Starting phenix.real_space_refine on Sun Jul 5 20:02:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sb5_24970/07_2026/7sb5_24970.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sb5_24970/07_2026/7sb5_24970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7sb5_24970/07_2026/7sb5_24970.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sb5_24970/07_2026/7sb5_24970.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sb5_24970/07_2026/7sb5_24970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sb5_24970/07_2026/7sb5_24970.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sb5_24970/07_2026/7sb5_24970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sb5_24970/07_2026/7sb5_24970.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 189 5.16 5 C 18696 2.51 5 N 4799 2.21 5 O 5773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29457 Number of models: 1 Model: "" Number of chains: 19 Chain: "C" Number of atoms: 9183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9183 Classifications: {'peptide': 1180} Link IDs: {'PTRANS': 52, 'TRANS': 1127} Chain breaks: 5 Chain: "B" Number of atoms: 9202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9202 Classifications: {'peptide': 1183} Link IDs: {'PTRANS': 51, 'TRANS': 1131} Chain breaks: 5 Chain: "A" Number of atoms: 9229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 9229 Classifications: {'peptide': 1187} Link IDs: {'PTRANS': 52, 'TRANS': 1134} Chain breaks: 5 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 485 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'TRANS': 96} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'UNK:plan-1': 97} Unresolved non-hydrogen planarities: 97 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 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 chiralities: 11 Chain: "B" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 176 Unusual residues: {'NAG': 10, 'PLM': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 158 Unusual residues: {'NAG': 10, 'PLM': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.80, per 1000 atoms: 0.23 Number of scatterers: 29457 At special positions: 0 Unit cell: (181.28, 169.95, 159.65, 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 189 16.00 O 5773 8.00 N 4799 7.00 C 18696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 260 " distance=2.09 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 368 " distance=2.02 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 439 " distance=2.05 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 614 " distance=2.04 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 499 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 576 " distance=2.02 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 548 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 578 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 597 " distance=2.04 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 683 " distance=2.04 Simple disulfide: pdb=" SG CYS C 708 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C 747 " - pdb=" SG CYS C 756 " distance=2.03 Simple disulfide: pdb=" SG CYS C 825 " - pdb=" SG CYS C 847 " distance=2.06 Simple disulfide: pdb=" SG CYS C 830 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 937 " - pdb=" SG CYS C 948 " distance=2.07 Simple disulfide: pdb=" SG CYS C1125 " - pdb=" SG CYS C1136 " distance=2.02 Simple disulfide: pdb=" SG CYS C1175 " - pdb=" SG CYS C1220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 260 " distance=2.04 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 308 " distance=2.04 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.10 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.04 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.06 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 576 " distance=2.02 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.07 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.05 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 756 " distance=2.06 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 847 " distance=2.07 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 937 " - pdb=" SG CYS B 948 " distance=2.04 Simple disulfide: pdb=" SG CYS B1125 " - pdb=" SG CYS B1136 " distance=2.02 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1220 " distance=2.02 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 173 " distance=2.02 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 260 " distance=2.04 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.02 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.04 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.04 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 522 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.04 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.05 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.04 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 756 " distance=2.03 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 847 " distance=2.06 Simple disulfide: pdb=" SG CYS A 830 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 937 " - pdb=" SG CYS A 948 " distance=2.04 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.04 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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-ASN " NAG A1401 " - " ASN A 212 " " NAG A1402 " - " ASN A 449 " " NAG A1403 " - " ASN A 713 " " NAG A1404 " - " ASN A 787 " " NAG A1405 " - " ASN A 936 " " NAG A1406 " - " ASN A1193 " " NAG A1407 " - " ASN A 675 " " NAG A1408 " - " ASN A 695 " " NAG A1409 " - " ASN A 648 " " NAG A1410 " - " ASN A1223 " " NAG B1401 " - " ASN B 212 " " NAG B1402 " - " ASN B 449 " " NAG B1403 " - " ASN B 713 " " NAG B1404 " - " ASN B 787 " " NAG B1405 " - " ASN B 936 " " NAG B1406 " - " ASN B 675 " " NAG B1407 " - " ASN B 695 " " NAG B1408 " - " ASN B 648 " " NAG B1409 " - " ASN B 371 " " NAG B1410 " - " ASN B1223 " " NAG C1401 " - " ASN C 137 " " NAG C1402 " - " ASN C 212 " " NAG C1403 " - " ASN C 713 " " NAG C1404 " - " ASN C 936 " " NAG C1405 " - " ASN C1193 " " NAG C1406 " - " ASN C 675 " " NAG C1407 " - " ASN C 695 " " NAG C1408 " - " ASN C 648 " " NAG C1409 " - " ASN C 449 " " NAG C1410 " - " ASN C1223 " " NAG C1411 " - " ASN C 787 " " NAG D 1 " - " ASN C 738 " " NAG E 1 " - " ASN C 206 " " NAG F 1 " - " ASN C 371 " " NAG G 1 " - " ASN B 137 " " NAG I 1 " - " ASN B 738 " " NAG J 1 " - " ASN B1193 " " NAG K 1 " - " ASN B 206 " " NAG M 1 " - " ASN A 137 " " NAG N 1 " - " ASN A 371 " " NAG O 1 " - " ASN A 738 " " NAG P 1 " - " ASN A 206 " Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.2 seconds 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7040 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 77 sheets defined 25.5% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'C' and resid 301 through 311 Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 357 through 360 removed outlier: 3.578A pdb=" N TRP C 360 " --> pdb=" O PRO C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 357 through 360' Processing helix chain 'C' and resid 371 through 379 removed outlier: 4.687A pdb=" N SER C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 424 through 429 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 458 through 464 Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 707 through 714 Processing helix chain 'C' and resid 824 through 830 Processing helix chain 'C' and resid 833 through 841 Processing helix chain 'C' and resid 843 through 874 removed outlier: 3.895A pdb=" N CYS C 847 " --> pdb=" O TYR C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 884 Processing helix chain 'C' and resid 913 through 921 Processing helix chain 'C' and resid 926 through 934 Processing helix chain 'C' and resid 945 through 953 Processing helix chain 'C' and resid 963 through 980 Processing helix chain 'C' and resid 990 through 1002 Processing helix chain 'C' and resid 1005 through 1012 Processing helix chain 'C' and resid 1012 through 1030 Processing helix chain 'C' and resid 1035 through 1059 removed outlier: 3.654A pdb=" N LEU C1059 " --> pdb=" O LEU C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1077 Processing helix chain 'C' and resid 1078 through 1125 removed outlier: 3.959A pdb=" N ALA C1084 " --> pdb=" O PRO C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1210 through 1212 No H-bonds generated for 'chain 'C' and resid 1210 through 1212' Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 344 through 350 Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 458 through 464 Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 707 through 714 Processing helix chain 'B' and resid 824 through 830 Processing helix chain 'B' and resid 833 through 841 Processing helix chain 'B' and resid 843 through 874 removed outlier: 3.668A pdb=" N CYS B 847 " --> pdb=" O TYR B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 884 Processing helix chain 'B' and resid 913 through 921 Processing helix chain 'B' and resid 926 through 935 Processing helix chain 'B' and resid 945 through 953 Processing helix chain 'B' and resid 963 through 977 Processing helix chain 'B' and resid 990 through 1001 Processing helix chain 'B' and resid 1005 through 1012 Processing helix chain 'B' and resid 1012 through 1030 Processing helix chain 'B' and resid 1035 through 1058 Processing helix chain 'B' and resid 1059 through 1061 No H-bonds generated for 'chain 'B' and resid 1059 through 1061' Processing helix chain 'B' and resid 1069 through 1077 Processing helix chain 'B' and resid 1078 through 1126 removed outlier: 4.933A pdb=" N ALA B1084 " --> pdb=" O PRO B1080 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN B1085 " --> pdb=" O GLU B1081 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1212 No H-bonds generated for 'chain 'B' and resid 1210 through 1212' Processing helix chain 'A' and resid 46 through 50 removed outlier: 4.438A pdb=" N ASN A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'A' and resid 371 through 379 Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 422 through 429 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 824 through 830 Processing helix chain 'A' and resid 833 through 840 Processing helix chain 'A' and resid 843 through 874 removed outlier: 3.514A pdb=" N CYS A 847 " --> pdb=" O TYR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 884 Processing helix chain 'A' and resid 913 through 921 Processing helix chain 'A' and resid 926 through 937 removed outlier: 4.222A pdb=" N ASN A 935 " --> pdb=" O VAL A 931 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N CYS A 937 " --> pdb=" O ALA A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 953 Processing helix chain 'A' and resid 963 through 980 Processing helix chain 'A' and resid 990 through 1001 Processing helix chain 'A' and resid 1006 through 1012 Processing helix chain 'A' and resid 1012 through 1030 Processing helix chain 'A' and resid 1035 through 1060 removed outlier: 3.500A pdb=" N VAL A1045 " --> pdb=" O ILE A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1077 Processing helix chain 'A' and resid 1078 through 1125 removed outlier: 4.132A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1212 No H-bonds generated for 'chain 'A' and resid 1210 through 1212' Processing helix chain 'H' and resid 69 through 73 Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 44 removed outlier: 4.066A pdb=" N ALA C 43 " --> pdb=" O TYR C 79 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N THR C 78 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE C 231 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N PHE C 240 " --> pdb=" O PHE C 231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 64 through 73 removed outlier: 3.576A pdb=" N ASN C 294 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.980A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.812A pdb=" N THR C 178 " --> pdb=" O THR C 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA6, first strand: chain 'C' and resid 114 through 118 Processing sheet with id=AA7, first strand: chain 'C' and resid 318 through 321 Processing sheet with id=AA8, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'C' and resid 331 through 335 removed outlier: 3.560A pdb=" N ALA C 331 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY C 668 " --> pdb=" O LEU C 659 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASN C 657 " --> pdb=" O ARG C 670 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASP A 58 " --> pdb=" O GLN C 656 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 353 through 355 removed outlier: 6.777A pdb=" N VAL C 354 " --> pdb=" O SER C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 361 through 365 removed outlier: 3.629A pdb=" N SER C 401 " --> pdb=" O HIS C 606 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 383 " --> pdb=" O TYR C 442 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASN C 444 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA C 381 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 361 through 365 removed outlier: 3.629A pdb=" N SER C 401 " --> pdb=" O HIS C 606 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 369 through 370 Processing sheet with id=AB5, first strand: chain 'C' and resid 485 through 488 Processing sheet with id=AB6, first strand: chain 'C' and resid 491 through 493 removed outlier: 4.354A pdb=" N CYS C 491 " --> pdb=" O SER C 553 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 565 through 566 Processing sheet with id=AB8, first strand: chain 'C' and resid 571 through 572 Processing sheet with id=AB9, first strand: chain 'C' and resid 701 through 704 Processing sheet with id=AC1, first strand: chain 'C' and resid 737 through 744 removed outlier: 5.864A pdb=" N ASN C 738 " --> pdb=" O TYR C 773 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE C 775 " --> pdb=" O ASN C 738 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR C 740 " --> pdb=" O PHE C 775 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASN C 777 " --> pdb=" O THR C 740 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE C 742 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR C 755 " --> pdb=" O VAL C 751 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 784 through 786 removed outlier: 6.383A pdb=" N ASN C 784 " --> pdb=" O LEU A 878 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 797 through 802 Processing sheet with id=AC4, first strand: chain 'C' and resid 805 through 815 removed outlier: 7.220A pdb=" N GLY C1152 " --> pdb=" O ASN C1148 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASN C1148 " --> pdb=" O GLY C1152 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR C1154 " --> pdb=" O VAL C1146 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL C1146 " --> pdb=" O TYR C1154 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C1156 " --> pdb=" O SER C1144 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER C1144 " --> pdb=" O ILE C1156 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE C1158 " --> pdb=" O ILE C1142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 820 through 823 removed outlier: 4.005A pdb=" N LYS C 820 " --> pdb=" O LEU C 958 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 877 through 879 Processing sheet with id=AC7, first strand: chain 'C' and resid 889 through 890 Processing sheet with id=AC8, first strand: chain 'C' and resid 1214 through 1217 removed outlier: 3.724A pdb=" N ARG C1180 " --> pdb=" O ILE C1176 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1187 through 1192 Processing sheet with id=AD1, first strand: chain 'B' and resid 29 through 30 removed outlier: 7.155A pdb=" N SER B 29 " --> pdb=" O LEU B 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 43 through 44 removed outlier: 4.215A pdb=" N ALA B 43 " --> pdb=" O TYR B 79 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR B 78 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE B 227 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN B 243 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA B 229 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 64 through 73 removed outlier: 7.726A pdb=" N GLN B 281 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP B 297 " --> pdb=" O GLN B 281 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU B 283 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA B 295 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA B 285 " --> pdb=" O PHE B 293 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 101 through 102 removed outlier: 6.261A pdb=" N LEU B 163 " --> pdb=" O ASN B 206 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN B 206 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B 165 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS B 204 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 167 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 114 through 118 Processing sheet with id=AD6, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.707A pdb=" N THR B 178 " --> pdb=" O THR B 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 318 through 326 removed outlier: 4.619A pdb=" N VAL B 688 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY B 324 " --> pdb=" O GLY B 686 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY B 686 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG B 687 " --> pdb=" O ARG B 704 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ARG B 704 " --> pdb=" O ARG B 687 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 353 through 355 Processing sheet with id=AD9, first strand: chain 'B' and resid 361 through 365 removed outlier: 6.621A pdb=" N PHE B 399 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 608 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 369 through 370 removed outlier: 6.621A pdb=" N PHE B 399 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 608 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 484 through 488 Processing sheet with id=AE3, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AE4, first strand: chain 'B' and resid 520 through 521 Processing sheet with id=AE5, first strand: chain 'B' and resid 565 through 566 Processing sheet with id=AE6, first strand: chain 'B' and resid 743 through 744 removed outlier: 6.537A pdb=" N TYR B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 749 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 797 through 802 Processing sheet with id=AE8, first strand: chain 'B' and resid 805 through 815 removed outlier: 7.174A pdb=" N GLY B1152 " --> pdb=" O ASN B1148 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASN B1148 " --> pdb=" O GLY B1152 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR B1154 " --> pdb=" O VAL B1146 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL B1146 " --> pdb=" O TYR B1154 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B1156 " --> pdb=" O SER B1144 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER B1144 " --> pdb=" O ILE B1156 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE B1158 " --> pdb=" O ILE B1142 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 820 through 823 removed outlier: 3.978A pdb=" N LYS B 820 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 877 through 879 Processing sheet with id=AF2, first strand: chain 'B' and resid 889 through 890 Processing sheet with id=AF3, first strand: chain 'B' and resid 1214 through 1216 Processing sheet with id=AF4, first strand: chain 'B' and resid 1187 through 1192 Processing sheet with id=AF5, first strand: chain 'A' and resid 29 through 30 removed outlier: 7.335A pdb=" N SER A 29 " --> pdb=" O LEU A 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.956A pdb=" N ALA A 43 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N THR A 78 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE A 227 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN A 243 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA A 229 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 64 through 72 removed outlier: 7.933A pdb=" N GLN A 281 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP A 297 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A 283 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 295 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 285 " --> pdb=" O PHE A 293 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 114 through 118 Processing sheet with id=AF9, first strand: chain 'A' and resid 201 through 208 removed outlier: 6.736A pdb=" N VAL A 167 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS A 204 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL A 165 " --> pdb=" O LYS A 204 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN A 206 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 163 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.563A pdb=" N THR A 178 " --> pdb=" O THR A 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'A' and resid 318 through 321 Processing sheet with id=AG3, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AG4, first strand: chain 'A' and resid 332 through 335 removed outlier: 5.857A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.389A pdb=" N VAL A 354 " --> pdb=" O SER A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'A' and resid 361 through 365 removed outlier: 4.162A pdb=" N GLU A 361 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 361 through 365 removed outlier: 4.162A pdb=" N GLU A 361 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AG9, first strand: chain 'A' and resid 485 through 488 removed outlier: 3.604A pdb=" N SER A 587 " --> pdb=" O TYR A 487 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AH2, first strand: chain 'A' and resid 520 through 521 removed outlier: 3.795A pdb=" N THR A 577 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 565 through 566 Processing sheet with id=AH4, first strand: chain 'A' and resid 737 through 744 removed outlier: 6.627A pdb=" N TYR A 737 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N ASN A 777 " --> pdb=" O TYR A 737 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N SER A 739 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR A 755 " --> pdb=" O VAL A 751 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 797 through 815 removed outlier: 6.847A pdb=" N GLU A 798 " --> pdb=" O LYS A1169 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS A1169 " --> pdb=" O GLU A 798 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLN A 800 " --> pdb=" O THR A1167 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A1167 " --> pdb=" O GLN A 800 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR A1165 " --> pdb=" O PRO A 802 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU A 804 " --> pdb=" O THR A1163 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY A1152 " --> pdb=" O ASN A1148 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASN A1148 " --> pdb=" O GLY A1152 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR A1154 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL A1146 " --> pdb=" O TYR A1154 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A1156 " --> pdb=" O SER A1144 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER A1144 " --> pdb=" O ILE A1156 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE A1158 " --> pdb=" O ILE A1142 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 820 through 823 removed outlier: 4.295A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'A' and resid 889 through 890 Processing sheet with id=AH8, first strand: chain 'A' and resid 1214 through 1217 removed outlier: 5.748A pdb=" N CYS A1175 " --> pdb=" O ALA A1227 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'A' and resid 1187 through 1192 Processing sheet with id=AI1, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AI2, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.848A pdb=" N UNK H 37 " --> pdb=" O UNK H 89 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 32 through 33 removed outlier: 5.355A pdb=" N UNK L 83 " --> pdb=" O UNK L 97 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N UNK L 97 " --> pdb=" O UNK L 83 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N UNK L 85 " --> pdb=" O UNK L 95 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 35 through 36 Processing sheet with id=AI5, first strand: chain 'L' and resid 47 through 48 1164 hydrogen bonds defined for protein. 3174 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.82 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 7999 1.33 - 1.47: 9749 1.47 - 1.62: 12087 1.62 - 1.76: 32 1.76 - 1.91: 223 Bond restraints: 30090 Sorted by residual: bond pdb=" C6 PLM B1411 " pdb=" C7 PLM B1411 " ideal model delta sigma weight residual 1.525 1.360 0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" C6 PLM B1412 " pdb=" C7 PLM B1412 " ideal model delta sigma weight residual 1.525 1.361 0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" C6 PLM A1411 " pdb=" C7 PLM A1411 " ideal model delta sigma weight residual 1.525 1.361 0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" CB HIS B 483 " pdb=" CG HIS B 483 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.51e+01 bond pdb=" CB HIS B1141 " pdb=" CG HIS B1141 " ideal model delta sigma weight residual 1.497 1.405 0.092 1.40e-02 5.10e+03 4.32e+01 ... (remaining 30085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 37087 2.90 - 5.80: 3497 5.80 - 8.70: 354 8.70 - 11.60: 36 11.60 - 14.50: 4 Bond angle restraints: 40978 Sorted by residual: angle pdb=" C ALA C 314 " pdb=" N PRO C 315 " pdb=" CA PRO C 315 " ideal model delta sigma weight residual 119.66 126.51 -6.85 7.30e-01 1.88e+00 8.81e+01 angle pdb=" C PRO A 959 " pdb=" N PRO A 960 " pdb=" CA PRO A 960 " ideal model delta sigma weight residual 120.21 129.05 -8.84 9.60e-01 1.09e+00 8.49e+01 angle pdb=" C PRO C 959 " pdb=" N PRO C 960 " pdb=" CA PRO C 960 " ideal model delta sigma weight residual 120.03 128.83 -8.80 9.90e-01 1.02e+00 7.89e+01 angle pdb=" C PRO B 959 " pdb=" N PRO B 960 " pdb=" CA PRO B 960 " ideal model delta sigma weight residual 120.21 128.37 -8.16 9.60e-01 1.09e+00 7.23e+01 angle pdb=" C GLY C 544 " pdb=" N PRO C 545 " pdb=" CA PRO C 545 " ideal model delta sigma weight residual 120.04 128.79 -8.75 1.08e+00 8.57e-01 6.56e+01 ... (remaining 40973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 16820 17.47 - 34.93: 487 34.93 - 52.40: 117 52.40 - 69.86: 55 69.86 - 87.33: 18 Dihedral angle restraints: 17497 sinusoidal: 6515 harmonic: 10982 Sorted by residual: dihedral pdb=" CB CYS A 830 " pdb=" SG CYS A 830 " pdb=" SG CYS A 836 " pdb=" CB CYS A 836 " ideal model delta sinusoidal sigma weight residual 93.00 164.23 -71.23 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" N SER C 739 " pdb=" C SER C 739 " pdb=" CA SER C 739 " pdb=" CB SER C 739 " ideal model delta harmonic sigma weight residual 122.80 102.76 20.04 0 2.50e+00 1.60e-01 6.43e+01 dihedral pdb=" CB CYS B 747 " pdb=" SG CYS B 747 " pdb=" SG CYS B 756 " pdb=" CB CYS B 756 " ideal model delta sinusoidal sigma weight residual 93.00 27.74 65.26 1 1.00e+01 1.00e-02 5.58e+01 ... (remaining 17494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 3819 0.126 - 0.252: 809 0.252 - 0.377: 128 0.377 - 0.503: 56 0.503 - 0.629: 3 Chirality restraints: 4815 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.64e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.05e+02 ... (remaining 4812 not shown) Planarity restraints: 5270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1404 " 0.345 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG B1404 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1404 " 0.141 2.00e-02 2.50e+03 pdb=" N2 NAG B1404 " -0.528 2.00e-02 2.50e+03 pdb=" O7 NAG B1404 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1404 " 0.186 2.00e-02 2.50e+03 1.55e-01 2.99e+02 pdb=" C7 NAG A1404 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG A1404 " 0.135 2.00e-02 2.50e+03 pdb=" N2 NAG A1404 " -0.252 2.00e-02 2.50e+03 pdb=" O7 NAG A1404 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.145 2.00e-02 2.50e+03 1.23e-01 1.88e+02 pdb=" C7 NAG F 2 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.196 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.116 2.00e-02 2.50e+03 ... (remaining 5267 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1602 2.69 - 3.24: 29205 3.24 - 3.80: 48939 3.80 - 4.35: 63615 4.35 - 4.90: 101395 Nonbonded interactions: 244756 Sorted by model distance: nonbonded pdb=" O3 NAG C1403 " pdb=" O7 NAG C1403 " model vdw 2.138 3.040 nonbonded pdb=" O3 NAG C1409 " pdb=" O7 NAG C1409 " model vdw 2.158 3.040 nonbonded pdb=" O3 NAG B1402 " pdb=" O7 NAG B1402 " model vdw 2.182 3.040 nonbonded pdb=" O3 NAG P 1 " pdb=" O7 NAG P 1 " model vdw 2.187 3.040 nonbonded pdb=" O3 NAG G 2 " pdb=" O7 NAG G 2 " model vdw 2.204 3.040 ... (remaining 244751 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 15 through 150 or resid 158 through 473 or resid 480 throu \ gh 762 or resid 772 through 1410)) selection = (chain 'B' and (resid 15 through 504 or resid 517 through 762 or resid 772 throu \ gh 1410)) selection = (chain 'C' and (resid 15 through 473 or resid 480 through 1410)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = (chain 'H' and resid 13 through 109) selection = chain 'L' } 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 30.780 Find NCS groups from input model: 0.930 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 : 0.021 0.190 30208 Z= 1.123 Angle : 1.782 14.503 41269 Z= 1.182 Chirality : 0.113 0.629 4815 Planarity : 0.010 0.297 5228 Dihedral : 9.999 87.326 10268 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.13), residues: 3514 helix: 0.32 (0.16), residues: 819 sheet: 1.25 (0.17), residues: 731 loop : 0.18 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 774 TYR 0.072 0.008 TYR A 430 PHE 0.061 0.006 PHE A 472 TRP 0.086 0.008 TRP B 360 HIS 0.016 0.003 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.02076 / 1.12 (30090) covalent geometry : angle 1.77163 / 1.18 (40978) SS BOND : bond 0.01786 / 1.08 ( 63) SS BOND : angle 2.35976 / 1.58 ( 126) hydrogen bonds : bond 0.15697 / 10.52 ( 1132) hydrogen bonds : angle 7.57076 / 5.25 ( 3174) link_BETA1-4 : bond 0.05827 / 3.57 ( 13) link_BETA1-4 : angle 4.08304 / 2.81 ( 39) link_NAG-ASN : bond 0.06297 / 4.00 ( 42) link_NAG-ASN : angle 2.94039 / 2.03 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 376 MET cc_start: 0.8725 (mtm) cc_final: 0.7993 (mtp) REVERT: C 397 MET cc_start: 0.9011 (ttm) cc_final: 0.8721 (ttp) REVERT: B 397 MET cc_start: 0.8675 (ttm) cc_final: 0.8345 (ttm) REVERT: B 1217 MET cc_start: 0.9093 (mtm) cc_final: 0.8844 (mtm) REVERT: A 82 MET cc_start: 0.9424 (mmm) cc_final: 0.9177 (mmp) REVERT: A 172 MET cc_start: 0.9330 (mtp) cc_final: 0.9125 (mtm) REVERT: A 194 MET cc_start: 0.7652 (tpp) cc_final: 0.7411 (tpp) REVERT: A 256 MET cc_start: 0.8953 (mtm) cc_final: 0.8367 (mpp) REVERT: A 372 MET cc_start: 0.8909 (mmm) cc_final: 0.8439 (tpp) REVERT: A 376 MET cc_start: 0.8693 (mtm) cc_final: 0.8180 (mtp) REVERT: A 397 MET cc_start: 0.8979 (mtp) cc_final: 0.8366 (mtp) REVERT: A 882 LEU cc_start: 0.9252 (mt) cc_final: 0.9037 (mt) REVERT: A 1217 MET cc_start: 0.7681 (mtm) cc_final: 0.7354 (mpp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1838 time to fit residues: 31.4853 Evaluate side-chains 67 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN C 606 HIS C 714 ASN C 996 GLN C1138 ASN B 342 ASN B 482 ASN B 606 HIS B 996 GLN B1028 GLN B1138 ASN B1141 HIS A 219 HIS A 387 ASN A 440 GLN A 461 ASN A 560 HIS A 609 ASN A 714 ASN A 994 ASN A 996 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.029428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.024162 restraints weight = 307539.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.024918 restraints weight = 160316.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.025423 restraints weight = 100710.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.025772 restraints weight = 71735.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.026010 restraints weight = 55932.127| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 30208 Z= 0.270 Angle : 0.776 12.622 41269 Z= 0.392 Chirality : 0.047 0.548 4815 Planarity : 0.004 0.040 5228 Dihedral : 6.368 59.700 4077 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.03 % Allowed : 0.97 % Favored : 99.00 % 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: 0.68 (0.14), residues: 3514 helix: 1.66 (0.18), residues: 822 sheet: 0.57 (0.18), residues: 749 loop : -0.06 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 676 TYR 0.022 0.002 TYR A 430 PHE 0.019 0.002 PHE A1135 TRP 0.051 0.003 TRP A 360 HIS 0.010 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.27 (30090) covalent geometry : angle 0.75414 / 0.39 (40978) SS BOND : bond 0.00339 / 0.25 ( 63) SS BOND : angle 0.93357 / 0.63 ( 126) hydrogen bonds : bond 0.05728 / 3.76 ( 1132) hydrogen bonds : angle 5.86189 / 4.10 ( 3174) link_BETA1-4 : bond 0.00438 / 0.32 ( 13) link_BETA1-4 : angle 2.33343 / 1.57 ( 39) link_NAG-ASN : bond 0.00669 / 0.45 ( 42) link_NAG-ASN : angle 3.08912 / 2.12 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.9511 (mmt) cc_final: 0.8961 (mmt) REVERT: C 194 MET cc_start: 0.8593 (ttp) cc_final: 0.8301 (ptm) REVERT: C 397 MET cc_start: 0.8625 (ttm) cc_final: 0.8373 (ttp) REVERT: B 372 MET cc_start: 0.7336 (mmm) cc_final: 0.7108 (tpp) REVERT: B 397 MET cc_start: 0.8327 (ttm) cc_final: 0.8124 (ttp) REVERT: B 679 MET cc_start: 0.8850 (mmp) cc_final: 0.8546 (mmp) REVERT: B 1217 MET cc_start: 0.8916 (mtm) cc_final: 0.8676 (mtm) REVERT: A 82 MET cc_start: 0.9229 (mmm) cc_final: 0.8915 (mmp) REVERT: A 172 MET cc_start: 0.9091 (mtp) cc_final: 0.8631 (mtp) REVERT: A 194 MET cc_start: 0.7471 (tpp) cc_final: 0.6614 (mtp) REVERT: A 248 MET cc_start: 0.9320 (mmm) cc_final: 0.8697 (mmt) REVERT: A 256 MET cc_start: 0.8926 (mtm) cc_final: 0.8071 (mpp) REVERT: A 372 MET cc_start: 0.9241 (mmm) cc_final: 0.8814 (tpp) REVERT: A 376 MET cc_start: 0.8438 (mtm) cc_final: 0.7995 (mtp) REVERT: A 397 MET cc_start: 0.8897 (mtp) cc_final: 0.8492 (mtp) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1778 time to fit residues: 24.1946 Evaluate side-chains 66 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 42 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 274 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 306 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 175 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN C 641 GLN C1138 ASN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A1071 GLN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.027547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.022335 restraints weight = 316156.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.023026 restraints weight = 168354.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.023496 restraints weight = 107616.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.023817 restraints weight = 77618.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.024041 restraints weight = 61281.628| |-----------------------------------------------------------------------------| r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 30208 Z= 0.295 Angle : 0.745 13.342 41269 Z= 0.383 Chirality : 0.046 0.289 4815 Planarity : 0.005 0.047 5228 Dihedral : 6.088 58.560 4077 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.03 % Allowed : 1.84 % Favored : 98.12 % 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: 0.22 (0.14), residues: 3514 helix: 1.50 (0.18), residues: 835 sheet: 0.36 (0.18), residues: 741 loop : -0.52 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 59 TYR 0.031 0.002 TYR C 651 PHE 0.020 0.002 PHE A 268 TRP 0.043 0.003 TRP A 192 HIS 0.024 0.002 HIS B 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.30 (30090) covalent geometry : angle 0.72816 / 0.38 (40978) SS BOND : bond 0.00369 / 0.27 ( 63) SS BOND : angle 0.87076 / 0.57 ( 126) hydrogen bonds : bond 0.05418 / 3.54 ( 1132) hydrogen bonds : angle 5.56880 / 3.89 ( 3174) link_BETA1-4 : bond 0.00478 / 0.27 ( 13) link_BETA1-4 : angle 1.50299 / 0.94 ( 39) link_NAG-ASN : bond 0.00639 / 0.46 ( 42) link_NAG-ASN : angle 2.82432 / 2.04 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 122 MET cc_start: 0.7939 (tpp) cc_final: 0.7501 (tpt) REVERT: C 1006 MET cc_start: 0.8678 (tpp) cc_final: 0.8447 (tpt) REVERT: C 1012 ASN cc_start: 0.8811 (m-40) cc_final: 0.8370 (p0) REVERT: B 256 MET cc_start: 0.9043 (pmm) cc_final: 0.8750 (pmm) REVERT: B 376 MET cc_start: 0.9152 (mtt) cc_final: 0.7981 (mtt) REVERT: B 679 MET cc_start: 0.8989 (mmp) cc_final: 0.8745 (mmp) REVERT: B 1217 MET cc_start: 0.8863 (mtm) cc_final: 0.8643 (mtm) REVERT: A 82 MET cc_start: 0.9235 (mmm) cc_final: 0.9027 (mmp) REVERT: A 194 MET cc_start: 0.7383 (tpp) cc_final: 0.6526 (mtp) REVERT: A 303 MET cc_start: 0.9264 (mmm) cc_final: 0.8682 (tpp) REVERT: A 372 MET cc_start: 0.9300 (mmm) cc_final: 0.8654 (tpp) REVERT: A 376 MET cc_start: 0.8450 (mtm) cc_final: 0.7894 (mtp) REVERT: A 397 MET cc_start: 0.8990 (mtp) cc_final: 0.8726 (mtp) REVERT: A 1231 MET cc_start: 0.7620 (ppp) cc_final: 0.7213 (ppp) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.1627 time to fit residues: 20.5341 Evaluate side-chains 63 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 112 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 213 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 147 optimal weight: 0.0010 chunk 289 optimal weight: 8.9990 chunk 246 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 641 GLN C1012 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.028111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.022853 restraints weight = 306542.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.023573 restraints weight = 161569.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.024054 restraints weight = 102420.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.024384 restraints weight = 73609.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.024615 restraints weight = 57980.491| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 30208 Z= 0.146 Angle : 0.585 11.305 41269 Z= 0.297 Chirality : 0.043 0.298 4815 Planarity : 0.004 0.040 5228 Dihedral : 5.818 59.895 4077 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: 0.38 (0.14), residues: 3514 helix: 1.75 (0.18), residues: 850 sheet: 0.36 (0.19), residues: 743 loop : -0.45 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1062 TYR 0.014 0.001 TYR C 997 PHE 0.013 0.001 PHE C 980 TRP 0.014 0.001 TRP C 460 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (30090) covalent geometry : angle 0.56458 / 0.29 (40978) SS BOND : bond 0.00211 / 0.15 ( 63) SS BOND : angle 0.74809 / 0.47 ( 126) hydrogen bonds : bond 0.04522 / 2.94 ( 1132) hydrogen bonds : angle 5.12320 / 3.59 ( 3174) link_BETA1-4 : bond 0.00308 / 0.18 ( 13) link_BETA1-4 : angle 1.42407 / 0.93 ( 39) link_NAG-ASN : bond 0.00446 / 0.32 ( 42) link_NAG-ASN : angle 2.70947 / 1.81 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.9490 (mmt) cc_final: 0.9147 (mmm) REVERT: C 372 MET cc_start: 0.9227 (mmp) cc_final: 0.8337 (mmm) REVERT: C 376 MET cc_start: 0.8561 (mtm) cc_final: 0.7401 (mtm) REVERT: C 669 PHE cc_start: 0.8572 (t80) cc_final: 0.8243 (t80) REVERT: C 1006 MET cc_start: 0.8552 (tpp) cc_final: 0.8300 (tpt) REVERT: C 1012 ASN cc_start: 0.8655 (m110) cc_final: 0.8268 (p0) REVERT: B 256 MET cc_start: 0.9056 (pmm) cc_final: 0.8700 (pmm) REVERT: B 679 MET cc_start: 0.8875 (mmp) cc_final: 0.8593 (mmp) REVERT: B 1217 MET cc_start: 0.8907 (mtm) cc_final: 0.8643 (mtp) REVERT: A 82 MET cc_start: 0.9127 (mmm) cc_final: 0.8808 (mmm) REVERT: A 372 MET cc_start: 0.9319 (mmm) cc_final: 0.8653 (tpp) REVERT: A 376 MET cc_start: 0.8337 (mtm) cc_final: 0.7896 (mtp) REVERT: A 397 MET cc_start: 0.8939 (mtp) cc_final: 0.8714 (mtp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1772 time to fit residues: 21.2369 Evaluate side-chains 64 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 346 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 358 optimal weight: 50.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** 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 = 0.2786 r_free = 0.2786 target = 0.027794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.022596 restraints weight = 310394.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.023302 restraints weight = 163230.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.023780 restraints weight = 103480.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.024109 restraints weight = 74115.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.024337 restraints weight = 58090.579| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 30208 Z= 0.185 Angle : 0.591 11.360 41269 Z= 0.300 Chirality : 0.042 0.279 4815 Planarity : 0.004 0.041 5228 Dihedral : 5.730 59.315 4077 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 0.39 (0.14), residues: 3514 helix: 1.88 (0.18), residues: 836 sheet: 0.36 (0.19), residues: 748 loop : -0.49 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 59 TYR 0.015 0.001 TYR A 651 PHE 0.014 0.001 PHE B 980 TRP 0.011 0.002 TRP C 460 HIS 0.005 0.001 HIS B 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (30090) covalent geometry : angle 0.57216 / 0.30 (40978) SS BOND : bond 0.00348 / 0.21 ( 63) SS BOND : angle 0.79276 / 0.54 ( 126) hydrogen bonds : bond 0.04492 / 2.93 ( 1132) hydrogen bonds : angle 5.09178 / 3.56 ( 3174) link_BETA1-4 : bond 0.00347 / 0.20 ( 13) link_BETA1-4 : angle 1.44432 / 0.92 ( 39) link_NAG-ASN : bond 0.00396 / 0.28 ( 42) link_NAG-ASN : angle 2.55494 / 1.71 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.9422 (mmt) cc_final: 0.9058 (mmm) REVERT: C 122 MET cc_start: 0.7881 (tpp) cc_final: 0.7550 (tpt) REVERT: C 372 MET cc_start: 0.9242 (mmp) cc_final: 0.8745 (mmt) REVERT: C 376 MET cc_start: 0.8684 (mtm) cc_final: 0.8164 (mtp) REVERT: C 669 PHE cc_start: 0.8641 (t80) cc_final: 0.8337 (t80) REVERT: C 679 MET cc_start: 0.9013 (mmm) cc_final: 0.8776 (mmm) REVERT: C 873 MET cc_start: 0.9072 (mmm) cc_final: 0.8842 (mmm) REVERT: C 1006 MET cc_start: 0.8620 (tpp) cc_final: 0.8358 (tpt) REVERT: C 1012 ASN cc_start: 0.8743 (m110) cc_final: 0.8335 (p0) REVERT: B 256 MET cc_start: 0.9061 (pmm) cc_final: 0.8819 (pmm) REVERT: B 397 MET cc_start: 0.8317 (ttm) cc_final: 0.8079 (ttp) REVERT: B 679 MET cc_start: 0.8886 (mmp) cc_final: 0.8593 (mmm) REVERT: B 1217 MET cc_start: 0.8854 (mtm) cc_final: 0.8635 (mtm) REVERT: A 82 MET cc_start: 0.9137 (mmm) cc_final: 0.8811 (mmm) REVERT: A 303 MET cc_start: 0.8935 (tpp) cc_final: 0.8649 (tpp) REVERT: A 372 MET cc_start: 0.9324 (mmm) cc_final: 0.8673 (tpp) REVERT: A 376 MET cc_start: 0.8395 (mtm) cc_final: 0.7989 (mtp) REVERT: A 397 MET cc_start: 0.8915 (mtp) cc_final: 0.8681 (mtp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1782 time to fit residues: 21.9751 Evaluate side-chains 63 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 224 optimal weight: 0.8980 chunk 211 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 315 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 260 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 299 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 527 ASN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.027683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.022468 restraints weight = 312772.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.023165 restraints weight = 165576.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.023638 restraints weight = 105503.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.023963 restraints weight = 75832.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.024185 restraints weight = 59655.267| |-----------------------------------------------------------------------------| r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 30208 Z= 0.176 Angle : 0.587 11.342 41269 Z= 0.297 Chirality : 0.042 0.267 4815 Planarity : 0.004 0.043 5228 Dihedral : 5.634 59.620 4077 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.82 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: 0.35 (0.14), residues: 3514 helix: 1.85 (0.18), residues: 836 sheet: 0.37 (0.19), residues: 748 loop : -0.53 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 59 TYR 0.012 0.001 TYR A 79 PHE 0.014 0.001 PHE B 980 TRP 0.014 0.002 TRP A 348 HIS 0.006 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (30090) covalent geometry : angle 0.56709 / 0.29 (40978) SS BOND : bond 0.00222 / 0.16 ( 63) SS BOND : angle 0.68399 / 0.45 ( 126) hydrogen bonds : bond 0.04344 / 2.82 ( 1132) hydrogen bonds : angle 5.04012 / 3.53 ( 3174) link_BETA1-4 : bond 0.00340 / 0.20 ( 13) link_BETA1-4 : angle 1.40935 / 0.90 ( 39) link_NAG-ASN : bond 0.00426 / 0.29 ( 42) link_NAG-ASN : angle 2.67592 / 1.75 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 MET cc_start: 0.7856 (tpp) cc_final: 0.7595 (tpt) REVERT: C 299 MET cc_start: 0.8640 (mmt) cc_final: 0.8345 (mmm) REVERT: C 372 MET cc_start: 0.9212 (mmp) cc_final: 0.8959 (mmt) REVERT: C 1006 MET cc_start: 0.8565 (tpp) cc_final: 0.8278 (tpt) REVERT: C 1012 ASN cc_start: 0.8801 (m110) cc_final: 0.8454 (p0) REVERT: C 1217 MET cc_start: 0.8420 (mtp) cc_final: 0.7830 (mmm) REVERT: B 256 MET cc_start: 0.9063 (pmm) cc_final: 0.8794 (pmm) REVERT: B 397 MET cc_start: 0.8301 (ttm) cc_final: 0.8059 (ttp) REVERT: B 679 MET cc_start: 0.8878 (mmp) cc_final: 0.8554 (mmm) REVERT: B 1217 MET cc_start: 0.8800 (mtm) cc_final: 0.8400 (mtp) REVERT: A 82 MET cc_start: 0.9073 (mmm) cc_final: 0.8787 (mmm) REVERT: A 256 MET cc_start: 0.9462 (mmm) cc_final: 0.9078 (mmm) REVERT: A 303 MET cc_start: 0.8906 (tpp) cc_final: 0.8320 (tpp) REVERT: A 372 MET cc_start: 0.9327 (mmm) cc_final: 0.8705 (tpp) REVERT: A 376 MET cc_start: 0.8368 (mtm) cc_final: 0.7977 (mtp) REVERT: A 1231 MET cc_start: 0.7595 (ppp) cc_final: 0.7220 (ppp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1780 time to fit residues: 22.4354 Evaluate side-chains 66 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 69 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 292 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 325 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 290 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 315 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 HIS B 426 GLN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.027233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.022062 restraints weight = 317103.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.022746 restraints weight = 168477.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.023210 restraints weight = 107549.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.023528 restraints weight = 77291.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.023749 restraints weight = 60971.704| |-----------------------------------------------------------------------------| r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 30208 Z= 0.232 Angle : 0.648 11.450 41269 Z= 0.325 Chirality : 0.043 0.275 4815 Planarity : 0.004 0.042 5228 Dihedral : 5.790 58.347 4077 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % 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: 0.12 (0.14), residues: 3514 helix: 1.67 (0.18), residues: 838 sheet: 0.07 (0.18), residues: 773 loop : -0.62 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 59 TYR 0.015 0.002 TYR A 651 PHE 0.017 0.002 PHE B 980 TRP 0.014 0.002 TRP A 348 HIS 0.008 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.23 (30090) covalent geometry : angle 0.62922 / 0.32 (40978) SS BOND : bond 0.00291 / 0.22 ( 63) SS BOND : angle 0.89501 / 0.60 ( 126) hydrogen bonds : bond 0.04632 / 3.03 ( 1132) hydrogen bonds : angle 5.17880 / 3.63 ( 3174) link_BETA1-4 : bond 0.00328 / 0.18 ( 13) link_BETA1-4 : angle 1.55020 / 0.96 ( 39) link_NAG-ASN : bond 0.00388 / 0.27 ( 42) link_NAG-ASN : angle 2.69630 / 1.79 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 MET cc_start: 0.9248 (mmt) cc_final: 0.8929 (mmp) REVERT: C 122 MET cc_start: 0.7799 (tpp) cc_final: 0.7594 (tpt) REVERT: C 376 MET cc_start: 0.8825 (mtm) cc_final: 0.8608 (mtp) REVERT: C 679 MET cc_start: 0.9017 (mmm) cc_final: 0.8783 (mmm) REVERT: C 1006 MET cc_start: 0.8548 (tpp) cc_final: 0.8246 (tpt) REVERT: C 1012 ASN cc_start: 0.8878 (m110) cc_final: 0.8414 (p0) REVERT: B 256 MET cc_start: 0.9062 (pmm) cc_final: 0.8774 (pmm) REVERT: B 397 MET cc_start: 0.8329 (ttm) cc_final: 0.8065 (ttp) REVERT: B 679 MET cc_start: 0.8926 (mmp) cc_final: 0.8633 (mmm) REVERT: B 1217 MET cc_start: 0.8577 (mtm) cc_final: 0.8216 (mtm) REVERT: A 82 MET cc_start: 0.9055 (mmm) cc_final: 0.8799 (mmm) REVERT: A 194 MET cc_start: 0.8244 (mtm) cc_final: 0.7469 (mtp) REVERT: A 256 MET cc_start: 0.9425 (mmm) cc_final: 0.8983 (mmm) REVERT: A 372 MET cc_start: 0.9350 (mmm) cc_final: 0.8049 (tpp) REVERT: A 376 MET cc_start: 0.8368 (mtm) cc_final: 0.7971 (mpp) REVERT: A 1231 MET cc_start: 0.7694 (ppp) cc_final: 0.7273 (ppp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1730 time to fit residues: 21.1671 Evaluate side-chains 65 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 365 optimal weight: 50.0000 chunk 254 optimal weight: 7.9990 chunk 311 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 321 optimal weight: 7.9990 chunk 292 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 270 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.027538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.022412 restraints weight = 310218.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.023105 restraints weight = 164835.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.023574 restraints weight = 105088.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.023887 restraints weight = 75411.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.024118 restraints weight = 59582.412| |-----------------------------------------------------------------------------| r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 30208 Z= 0.154 Angle : 0.573 11.245 41269 Z= 0.289 Chirality : 0.042 0.245 4815 Planarity : 0.004 0.046 5228 Dihedral : 5.658 59.771 4077 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 0.23 (0.14), residues: 3514 helix: 1.81 (0.18), residues: 837 sheet: 0.10 (0.18), residues: 760 loop : -0.55 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 362 TYR 0.013 0.001 TYR A 79 PHE 0.012 0.001 PHE A 268 TRP 0.012 0.001 TRP A 348 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (30090) covalent geometry : angle 0.55189 / 0.28 (40978) SS BOND : bond 0.00244 / 0.17 ( 63) SS BOND : angle 0.86408 / 0.55 ( 126) hydrogen bonds : bond 0.04274 / 2.78 ( 1132) hydrogen bonds : angle 5.00792 / 3.51 ( 3174) link_BETA1-4 : bond 0.00358 / 0.22 ( 13) link_BETA1-4 : angle 1.40717 / 0.89 ( 39) link_NAG-ASN : bond 0.00392 / 0.27 ( 42) link_NAG-ASN : angle 2.68628 / 1.74 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1006 MET cc_start: 0.8507 (tpp) cc_final: 0.8215 (tpt) REVERT: C 1012 ASN cc_start: 0.8868 (m110) cc_final: 0.8404 (p0) REVERT: B 248 MET cc_start: 0.8744 (mmm) cc_final: 0.8500 (mmm) REVERT: B 256 MET cc_start: 0.9073 (pmm) cc_final: 0.8773 (pmm) REVERT: B 397 MET cc_start: 0.8310 (ttm) cc_final: 0.8038 (ttp) REVERT: B 679 MET cc_start: 0.8902 (mmp) cc_final: 0.8560 (mmm) REVERT: B 1119 MET cc_start: 0.8920 (mmt) cc_final: 0.8627 (mmt) REVERT: B 1217 MET cc_start: 0.8559 (mtm) cc_final: 0.8183 (mtm) REVERT: A 82 MET cc_start: 0.9015 (mmm) cc_final: 0.8635 (mmm) REVERT: A 256 MET cc_start: 0.9433 (mmm) cc_final: 0.9103 (mmm) REVERT: A 372 MET cc_start: 0.9319 (mmm) cc_final: 0.8701 (tpp) REVERT: A 376 MET cc_start: 0.8305 (mtm) cc_final: 0.8036 (mtp) REVERT: A 1231 MET cc_start: 0.7656 (ppp) cc_final: 0.7250 (ppp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1601 time to fit residues: 19.1749 Evaluate side-chains 64 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 195 optimal weight: 7.9990 chunk 276 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 351 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 299 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** 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 = 0.2771 r_free = 0.2771 target = 0.027452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.022291 restraints weight = 315083.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.022985 restraints weight = 167102.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.023454 restraints weight = 106160.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.023778 restraints weight = 76260.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.023999 restraints weight = 59891.281| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 30208 Z= 0.177 Angle : 0.580 11.207 41269 Z= 0.293 Chirality : 0.042 0.240 4815 Planarity : 0.004 0.046 5228 Dihedral : 5.587 59.059 4077 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 0.21 (0.14), residues: 3514 helix: 1.82 (0.18), residues: 832 sheet: 0.03 (0.18), residues: 769 loop : -0.54 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 431 TYR 0.013 0.001 TYR A 79 PHE 0.014 0.001 PHE B 980 TRP 0.015 0.002 TRP B 360 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (30090) covalent geometry : angle 0.56046 / 0.29 (40978) SS BOND : bond 0.00241 / 0.18 ( 63) SS BOND : angle 0.77075 / 0.51 ( 126) hydrogen bonds : bond 0.04282 / 2.79 ( 1132) hydrogen bonds : angle 5.01660 / 3.51 ( 3174) link_BETA1-4 : bond 0.00351 / 0.21 ( 13) link_BETA1-4 : angle 1.43696 / 0.91 ( 39) link_NAG-ASN : bond 0.00369 / 0.26 ( 42) link_NAG-ASN : angle 2.62868 / 1.71 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 372 MET cc_start: 0.9256 (mmm) cc_final: 0.8977 (mmm) REVERT: C 376 MET cc_start: 0.8769 (mtm) cc_final: 0.8297 (tpt) REVERT: C 1006 MET cc_start: 0.8479 (tpp) cc_final: 0.8266 (tpt) REVERT: C 1012 ASN cc_start: 0.8882 (m110) cc_final: 0.8407 (p0) REVERT: B 248 MET cc_start: 0.8773 (mmm) cc_final: 0.8521 (mmm) REVERT: B 256 MET cc_start: 0.9065 (pmm) cc_final: 0.8751 (pmm) REVERT: B 397 MET cc_start: 0.8298 (ttm) cc_final: 0.8019 (ttp) REVERT: B 679 MET cc_start: 0.8911 (mmp) cc_final: 0.8625 (mmm) REVERT: B 1217 MET cc_start: 0.8548 (mtm) cc_final: 0.8227 (mtm) REVERT: A 82 MET cc_start: 0.9004 (mmm) cc_final: 0.8632 (mmm) REVERT: A 194 MET cc_start: 0.8236 (mtm) cc_final: 0.7870 (mtm) REVERT: A 256 MET cc_start: 0.9424 (mmm) cc_final: 0.8945 (mmm) REVERT: A 303 MET cc_start: 0.8999 (tpp) cc_final: 0.8622 (tpp) REVERT: A 372 MET cc_start: 0.9302 (mmm) cc_final: 0.8733 (tpp) REVERT: A 376 MET cc_start: 0.8313 (mtm) cc_final: 0.8063 (mtp) REVERT: A 1231 MET cc_start: 0.7664 (ppp) cc_final: 0.7229 (ppp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1616 time to fit residues: 19.5097 Evaluate side-chains 64 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 140 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 264 optimal weight: 0.8980 chunk 357 optimal weight: 50.0000 chunk 35 optimal weight: 1.9990 chunk 317 optimal weight: 5.9990 chunk 364 optimal weight: 50.0000 chunk 61 optimal weight: 0.6980 chunk 325 optimal weight: 0.3980 chunk 6 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN B 387 ASN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.028015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.022885 restraints weight = 309174.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.023596 restraints weight = 163709.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.024078 restraints weight = 103767.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.024409 restraints weight = 74196.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.024637 restraints weight = 58019.737| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30208 Z= 0.101 Angle : 0.536 11.460 41269 Z= 0.270 Chirality : 0.042 0.231 4815 Planarity : 0.003 0.048 5228 Dihedral : 5.310 59.966 4077 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.35 (0.14), residues: 3514 helix: 1.94 (0.18), residues: 839 sheet: 0.26 (0.19), residues: 725 loop : -0.52 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 362 TYR 0.014 0.001 TYR A 79 PHE 0.009 0.001 PHE B 775 TRP 0.013 0.001 TRP C 192 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (30090) covalent geometry : angle 0.51495 / 0.27 (40978) SS BOND : bond 0.00176 / 0.13 ( 63) SS BOND : angle 0.67927 / 0.45 ( 126) hydrogen bonds : bond 0.03916 / 2.54 ( 1132) hydrogen bonds : angle 4.80536 / 3.37 ( 3174) link_BETA1-4 : bond 0.00393 / 0.24 ( 13) link_BETA1-4 : angle 1.25577 / 0.82 ( 39) link_NAG-ASN : bond 0.00441 / 0.32 ( 42) link_NAG-ASN : angle 2.60985 / 1.66 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7028 Ramachandran restraints generated. 3514 Oldfield, 0 Emsley, 3514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 122 MET cc_start: 0.7845 (tpp) cc_final: 0.7586 (tpp) REVERT: C 372 MET cc_start: 0.9240 (mmm) cc_final: 0.8909 (mmm) REVERT: C 376 MET cc_start: 0.8683 (mtm) cc_final: 0.8205 (tpt) REVERT: C 873 MET cc_start: 0.8683 (mmm) cc_final: 0.8450 (mmm) REVERT: C 1006 MET cc_start: 0.8413 (tpp) cc_final: 0.8124 (tpt) REVERT: C 1012 ASN cc_start: 0.8773 (m110) cc_final: 0.8356 (p0) REVERT: B 248 MET cc_start: 0.8749 (mmm) cc_final: 0.8501 (mmm) REVERT: B 256 MET cc_start: 0.9048 (pmm) cc_final: 0.8726 (pmm) REVERT: B 397 MET cc_start: 0.8262 (ttm) cc_final: 0.7980 (ttp) REVERT: B 679 MET cc_start: 0.8880 (mmp) cc_final: 0.8538 (mmp) REVERT: B 1217 MET cc_start: 0.8574 (mtm) cc_final: 0.8082 (mtp) REVERT: A 82 MET cc_start: 0.8939 (mmm) cc_final: 0.8582 (mmm) REVERT: A 194 MET cc_start: 0.8255 (mtm) cc_final: 0.7766 (ptp) REVERT: A 256 MET cc_start: 0.9394 (mmm) cc_final: 0.9064 (mmm) REVERT: A 303 MET cc_start: 0.8866 (tpp) cc_final: 0.8608 (tpp) REVERT: A 372 MET cc_start: 0.9297 (mmm) cc_final: 0.8680 (tpp) REVERT: A 376 MET cc_start: 0.8234 (mtm) cc_final: 0.7989 (mtp) REVERT: A 1231 MET cc_start: 0.7701 (ppp) cc_final: 0.7278 (ppp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1632 time to fit residues: 20.4434 Evaluate side-chains 64 residues out of total 3090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 17 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 343 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 chunk 149 optimal weight: 0.0670 chunk 311 optimal weight: 0.9980 chunk 277 optimal weight: 5.9990 overall best weight: 2.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** 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 = 0.2791 r_free = 0.2791 target = 0.027875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.022781 restraints weight = 311022.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.023483 restraints weight = 164877.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.023965 restraints weight = 104640.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.024300 restraints weight = 74715.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.024533 restraints weight = 58314.686| |-----------------------------------------------------------------------------| r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30208 Z= 0.129 Angle : 0.537 10.956 41269 Z= 0.271 Chirality : 0.041 0.223 4815 Planarity : 0.003 0.046 5228 Dihedral : 5.210 59.706 4077 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 0.37 (0.14), residues: 3514 helix: 2.00 (0.19), residues: 833 sheet: 0.14 (0.19), residues: 746 loop : -0.47 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1132 TYR 0.012 0.001 TYR A 79 PHE 0.011 0.001 PHE B 980 TRP 0.011 0.001 TRP C 192 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (30090) covalent geometry : angle 0.51670 / 0.27 (40978) SS BOND : bond 0.00184 / 0.13 ( 63) SS BOND : angle 0.65741 / 0.45 ( 126) hydrogen bonds : bond 0.03953 / 2.58 ( 1132) hydrogen bonds : angle 4.79678 / 3.36 ( 3174) link_BETA1-4 : bond 0.00372 / 0.23 ( 13) link_BETA1-4 : angle 1.31088 / 0.85 ( 39) link_NAG-ASN : bond 0.00354 / 0.25 ( 42) link_NAG-ASN : angle 2.54624 / 1.63 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3410.47 seconds wall clock time: 60 minutes 49.30 seconds (3649.30 seconds total)