )) 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 through 494 or (resid 495 and (name \ N or name CA or name C or name O or name CB )) or resid 496 or (resid 497 throug \ h 498 and (name N or name CA or name C or name O or name CB )) or resid 504 thro \ ugh 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 (name N or name CA or name C or name O \ or name CB )) or resid 525 through 527 or (resid 528 through 537 and (name N or \ name CA or name C or name O or name CB )) or resid 538 through 553 or (resid 554 \ through 557 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 58 through 564 or (resid 565 and (name N or name CA or name C or name O or name \ CB )) or resid 566 through 570 or (resid 571 and (name N or name CA or name C or \ name O or name CB )) or resid 572 through 573 or (resid 574 through 575 and (na \ me N or name CA or name C or name O or name CB )) or resid 576 through 577 or (r \ esid 578 and (name N or name CA or name C or name O or name CB )) or resid 579 t \ hrough 582 or (resid 583 and (name N or name CA or name C or name O or name CB ) \ ) or resid 584 through 658 or (resid 659 and (name N or name CA or name C or nam \ e O or name CB )) or resid 660 through 675 or (resid 676 and (name N or name CA \ or name C or name O or name CB )) or resid 690 through 724 or (resid 725 and (na \ me N or name CA or name C or name O or name CB )) or resid 726 through 775 or (r \ esid 776 and (name N or name CA or name C or name O or name CB )) or resid 777 t \ hrough 779 or (resid 780 and (name N or name CA or name C or name O or name CB ) \ ) or resid 781 through 810 or (resid 811 and (name N or name CA or name C or nam \ e O or name CB )) or resid 813 through 827 or (resid 856 and (name N or name CA \ or name C or name O or name CB )) or resid 857 through 871 or (resid 872 and (na \ me N or name CA or name C or name O or name CB )) or resid 873 through 903 or (r \ esid 904 and (name N or name CA or name C or name O or name CB )) or resid 905 t \ hrough 939 or (resid 940 and (name N or name CA or name C or name O or name CB ) \ ) or resid 941 through 942 or (resid 943 through 944 and (name N or name CA or n \ ame C or name O or name CB )) or resid 945 through 984 or (resid 985 and (name N \ or name CA or name C or name O or name CB )) or resid 986 through 1030 or (resi \ d 1031 and (name N or name CA or name C or name O or name CB )) or resid 1032 th \ rough 1040 or (resid 1041 and (name N or name CA or name C or name O or name CB \ )) or resid 1042 through 1044 or (resid 1045 and (name N or name CA or name C or \ name O or name CB )) or resid 1046 through 1082 or (resid 1083 through 1084 and \ (name N or name CA or name C or name O or name CB )) or resid 1085 through 1096 \ or (resid 1097 and (name N or name CA or name C or name O or name CB )) or resi \ d 1098 through 1099 or (resid 1100 and (name N or name CA or name C or name O or \ name CB )) or resid 1101 through 1134 or (resid 1135 and (name N or name CA or \ name C or name O or name CB )) or resid 1136 through 1317)) selection = (chain 'B' and (resid 27 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 44 or (resid 45 through 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 50 or (res \ id 51 and (name N or name CA or name C or name O or name CB )) or resid 52 throu \ gh 59 or (resid 60 and (name N or name CA or name C or name O or name CB )) or r \ esid 61 through 66 or resid 82 through 94 or (resid 95 through 102 and (name N o \ r name CA or name C or name O or name CB )) or resid 103 through 104 or (resid 1 \ 05 and (name N or name CA or name C or name O or name CB )) or resid 106 through \ 110 or (resid 116 through 118 and (name N or name CA or name C or name O or nam \ e CB )) or resid 119 through 120 or (resid 121 and (name N or name CA or name C \ or name O or name CB )) or resid 122 through 129 or (resid 130 and (name N or na \ me CA or name C or name O or name CB )) or resid 131 through 136 or resid 138 th \ rough 139 or (resid 140 and (name N or name CA or name C or name O or name CB )) \ or resid 166 through 167 or (resid 168 through 188 and (name N or name CA or na \ me C or name O or name CB )) or resid 189 or (resid 190 through 191 and (name N \ or name CA or name C or name O or name CB )) or resid 192 through 209 or (resid \ 210 through 216 and (name N or name CA or name C or name O or name CB )) or resi \ d 217 through 232 or (resid 233 and (name N or name CA or name C or name O or na \ me CB )) or resid 234 through 238 or (resid 239 through 263 and (name N or name \ CA or name C or name O or name CB )) or resid 265 through 280 or (resid 281 and \ (name N or name CA or name C or name O or name CB )) or resid 282 through 286 or \ (resid 287 through 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 or (resid 290 and (name N or name CA or name C or name O or name C \ B )) or resid 291 through 293 or (resid 294 and (name N or name CA or name C or \ name O or name CB )) or resid 295 through 316 or (resid 317 and (name N or name \ CA or name C or name O or name CB )) or resid 318 through 320 or (resid 321 and \ (name N or name CA or name C or name O or name CB )) or resid 322 through 323 or \ (resid 324 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 5 through 442 or resid 463 through 498 or resid 504 through 568 or (resid 569 th \ rough 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 resid 584 through 591 or (resid 592 and (name N or name CA or \ name C or name O or name CB )) or resid 593 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 (resi \ d 646 through 647 and (name N or name CA or name C or name O or name CB )) or re \ sid 648 through 658 or (resid 659 and (name N or name CA or name C or name O or \ name CB )) or resid 660 through 662 or (resid 663 and (name N or name CA or name \ C or name O or name CB )) or resid 664 through 675 or (resid 676 and (name N or \ name CA or name C or name O or name CB )) or resid 690 through 724 or (resid 72 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 726 through \ 736 or (resid 737 and (name N or name CA or name C or name O or name CB )) or re \ sid 738 through 772 or (resid 773 and (name N or name CA or name C or name O or \ name CB )) or resid 774 through 775 or (resid 776 and (name N or name CA or name \ C or name O or name CB )) or resid 777 through 789 or (resid 790 and (name N or \ name CA or name C or name O or name CB )) or resid 791 through 827 or (resid 85 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 857 through \ 871 or (resid 872 and (name N or name CA or name C or name O or name CB )) or re \ sid 873 through 903 or (resid 904 and (name N or name CA or name C or name O or \ name CB )) or resid 905 through 917 or (resid 918 and (name N or name CA or name \ C or name O or name CB )) or resid 919 through 920 or (resid 921 and (name N or \ name CA or name C or name O or name CB )) or resid 922 through 932 or (resid 93 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 934 through \ 935 or (resid 936 and (name N or name CA or name C or name O or name CB )) or re \ sid 937 through 939 or (resid 940 and (name N or name CA or name C or name O or \ name CB )) or resid 941 through 942 or (resid 943 through 944 and (name N or nam \ e CA or name C or name O or name CB )) or resid 945 through 984 or (resid 985 an \ d (name N or name CA or name C or name O or name CB )) or resid 986 through 987 \ or (resid 988 through 990 and (name N or name CA or name C or name O or name CB \ )) or resid 991 through 1016 or (resid 1017 and (name N or name CA or name C or \ name O or name CB )) or resid 1018 through 1082 or (resid 1083 through 1084 and \ (name N or name CA or name C or name O or name CB )) or resid 1085 through 1096 \ or (resid 1097 and (name N or name CA or name C or name O or name CB )) or resid \ 1098 through 1110 or (resid 1111 and (name N or name CA or name C or name O or \ name CB )) or resid 1112 through 1137 or resid 1303 through 1319)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 97 or (resi \ d 98 through 102 and (name N or name CA or name C or name O or name CB )) or res \ id 103 through 110 or (resid 116 through 118 and (name N or name CA or name C or \ name O or name CB )) or resid 119 through 136 or resid 138 through 140 or resid \ 166 through 172 or resid 188 through 190 or (resid 191 and (name N or name CA o \ r name C or name O or name CB )) or resid 192 through 196 or (resid 200 through \ 203 and (name N or name CA or name C or name O or name CB )) or resid 204 throug \ h 210 or resid 216 through 223 or (resid 224 and (name N or name CA or name C or \ name O or name CB )) or resid 225 through 230 or (resid 231 and (name N or name \ CA or name C or name O or name CB )) or resid 232 or (resid 233 and (name N or \ name CA or name C or name O or name CB )) or resid 234 through 273 or (resid 274 \ and (name N or name CA or name C or name O or name CB )) or resid 275 through 2 \ 79 or (resid 280 through 281 and (name N or name CA or name C or name O or name \ CB )) or resid 282 through 283 or (resid 284 and (name N or name CA or name C or \ name O or name CB )) or resid 285 through 293 or (resid 294 and (name N or name \ CA or name C or name O or name CB )) or resid 295 through 320 or (resid 321 and \ (name N or name CA or name C or name O or name CB )) or resid 322 through 339 o \ r (resid 340 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 41 through 344 or (resid 345 through 360 and (name N or name CA or name C or nam \ e O or name CB )) or resid 361 or (resid 362 through 378 and (name N or name CA \ or name C or name O or name CB )) or resid 379 or (resid 380 and (name N or name \ CA or name C or name O or name CB )) or resid 381 or (resid 382 through 383 and \ (name N or name CA or name C or name O or name CB )) or resid 384 or (resid 385 \ through 390 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 91 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 na \ me 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 na \ me CA or name C or name O or name CB )) or resid 426 or (resid 427 through 430 a \ nd (name 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 \ )) or resid 463 or (resid 464 through 466 and (name N or name CA or name C or n \ ame O or name CB )) or resid 491 or (resid 492 through 495 and (name N or name C \ A 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 or name CB )) or (resid 504 through 506 an \ d (name N or name CA or name C or name O or name CB )) or resid 507 or (resid 50 \ 8 through 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 res \ id 525 through 527 or (resid 528 through 537 and (name N or name CA or name C or \ name O or name CB )) or resid 538 through 554 or (resid 555 through 557 and (na \ me N or name CA or name C or name O or name CB )) or resid 558 through 563 or (r \ esid 564 through 565 and (name N or name CA or name C or name O or name CB )) or \ resid 566 through 567 or (resid 568 through 571 and (name N or name CA or name \ C or name O or name CB )) or resid 572 through 573 or (resid 574 through 575 and \ (name N or name CA or name C or name O or name CB )) or resid 576 through 581 o \ r (resid 582 through 583 and (name N or name CA or name C or name O or name CB ) \ ) or resid 584 through 591 or (resid 592 and (name N or name CA or name C or nam \ e O or name CB )) or resid 593 through 645 or (resid 646 through 647 and (name N \ or name CA or name C or name O or name CB )) or resid 648 through 657 or (resid \ 658 through 659 and (name N or name CA or name C or name O or name CB )) or res \ id 660 or (resid 661 and (name N or name CA or name C or name O or name CB )) or \ resid 662 or (resid 663 and (name N or name CA or name C or name O or name CB ) \ ) or resid 664 through 674 or (resid 675 through 676 and (name N or name CA or n \ ame C or name O or name CB )) or resid 690 through 701 or (resid 702 and (name N \ or name CA or name C or name O or name CB )) or resid 703 through 736 or (resid \ 737 and (name N or name CA or name C or name O or name CB )) or resid 738 throu \ gh 747 or (resid 748 and (name N or name CA or name C or name O or name CB )) or \ resid 749 through 772 or (resid 773 and (name N or name CA or name C or name O \ or name CB )) or resid 774 through 779 or (resid 780 and (name N or name CA or n \ ame C or name O or name CB )) or resid 781 through 793 or (resid 794 and (name N \ or name CA or name C or name O or name CB )) or resid 795 or (resid 796 and (na \ me N or name CA or name C or name O or name CB )) or resid 797 through 810 or (r \ esid 811 and (name N or name CA or name C or name O or name CB )) or resid 813 t \ hrough 866 or (resid 867 and (name N or name CA or name C or name O or name CB ) \ ) or resid 868 through 917 or (resid 918 and (name N or name CA or name C or nam \ e O or name CB )) or resid 919 through 920 or (resid 921 and (name N or name CA \ or name C or name O or name CB )) or resid 922 through 932 or (resid 933 and (na \ me N or name CA or name C or name O or name CB )) or resid 934 through 935 or (r \ esid 936 and (name N or name CA or name C or name O or name CB )) or resid 937 t \ hrough 978 or (resid 979 and (name N or name CA or name C or name O or name CB ) \ ) or resid 980 through 987 or (resid 988 through 990 and (name N or name CA or n \ ame C or name O or name CB )) or resid 991 through 1016 or (resid 1017 and (name \ N or name CA or name C or name O or name CB )) or resid 1018 through 1030 or (r \ esid 1031 and (name N or name CA or name C or name O or name CB )) or resid 1032 \ through 1040 or (resid 1041 and (name N or name CA or name C or name O or name \ CB )) or resid 1042 through 1110 or (resid 1111 and (name N or name CA or name C \ or name O or name CB )) or resid 1112 through 1134 or (resid 1135 and (name N o \ r name CA or name C or name O or name CB )) or resid 1136 through 1137 or resid \ 1301 through 1319)) } ncs_group { reference = (chain 'D' and (resid 2 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 83 or (resid 84 through 93 and (nam \ e N or name CA or name C or name O or name CB )) or resid 94 through 124)) selection = (chain 'H' and ((resid 2 through 7 and (name N or name CA or name C or name O or \ name CB )) or (resid 8 through 13 and (name N or name CA or name C or name O or \ name CB )) or resid 14 through 17 or (resid 18 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 36 or (resid 37 and (nam \ e N or name CA or name C or name O or name CB )) or resid 38 through 47 or (resi \ d 48 and (name N or name CA or name C or name O or name CB )) or resid 49 throug \ h 52 or (resid 53 and (name N or name CA or name C or name O or name CB )) or re \ sid 54 or (resid 55 and (name N or name CA or name C or name O or name CB )) or \ resid 56 through 57 or (resid 58 and (name N or name CA or name C or name O or n \ ame CB )) or resid 59 through 64 or (resid 65 and (name N or name CA or name C o \ r name O or name CB )) or resid 66 or (resid 67 through 71 and (name N or name C \ A or name C or name O or name CB )) or resid 72 through 73 or (resid 74 through \ 78 and (name N or name CA or name C or name O or name CB )) or resid 79 or (resi \ d 80 through 93 and (name N or name CA or name C or name O or name CB )) or resi \ d 94 through 98 or (resid 99 and (name N or name CA or name C or name O or name \ CB )) or resid 100 or (resid 101 and (name N or name CA or name C or name O or n \ ame CB )) or resid 102 through 107 or (resid 108 through 109 and (name N or name \ CA or name C or name O or name CB )) or resid 110 or (resid 111 and (name N or \ name CA or name C or name O or name CB )) or resid 112 through 114 or (resid 115 \ through 116 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 17 through 124)) } ncs_group { reference = (chain 'E' and (resid 2 through 7 or (resid 11 through 12 and (name N or name CA \ or name C or name O or name CB )) or resid 13 through 19 or (resid 20 through 2 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 23 through 2 \ 6 or (resid 27 through 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 45 or (resid 46 and (name N or name CA or name C or name \ O or name CB )) or resid 47 through 59 or resid 62 through 90 or (resid 91 and ( \ name N or name CA or name C or name O or name CB )) or resid 92 through 101)) selection = (chain 'L' and ((resid 2 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 through 28 or (resid 29 through 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 38 or (resid 39 through \ 40 and (name N or name CA or name C or name O or name CB )) or resid 41 through \ 47 or (resid 48 through 49 and (name N or name CA or name C or name O or name C \ B )) or resid 50 through 82 or (resid 83 through 86 and (name N or name CA or na \ me C or name O or name CB )) or resid 87 through 89 or (resid 90 through 91 and \ (name N or name CA or name C or name O or name CB )) or resid 92 through 94 or ( \ resid 95 through 97 and (name N or name CA or name C or name O or name CB )) or \ resid 98 through 101)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.140 Find NCS groups from input model: 0.730 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 : 0.013 0.148 24919 Z= 0.677 Angle : 1.363 8.273 34179 Z= 0.911 Chirality : 0.091 0.443 4184 Planarity : 0.005 0.025 4304 Dihedral : 10.414 107.371 9201 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 0.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % Rotamer: Outliers : 0.09 % Allowed : 0.59 % Favored : 99.32 % 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: 0.62 (0.14), residues: 3181 helix: 0.17 (0.18), residues: 691 sheet: 1.21 (0.17), residues: 767 loop : 0.26 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 509 TYR 0.044 0.005 TYR A 266 PHE 0.024 0.004 PHE L 98 TRP 0.030 0.007 TRP C 886 HIS 0.004 0.001 HIS C 655 Details of bonding type rmsd covalent geometry : bond 0.01221 (24814) covalent geometry : angle 1.34650 (33904) SS BOND : bond 0.02981 ( 40) SS BOND : angle 3.24590 ( 80) hydrogen bonds : bond 0.16886 ( 1129) hydrogen bonds : angle 7.89172 ( 3153) link_ALPHA1-3 : bond 0.05908 ( 1) link_ALPHA1-3 : angle 2.30383 ( 3) link_ALPHA1-6 : bond 0.04473 ( 1) link_ALPHA1-6 : angle 1.95154 ( 3) link_BETA1-4 : bond 0.05394 ( 14) link_BETA1-4 : angle 3.09074 ( 42) link_BETA1-6 : bond 0.04433 ( 2) link_BETA1-6 : angle 1.94555 ( 6) link_NAG-ASN : bond 0.05670 ( 47) link_NAG-ASN : angle 2.28445 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 438 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8326 (mm) cc_final: 0.7982 (mp) REVERT: A 758 SER cc_start: 0.8248 (m) cc_final: 0.7916 (t) REVERT: C 423 TYR cc_start: 0.7001 (t80) cc_final: 0.6618 (t80) REVERT: C 740 MET cc_start: 0.7590 (ttt) cc_final: 0.7354 (ttt) REVERT: C 751 ASN cc_start: 0.7777 (m-40) cc_final: 0.7399 (t0) REVERT: C 778 THR cc_start: 0.9036 (m) cc_final: 0.8787 (p) REVERT: C 870 ILE cc_start: 0.8962 (mm) cc_final: 0.8682 (mt) REVERT: H 34 ILE cc_start: 0.8951 (mt) cc_final: 0.8564 (tt) REVERT: H 47 TRP cc_start: 0.8182 (t60) cc_final: 0.7963 (t60) REVERT: H 48 MET cc_start: 0.8100 (mtp) cc_final: 0.7605 (mtp) REVERT: H 117 TRP cc_start: 0.8369 (m100) cc_final: 0.8077 (m100) REVERT: D 57 ASN cc_start: 0.8411 (t0) cc_final: 0.8198 (p0) outliers start: 2 outliers final: 0 residues processed: 440 average time/residue: 0.1592 time to fit residues: 111.4724 Evaluate side-chains 161 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 914 ASN A 957 GLN A 978 ASN A1010 GLN A1048 HIS A1119 ASN B 542 ASN B 606 ASN C 87 ASN C 804 GLN C 926 GLN C 935 GLN C 955 ASN C1002 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.108030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.088713 restraints weight = 64279.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.089514 restraints weight = 44287.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.090300 restraints weight = 33797.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.090595 restraints weight = 27665.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.090705 restraints weight = 25164.983| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24919 Z= 0.164 Angle : 0.632 9.594 34179 Z= 0.335 Chirality : 0.046 0.407 4184 Planarity : 0.004 0.049 4304 Dihedral : 6.322 75.622 4787 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.32 % Favored : 98.59 % Rotamer: Outliers : 1.86 % Allowed : 7.26 % Favored : 90.88 % 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: 0.89 (0.14), residues: 3181 helix: 1.45 (0.20), residues: 697 sheet: 0.87 (0.16), residues: 869 loop : 0.14 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 273 TYR 0.025 0.002 TYR B1067 PHE 0.023 0.002 PHE A 318 TRP 0.014 0.002 TRP L 36 HIS 0.004 0.001 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00354 (24814) covalent geometry : angle 0.60867 (33904) SS BOND : bond 0.00563 ( 40) SS BOND : angle 1.63199 ( 80) hydrogen bonds : bond 0.05231 ( 1129) hydrogen bonds : angle 6.09613 ( 3153) link_ALPHA1-3 : bond 0.01008 ( 1) link_ALPHA1-3 : angle 2.16780 ( 3) link_ALPHA1-6 : bond 0.00480 ( 1) link_ALPHA1-6 : angle 1.50476 ( 3) link_BETA1-4 : bond 0.00634 ( 14) link_BETA1-4 : angle 1.95753 ( 42) link_BETA1-6 : bond 0.00633 ( 2) link_BETA1-6 : angle 1.06163 ( 6) link_NAG-ASN : bond 0.00703 ( 47) link_NAG-ASN : angle 2.20603 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1029 MET cc_start: 0.7753 (ttm) cc_final: 0.7339 (mtt) REVERT: C 423 TYR cc_start: 0.7069 (t80) cc_final: 0.6521 (t80) REVERT: C 751 ASN cc_start: 0.8332 (m-40) cc_final: 0.8012 (t0) REVERT: C 870 ILE cc_start: 0.8789 (mm) cc_final: 0.8560 (mt) REVERT: H 101 THR cc_start: 0.8604 (p) cc_final: 0.8223 (p) outliers start: 41 outliers final: 21 residues processed: 216 average time/residue: 0.1484 time to fit residues: 53.0089 Evaluate side-chains 144 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 940 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 87 optimal weight: 0.6980 chunk 243 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 230 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 chunk 308 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 282 optimal weight: 5.9990 chunk 186 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C1048 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.106582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.087002 restraints weight = 64735.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.088121 restraints weight = 42440.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.089023 restraints weight = 30970.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.089194 restraints weight = 25700.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.089226 restraints weight = 24311.050| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24919 Z= 0.133 Angle : 0.558 9.515 34179 Z= 0.288 Chirality : 0.044 0.236 4184 Planarity : 0.003 0.043 4304 Dihedral : 5.106 61.351 4787 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.98 % Favored : 97.96 % Rotamer: Outliers : 1.95 % Allowed : 8.03 % Favored : 90.02 % 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: 0.95 (0.14), residues: 3181 helix: 2.03 (0.21), residues: 681 sheet: 0.68 (0.16), residues: 877 loop : 0.07 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.023 0.001 TYR B1067 PHE 0.020 0.002 PHE C 565 TRP 0.029 0.002 TRP L 36 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00292 (24814) covalent geometry : angle 0.53682 (33904) SS BOND : bond 0.00469 ( 40) SS BOND : angle 1.46271 ( 80) hydrogen bonds : bond 0.04247 ( 1129) hydrogen bonds : angle 5.55479 ( 3153) link_ALPHA1-3 : bond 0.01470 ( 1) link_ALPHA1-3 : angle 1.36861 ( 3) link_ALPHA1-6 : bond 0.00409 ( 1) link_ALPHA1-6 : angle 1.54118 ( 3) link_BETA1-4 : bond 0.00571 ( 14) link_BETA1-4 : angle 1.41170 ( 42) link_BETA1-6 : bond 0.00454 ( 2) link_BETA1-6 : angle 1.19214 ( 6) link_NAG-ASN : bond 0.00579 ( 47) link_NAG-ASN : angle 2.02307 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1029 MET cc_start: 0.7888 (ttm) cc_final: 0.7419 (mtt) REVERT: C 870 ILE cc_start: 0.8946 (mm) cc_final: 0.8716 (mt) REVERT: H 101 THR cc_start: 0.8649 (p) cc_final: 0.8230 (p) outliers start: 43 outliers final: 23 residues processed: 187 average time/residue: 0.1381 time to fit residues: 43.3055 Evaluate side-chains 147 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain E residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 224 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 315 optimal weight: 0.0770 chunk 154 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 295 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 ASN A1119 ASN B 955 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN C1064 HIS L 90 GLN L 92 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.104361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.084073 restraints weight = 64575.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.085418 restraints weight = 41127.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.086045 restraints weight = 29508.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.086417 restraints weight = 26891.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.086544 restraints weight = 24530.883| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24919 Z= 0.154 Angle : 0.562 9.760 34179 Z= 0.289 Chirality : 0.045 0.293 4184 Planarity : 0.004 0.040 4304 Dihedral : 4.625 45.535 4787 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.63 % Favored : 98.30 % Rotamer: Outliers : 2.40 % Allowed : 8.17 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.82 (0.14), residues: 3181 helix: 1.93 (0.20), residues: 681 sheet: 0.47 (0.16), residues: 859 loop : 0.08 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 84 TYR 0.024 0.002 TYR B1067 PHE 0.019 0.002 PHE A 318 TRP 0.026 0.001 TRP D 117 HIS 0.005 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00348 (24814) covalent geometry : angle 0.53946 (33904) SS BOND : bond 0.00336 ( 40) SS BOND : angle 1.85036 ( 80) hydrogen bonds : bond 0.03930 ( 1129) hydrogen bonds : angle 5.36696 ( 3153) link_ALPHA1-3 : bond 0.01468 ( 1) link_ALPHA1-3 : angle 1.61138 ( 3) link_ALPHA1-6 : bond 0.00508 ( 1) link_ALPHA1-6 : angle 1.47553 ( 3) link_BETA1-4 : bond 0.00402 ( 14) link_BETA1-4 : angle 1.24507 ( 42) link_BETA1-6 : bond 0.00319 ( 2) link_BETA1-6 : angle 1.36314 ( 6) link_NAG-ASN : bond 0.00376 ( 47) link_NAG-ASN : angle 2.02819 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 869 MET cc_start: 0.7968 (mmm) cc_final: 0.7602 (mmm) REVERT: C 870 ILE cc_start: 0.8866 (mm) cc_final: 0.8629 (mt) REVERT: C 900 MET cc_start: 0.8033 (mtm) cc_final: 0.7565 (mtm) REVERT: H 29 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7373 (t80) REVERT: H 54 TYR cc_start: 0.7832 (t80) cc_final: 0.7515 (t80) outliers start: 53 outliers final: 32 residues processed: 185 average time/residue: 0.1356 time to fit residues: 42.8902 Evaluate side-chains 161 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 141 optimal weight: 9.9990 chunk 131 optimal weight: 40.0000 chunk 20 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 316 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 234 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 247 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.099533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.075583 restraints weight = 63672.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.077888 restraints weight = 34504.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.079388 restraints weight = 22852.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.080393 restraints weight = 17353.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.081018 restraints weight = 14390.895| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24919 Z= 0.121 Angle : 0.524 9.563 34179 Z= 0.267 Chirality : 0.044 0.225 4184 Planarity : 0.003 0.040 4304 Dihedral : 4.360 37.910 4787 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.82 % Favored : 98.11 % Rotamer: Outliers : 1.86 % Allowed : 9.39 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.86 (0.15), residues: 3181 helix: 2.13 (0.20), residues: 677 sheet: 0.44 (0.17), residues: 849 loop : 0.06 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 84 TYR 0.022 0.001 TYR B1067 PHE 0.021 0.001 PHE A 140 TRP 0.026 0.001 TRP L 36 HIS 0.004 0.001 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00267 (24814) covalent geometry : angle 0.50413 (33904) SS BOND : bond 0.00291 ( 40) SS BOND : angle 1.60411 ( 80) hydrogen bonds : bond 0.03700 ( 1129) hydrogen bonds : angle 5.21718 ( 3153) link_ALPHA1-3 : bond 0.01405 ( 1) link_ALPHA1-3 : angle 1.27072 ( 3) link_ALPHA1-6 : bond 0.00576 ( 1) link_ALPHA1-6 : angle 1.41788 ( 3) link_BETA1-4 : bond 0.00439 ( 14) link_BETA1-4 : angle 1.12524 ( 42) link_BETA1-6 : bond 0.00352 ( 2) link_BETA1-6 : angle 1.21993 ( 6) link_NAG-ASN : bond 0.00369 ( 47) link_NAG-ASN : angle 1.88105 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8786 (ptm-80) cc_final: 0.8345 (ptp90) REVERT: C 869 MET cc_start: 0.7999 (mmm) cc_final: 0.7488 (mmm) REVERT: C 873 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: C 900 MET cc_start: 0.8176 (mtm) cc_final: 0.7618 (mtm) REVERT: H 36 TRP cc_start: 0.8419 (m100) cc_final: 0.7215 (m100) REVERT: H 54 TYR cc_start: 0.7963 (t80) cc_final: 0.7456 (t80) REVERT: E 36 TRP cc_start: 0.7221 (OUTLIER) cc_final: 0.6921 (m-10) outliers start: 41 outliers final: 23 residues processed: 169 average time/residue: 0.1384 time to fit residues: 39.6579 Evaluate side-chains 145 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain E residue 36 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 218 optimal weight: 0.8980 chunk 277 optimal weight: 0.4980 chunk 152 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 260 optimal weight: 2.9990 chunk 131 optimal weight: 40.0000 chunk 182 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN B 804 GLN B 901 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.104056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.085591 restraints weight = 66423.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085653 restraints weight = 49861.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.086435 restraints weight = 53435.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.086807 restraints weight = 36054.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.087440 restraints weight = 32777.403| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 24919 Z= 0.248 Angle : 0.648 9.500 34179 Z= 0.329 Chirality : 0.046 0.225 4184 Planarity : 0.004 0.043 4304 Dihedral : 4.900 39.057 4787 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 2.36 % Allowed : 9.62 % Favored : 88.02 % 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: 0.44 (0.14), residues: 3181 helix: 1.68 (0.20), residues: 668 sheet: 0.20 (0.17), residues: 844 loop : -0.14 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 815 TYR 0.026 0.002 TYR B1067 PHE 0.027 0.002 PHE B 906 TRP 0.013 0.002 TRP H 117 HIS 0.009 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00570 (24814) covalent geometry : angle 0.62575 (33904) SS BOND : bond 0.00377 ( 40) SS BOND : angle 1.95308 ( 80) hydrogen bonds : bond 0.04256 ( 1129) hydrogen bonds : angle 5.50970 ( 3153) link_ALPHA1-3 : bond 0.01253 ( 1) link_ALPHA1-3 : angle 1.22245 ( 3) link_ALPHA1-6 : bond 0.00658 ( 1) link_ALPHA1-6 : angle 1.27957 ( 3) link_BETA1-4 : bond 0.00423 ( 14) link_BETA1-4 : angle 1.26227 ( 42) link_BETA1-6 : bond 0.00199 ( 2) link_BETA1-6 : angle 1.58487 ( 6) link_NAG-ASN : bond 0.00537 ( 47) link_NAG-ASN : angle 2.21728 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 121 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 869 MET cc_start: 0.7365 (mmm) cc_final: 0.7077 (mmm) REVERT: C 873 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: C 900 MET cc_start: 0.8118 (mtm) cc_final: 0.7437 (mtm) REVERT: H 36 TRP cc_start: 0.8250 (m100) cc_final: 0.7347 (m100) REVERT: H 47 TRP cc_start: 0.8521 (t60) cc_final: 0.8006 (t60) REVERT: H 54 TYR cc_start: 0.7771 (t80) cc_final: 0.7325 (t80) outliers start: 52 outliers final: 39 residues processed: 154 average time/residue: 0.1333 time to fit residues: 35.6814 Evaluate side-chains 148 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain E residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 76 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 209 optimal weight: 9.9990 chunk 189 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 262 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 901 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.105829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.087059 restraints weight = 65927.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.088109 restraints weight = 51304.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.088605 restraints weight = 39737.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.088939 restraints weight = 34355.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.088996 restraints weight = 30841.044| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 24919 Z= 0.137 Angle : 0.566 17.978 34179 Z= 0.286 Chirality : 0.044 0.255 4184 Planarity : 0.003 0.046 4304 Dihedral : 4.589 37.488 4787 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.04 % Favored : 97.89 % Rotamer: Outliers : 1.81 % Allowed : 10.71 % Favored : 87.48 % 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: 3181 helix: 2.03 (0.21), residues: 674 sheet: 0.26 (0.17), residues: 837 loop : -0.15 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1019 TYR 0.022 0.001 TYR B 707 PHE 0.029 0.001 PHE A 140 TRP 0.011 0.001 TRP L 36 HIS 0.003 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00310 (24814) covalent geometry : angle 0.53456 (33904) SS BOND : bond 0.00351 ( 40) SS BOND : angle 2.67049 ( 80) hydrogen bonds : bond 0.03785 ( 1129) hydrogen bonds : angle 5.28608 ( 3153) link_ALPHA1-3 : bond 0.01672 ( 1) link_ALPHA1-3 : angle 1.27908 ( 3) link_ALPHA1-6 : bond 0.00662 ( 1) link_ALPHA1-6 : angle 1.29985 ( 3) link_BETA1-4 : bond 0.00502 ( 14) link_BETA1-4 : angle 1.14800 ( 42) link_BETA1-6 : bond 0.00325 ( 2) link_BETA1-6 : angle 1.23764 ( 6) link_NAG-ASN : bond 0.00382 ( 47) link_NAG-ASN : angle 2.07616 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8445 (ptm-80) cc_final: 0.8238 (ptp90) REVERT: A 780 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7115 (mm-30) REVERT: B 223 LEU cc_start: 0.7508 (mp) cc_final: 0.7247 (mt) REVERT: C 873 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7461 (m-80) REVERT: C 900 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7439 (mtm) REVERT: H 54 TYR cc_start: 0.7689 (t80) cc_final: 0.7302 (t80) outliers start: 40 outliers final: 27 residues processed: 155 average time/residue: 0.1371 time to fit residues: 36.6281 Evaluate side-chains 144 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 111 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 53 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 236 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C1071 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.106029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.087285 restraints weight = 65841.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.088122 restraints weight = 51482.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.088701 restraints weight = 40790.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089020 restraints weight = 33552.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.089167 restraints weight = 30905.571| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 24919 Z= 0.130 Angle : 0.552 12.076 34179 Z= 0.278 Chirality : 0.044 0.286 4184 Planarity : 0.004 0.086 4304 Dihedral : 4.415 36.789 4787 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.36 % Rotamer: Outliers : 1.86 % Allowed : 11.03 % Favored : 87.11 % 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: 0.66 (0.15), residues: 3181 helix: 2.02 (0.21), residues: 677 sheet: 0.28 (0.17), residues: 854 loop : -0.07 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1019 TYR 0.022 0.001 TYR B 707 PHE 0.030 0.001 PHE A 140 TRP 0.021 0.001 TRP H 47 HIS 0.002 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00296 (24814) covalent geometry : angle 0.52930 (33904) SS BOND : bond 0.00238 ( 40) SS BOND : angle 2.04829 ( 80) hydrogen bonds : bond 0.03659 ( 1129) hydrogen bonds : angle 5.22783 ( 3153) link_ALPHA1-3 : bond 0.01451 ( 1) link_ALPHA1-3 : angle 1.12199 ( 3) link_ALPHA1-6 : bond 0.00649 ( 1) link_ALPHA1-6 : angle 1.29908 ( 3) link_BETA1-4 : bond 0.00395 ( 14) link_BETA1-4 : angle 1.09625 ( 42) link_BETA1-6 : bond 0.00286 ( 2) link_BETA1-6 : angle 1.23776 ( 6) link_NAG-ASN : bond 0.00368 ( 47) link_NAG-ASN : angle 1.93696 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 223 LEU cc_start: 0.7492 (mp) cc_final: 0.7250 (mt) REVERT: B 902 MET cc_start: 0.9018 (tpp) cc_final: 0.8751 (tpp) REVERT: C 900 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7350 (mtm) REVERT: H 54 TYR cc_start: 0.7690 (t80) cc_final: 0.7282 (t80) outliers start: 41 outliers final: 36 residues processed: 146 average time/residue: 0.1354 time to fit residues: 34.4892 Evaluate side-chains 148 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 111 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 78 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 319 optimal weight: 0.0670 chunk 302 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 208 optimal weight: 0.6980 chunk 243 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C1064 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.106669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.087783 restraints weight = 66243.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.088715 restraints weight = 51295.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089114 restraints weight = 45814.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.090204 restraints weight = 35661.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.090112 restraints weight = 31010.322| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 24919 Z= 0.111 Angle : 0.524 12.024 34179 Z= 0.264 Chirality : 0.043 0.301 4184 Planarity : 0.003 0.039 4304 Dihedral : 4.243 36.404 4787 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.93 % Rotamer: Outliers : 1.72 % Allowed : 11.30 % Favored : 86.98 % 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: 0.74 (0.15), residues: 3181 helix: 2.14 (0.21), residues: 676 sheet: 0.31 (0.17), residues: 853 loop : -0.03 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1019 TYR 0.022 0.001 TYR B 707 PHE 0.030 0.001 PHE A 140 TRP 0.018 0.001 TRP H 47 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00247 (24814) covalent geometry : angle 0.50369 (33904) SS BOND : bond 0.00202 ( 40) SS BOND : angle 1.73860 ( 80) hydrogen bonds : bond 0.03502 ( 1129) hydrogen bonds : angle 5.12523 ( 3153) link_ALPHA1-3 : bond 0.01410 ( 1) link_ALPHA1-3 : angle 1.10689 ( 3) link_ALPHA1-6 : bond 0.00646 ( 1) link_ALPHA1-6 : angle 1.30299 ( 3) link_BETA1-4 : bond 0.00415 ( 14) link_BETA1-4 : angle 1.07500 ( 42) link_BETA1-6 : bond 0.00312 ( 2) link_BETA1-6 : angle 1.20919 ( 6) link_NAG-ASN : bond 0.00339 ( 47) link_NAG-ASN : angle 1.83432 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 223 LEU cc_start: 0.7461 (mp) cc_final: 0.7221 (mt) REVERT: C 900 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7393 (mtm) REVERT: H 47 TRP cc_start: 0.8390 (t60) cc_final: 0.7775 (t60) REVERT: H 54 TYR cc_start: 0.7635 (t80) cc_final: 0.7192 (t80) outliers start: 38 outliers final: 29 residues processed: 146 average time/residue: 0.1323 time to fit residues: 33.3854 Evaluate side-chains 143 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 27 optimal weight: 0.9980 chunk 296 optimal weight: 9.9990 chunk 257 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 50.0000 chunk 206 optimal weight: 0.0050 chunk 108 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 127 optimal weight: 50.0000 chunk 226 optimal weight: 0.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.106342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.087466 restraints weight = 66126.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.088522 restraints weight = 52417.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.089244 restraints weight = 42892.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.089541 restraints weight = 33506.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.089732 restraints weight = 30469.295| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24919 Z= 0.121 Angle : 0.523 12.114 34179 Z= 0.264 Chirality : 0.043 0.296 4184 Planarity : 0.003 0.039 4304 Dihedral : 4.161 35.565 4787 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.67 % Rotamer: Outliers : 1.63 % Allowed : 11.71 % Favored : 86.66 % 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: 0.74 (0.15), residues: 3181 helix: 2.14 (0.21), residues: 676 sheet: 0.32 (0.17), residues: 857 loop : -0.04 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.021 0.001 TYR B 707 PHE 0.030 0.001 PHE A 140 TRP 0.018 0.001 TRP H 47 HIS 0.002 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00274 (24814) covalent geometry : angle 0.50435 (33904) SS BOND : bond 0.00224 ( 40) SS BOND : angle 1.60944 ( 80) hydrogen bonds : bond 0.03480 ( 1129) hydrogen bonds : angle 5.07365 ( 3153) link_ALPHA1-3 : bond 0.01352 ( 1) link_ALPHA1-3 : angle 1.05388 ( 3) link_ALPHA1-6 : bond 0.00633 ( 1) link_ALPHA1-6 : angle 1.30003 ( 3) link_BETA1-4 : bond 0.00397 ( 14) link_BETA1-4 : angle 1.08576 ( 42) link_BETA1-6 : bond 0.00277 ( 2) link_BETA1-6 : angle 1.24733 ( 6) link_NAG-ASN : bond 0.00322 ( 47) link_NAG-ASN : angle 1.78047 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 223 LEU cc_start: 0.7453 (mp) cc_final: 0.7219 (mt) REVERT: C 900 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7365 (mtm) REVERT: H 47 TRP cc_start: 0.8394 (t60) cc_final: 0.7783 (t60) REVERT: H 54 TYR cc_start: 0.7709 (t80) cc_final: 0.7296 (t80) outliers start: 36 outliers final: 30 residues processed: 142 average time/residue: 0.1358 time to fit residues: 33.6379 Evaluate side-chains 141 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 28 optimal weight: 0.0070 chunk 87 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 309 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 295 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 264 optimal weight: 3.9990 chunk 250 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.106931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.087852 restraints weight = 66045.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.089059 restraints weight = 51864.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.089919 restraints weight = 37528.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.090224 restraints weight = 30664.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.090419 restraints weight = 29698.726| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 24919 Z= 0.104 Angle : 0.509 11.674 34179 Z= 0.257 Chirality : 0.043 0.307 4184 Planarity : 0.003 0.038 4304 Dihedral : 4.028 35.189 4787 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % Rotamer: Outliers : 1.68 % Allowed : 12.07 % Favored : 86.25 % 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: 0.81 (0.15), residues: 3181 helix: 2.19 (0.21), residues: 677 sheet: 0.33 (0.17), residues: 858 loop : 0.02 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1019 TYR 0.023 0.001 TYR B 707 PHE 0.034 0.001 PHE B 55 TRP 0.016 0.001 TRP H 47 HIS 0.003 0.001 HIS L 92 Details of bonding type rmsd covalent geometry : bond 0.00228 (24814) covalent geometry : angle 0.49259 (33904) SS BOND : bond 0.00200 ( 40) SS BOND : angle 1.47031 ( 80) hydrogen bonds : bond 0.03364 ( 1129) hydrogen bonds : angle 4.99262 ( 3153) link_ALPHA1-3 : bond 0.01040 ( 1) link_ALPHA1-3 : angle 0.92603 ( 3) link_ALPHA1-6 : bond 0.00626 ( 1) link_ALPHA1-6 : angle 1.30238 ( 3) link_BETA1-4 : bond 0.00431 ( 14) link_BETA1-4 : angle 1.07127 ( 42) link_BETA1-6 : bond 0.00313 ( 2) link_BETA1-6 : angle 1.23155 ( 6) link_NAG-ASN : bond 0.00314 ( 47) link_NAG-ASN : angle 1.69931 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3274.75 seconds wall clock time: 57 minutes 29.89 seconds (3449.89 seconds total)