Starting phenix.real_space_refine on Fri Mar 6 09:31:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sob_25265/03_2026/7sob_25265.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sob_25265/03_2026/7sob_25265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sob_25265/03_2026/7sob_25265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sob_25265/03_2026/7sob_25265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sob_25265/03_2026/7sob_25265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sob_25265/03_2026/7sob_25265.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.080 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 144 5.16 5 C 18564 2.51 5 N 5172 2.21 5 O 6120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30000 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7140 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 250} Link IDs: {'PTRANS': 57, 'TRANS': 967} Chain breaks: 8 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1179 Unresolved non-hydrogen dihedrals: 765 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 20, 'ASN:plan1': 22, 'ARG:plan': 14, 'GLU:plan': 20, 'PHE:plan': 16, 'TYR:plan': 16, 'HIS:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 584 Chain: "B" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 560 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'TRP:plan': 2, 'GLN:plan1': 7, 'ASP:plan': 7, 'ARG:plan': 3, 'PHE:plan': 6, 'ASN:plan1': 3, 'TYR:plan': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 163 Chain: "C" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 787 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 5, 'ARG:plan': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 94 Chain: "G" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 632 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 377 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 4, 'TYR:plan': 8, 'PHE:plan': 4, 'TRP:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 231 Chain: "I" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 501 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'ARG:plan': 6, 'TRP:plan': 1, 'TYR:plan': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 148 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "A" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "D" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "K" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Restraints were copied for chains: D, K, E, L, F, M, H, N, J, O Time building chain proxies: 8.82, per 1000 atoms: 0.29 Number of scatterers: 30000 At special positions: 0 Unit cell: (157.641, 158.484, 188.832, 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 144 16.00 O 6120 8.00 N 5172 7.00 C 18564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.08 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS K 985 " distance=2.46 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.07 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.16 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.12 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS D 383 " distance=2.46 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.00 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.01 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.04 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 136 " distance=2.04 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.02 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.02 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.08 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.08 Simple disulfide: pdb=" SG CYS K 383 " - pdb=" SG CYS D 985 " distance=2.46 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.07 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.07 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.01 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.01 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.04 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.04 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.05 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.05 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.16 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.16 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.12 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.12 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.02 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.02 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.00 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.00 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.01 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A1098 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A 717 " " NAG A1312 " - " ASN A 61 " " NAG A1313 " - " ASN A 122 " " NAG A1314 " - " ASN A 234 " " NAG A1315 " - " ASN A 17 " " NAG A1316 " - " ASN A 165 " " NAG A1317 " - " ASN A 343 " " NAG D1301 " - " ASN D 331 " " NAG D1302 " - " ASN D 603 " " NAG D1303 " - " ASN D 657 " " NAG D1304 " - " ASN D1074 " " NAG D1305 " - " ASN D1098 " " NAG D1306 " - " ASN D1134 " " NAG D1307 " - " ASN D 616 " " NAG D1308 " - " ASN D 709 " " NAG D1309 " - " ASN D 282 " " NAG D1310 " - " ASN D 801 " " NAG D1311 " - " ASN D 717 " " NAG D1312 " - " ASN D 61 " " NAG D1313 " - " ASN D 122 " " NAG D1314 " - " ASN D 234 " " NAG D1315 " - " ASN D 17 " " NAG D1316 " - " ASN D 165 " " NAG D1317 " - " ASN D 343 " " NAG K1301 " - " ASN K 331 " " NAG K1302 " - " ASN K 603 " " NAG K1303 " - " ASN K 657 " " NAG K1304 " - " ASN K1074 " " NAG K1305 " - " ASN K1098 " " NAG K1306 " - " ASN K1134 " " NAG K1307 " - " ASN K 616 " " NAG K1308 " - " ASN K 709 " " NAG K1309 " - " ASN K 282 " " NAG K1310 " - " ASN K 801 " " NAG K1311 " - " ASN K 717 " " NAG K1312 " - " ASN K 61 " " NAG K1313 " - " ASN K 122 " " NAG K1314 " - " ASN K 234 " " NAG K1315 " - " ASN K 17 " " NAG K1316 " - " ASN K 165 " " NAG K1317 " - " ASN K 343 " Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.4 seconds 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8208 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 81 sheets defined 19.7% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.652A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.418A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.657A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.510A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.601A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.581A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.073A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.015A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.532A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.374A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.062A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 30 through 32 No H-bonds generated for 'chain 'I' and resid 30 through 32' Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.835A pdb=" N PHE I 84 " --> pdb=" O PRO I 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 370 removed outlier: 3.652A pdb=" N ASN D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 389 Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.418A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.657A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 620 removed outlier: 3.509A pdb=" N VAL D 620 " --> pdb=" O CYS D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.601A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.581A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 856 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 912 through 919 removed outlier: 4.073A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 939 Processing helix chain 'D' and resid 945 through 965 removed outlier: 4.016A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 removed outlier: 3.532A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.374A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.062A pdb=" N ILE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.834A pdb=" N PHE J 84 " --> pdb=" O PRO J 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 303 Processing helix chain 'K' and resid 338 through 343 Processing helix chain 'K' and resid 365 through 370 removed outlier: 3.651A pdb=" N ASN K 370 " --> pdb=" O SER K 366 " (cutoff:3.500A) Processing helix chain 'K' and resid 386 through 389 Processing helix chain 'K' and resid 405 through 410 removed outlier: 4.418A pdb=" N ARG K 408 " --> pdb=" O ASP K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 422 Processing helix chain 'K' and resid 438 through 443 removed outlier: 3.657A pdb=" N SER K 443 " --> pdb=" O ASN K 439 " (cutoff:3.500A) Processing helix chain 'K' and resid 616 through 620 removed outlier: 3.509A pdb=" N VAL K 620 " --> pdb=" O CYS K 617 " (cutoff:3.500A) Processing helix chain 'K' and resid 737 through 744 Processing helix chain 'K' and resid 746 through 754 Processing helix chain 'K' and resid 755 through 757 No H-bonds generated for 'chain 'K' and resid 755 through 757' Processing helix chain 'K' and resid 758 through 783 removed outlier: 3.601A pdb=" N ASP K 775 " --> pdb=" O ALA K 771 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 826 removed outlier: 3.581A pdb=" N VAL K 826 " --> pdb=" O LEU K 822 " (cutoff:3.500A) Processing helix chain 'K' and resid 853 through 856 Processing helix chain 'K' and resid 866 through 885 Processing helix chain 'K' and resid 886 through 890 Processing helix chain 'K' and resid 897 through 908 Processing helix chain 'K' and resid 912 through 919 removed outlier: 4.073A pdb=" N LEU K 916 " --> pdb=" O THR K 912 " (cutoff:3.500A) Processing helix chain 'K' and resid 919 through 939 Processing helix chain 'K' and resid 945 through 965 removed outlier: 4.015A pdb=" N VAL K 951 " --> pdb=" O LYS K 947 " (cutoff:3.500A) Processing helix chain 'K' and resid 966 through 968 No H-bonds generated for 'chain 'K' and resid 966 through 968' Processing helix chain 'K' and resid 976 through 984 removed outlier: 3.532A pdb=" N ILE K 980 " --> pdb=" O VAL K 976 " (cutoff:3.500A) Processing helix chain 'K' and resid 985 through 1033 removed outlier: 4.374A pdb=" N VAL K 991 " --> pdb=" O PRO K 987 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN K 992 " --> pdb=" O GLU K 988 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.062A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 30 through 32 No H-bonds generated for 'chain 'O' and resid 30 through 32' Processing helix chain 'O' and resid 80 through 84 removed outlier: 3.834A pdb=" N PHE O 84 " --> pdb=" O PRO O 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.905A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.816A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.511A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.414A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.838A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.287A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.134A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.789A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.559A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.353A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.995A pdb=" N ILE A 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.651A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.716A pdb=" N LEU B 11 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU B 33 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.716A pdb=" N LEU B 11 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.636A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AC6, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.660A pdb=" N GLY G 33 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.975A pdb=" N ASN G 116 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'I' and resid 54 through 55 removed outlier: 6.586A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 27 through 31 removed outlier: 3.905A pdb=" N ALA D 27 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS D 207 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 9.817A pdb=" N ALA D 222 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.511A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN D 134 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN D 164 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N CYS D 136 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N SER D 162 " --> pdb=" O CYS D 136 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 84 through 85 removed outlier: 13.414A pdb=" N PHE D 238 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 12.838A pdb=" N ASN D 137 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR D 240 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 242 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN D 134 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN D 164 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N CYS D 136 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N SER D 162 " --> pdb=" O CYS D 136 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.287A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 324 through 328 removed outlier: 4.134A pdb=" N GLU D 324 " --> pdb=" O CYS D 538 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.789A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.559A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.353A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 788 through 790 removed outlier: 5.995A pdb=" N ILE D 788 " --> pdb=" O ASN K 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.651A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.716A pdb=" N LEU E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.716A pdb=" N LEU E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.636A pdb=" N MET F 34 " --> pdb=" O PHE F 50 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.660A pdb=" N GLY H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.975A pdb=" N ASN H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AG1, first strand: chain 'J' and resid 54 through 55 removed outlier: 6.587A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 27 through 31 removed outlier: 3.906A pdb=" N ALA K 27 " --> pdb=" O TRP K 64 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER K 60 " --> pdb=" O SER K 31 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS K 207 " --> pdb=" O ALA K 222 " (cutoff:3.500A) removed outlier: 9.817A pdb=" N ALA K 222 " --> pdb=" O HIS K 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL K 36 " --> pdb=" O LEU K 223 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP K 287 " --> pdb=" O LYS K 278 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 84 through 85 removed outlier: 6.511A pdb=" N ALA K 243 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE K 101 " --> pdb=" O ALA K 243 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG K 102 " --> pdb=" O ASN K 121 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU K 132 " --> pdb=" O CYS K 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS K 166 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN K 134 " --> pdb=" O ASN K 164 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN K 164 " --> pdb=" O GLN K 134 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N CYS K 136 " --> pdb=" O SER K 162 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N SER K 162 " --> pdb=" O CYS K 136 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N ASP K 138 " --> pdb=" O TYR K 160 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TYR K 160 " --> pdb=" O ASP K 138 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 84 through 85 removed outlier: 13.414A pdb=" N PHE K 238 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 12.838A pdb=" N ASN K 137 " --> pdb=" O PHE K 238 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR K 240 " --> pdb=" O ASN K 137 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU K 242 " --> pdb=" O PRO K 139 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU K 132 " --> pdb=" O CYS K 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS K 166 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN K 134 " --> pdb=" O ASN K 164 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN K 164 " --> pdb=" O GLN K 134 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N CYS K 136 " --> pdb=" O SER K 162 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N SER K 162 " --> pdb=" O CYS K 136 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N ASP K 138 " --> pdb=" O TYR K 160 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TYR K 160 " --> pdb=" O ASP K 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 311 through 319 removed outlier: 5.288A pdb=" N ILE K 312 " --> pdb=" O THR K 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR K 599 " --> pdb=" O ILE K 312 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN K 314 " --> pdb=" O VAL K 597 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL K 597 " --> pdb=" O GLN K 314 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER K 316 " --> pdb=" O VAL K 595 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY K 594 " --> pdb=" O GLN K 613 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 324 through 328 removed outlier: 4.134A pdb=" N GLU K 324 " --> pdb=" O CYS K 538 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP K 574 " --> pdb=" O ILE K 587 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA K 575 " --> pdb=" O GLY K 566 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 354 through 358 Processing sheet with id=AG9, first strand: chain 'K' and resid 361 through 362 removed outlier: 6.789A pdb=" N CYS K 361 " --> pdb=" O CYS K 525 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 452 through 454 Processing sheet with id=AH2, first strand: chain 'K' and resid 473 through 474 Processing sheet with id=AH3, first strand: chain 'K' and resid 654 through 655 removed outlier: 6.559A pdb=" N ILE K 670 " --> pdb=" O ILE K 666 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA K1078 " --> pdb=" O PHE K1095 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE K1095 " --> pdb=" O ALA K1078 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 733 through 736 removed outlier: 4.353A pdb=" N LYS K 733 " --> pdb=" O LEU K 861 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 1120 through 1125 removed outlier: 4.651A pdb=" N ALA K1087 " --> pdb=" O SER K1123 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AH9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.716A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.716A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AI3, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.636A pdb=" N MET M 34 " --> pdb=" O PHE M 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 10 through 12 Processing sheet with id=AI5, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AI6, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.660A pdb=" N GLY N 33 " --> pdb=" O ASP N 99 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE N 34 " --> pdb=" O TRP N 50 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP N 50 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP N 36 " --> pdb=" O MET N 48 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.975A pdb=" N ASN N 116 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AI9, first strand: chain 'O' and resid 54 through 55 removed outlier: 6.586A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR O 50 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) 1634 hydrogen bonds defined for protein. 4191 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: 9.56 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.24: 4880 1.24 - 1.40: 7355 1.40 - 1.55: 17587 1.55 - 1.71: 121 1.71 - 1.86: 174 Bond restraints: 30117 Sorted by residual: bond pdb=" N CYS D 985 " pdb=" CA CYS D 985 " ideal model delta sigma weight residual 1.453 1.663 -0.210 1.25e-02 6.40e+03 2.82e+02 bond pdb=" N CYS K 985 " pdb=" CA CYS K 985 " ideal model delta sigma weight residual 1.453 1.663 -0.210 1.25e-02 6.40e+03 2.81e+02 bond pdb=" N CYS A 985 " pdb=" CA CYS A 985 " ideal model delta sigma weight residual 1.453 1.662 -0.209 1.25e-02 6.40e+03 2.80e+02 bond pdb=" C CYS K1082 " pdb=" O CYS K1082 " ideal model delta sigma weight residual 1.236 1.383 -0.147 1.24e-02 6.50e+03 1.41e+02 bond pdb=" C CYS A1082 " pdb=" O CYS A1082 " ideal model delta sigma weight residual 1.236 1.383 -0.147 1.24e-02 6.50e+03 1.40e+02 ... (remaining 30112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 38801 2.44 - 4.88: 1974 4.88 - 7.32: 535 7.32 - 9.75: 54 9.75 - 12.19: 12 Bond angle restraints: 41376 Sorted by residual: angle pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " ideal model delta sigma weight residual 118.08 106.48 11.60 1.30e+00 5.92e-01 7.96e+01 angle pdb=" CA CYS K 617 " pdb=" C CYS K 617 " pdb=" N THR K 618 " ideal model delta sigma weight residual 118.08 106.50 11.58 1.30e+00 5.92e-01 7.94e+01 angle pdb=" CA CYS D 617 " pdb=" C CYS D 617 " pdb=" N THR D 618 " ideal model delta sigma weight residual 118.08 106.51 11.57 1.30e+00 5.92e-01 7.92e+01 angle pdb=" C THR A 791 " pdb=" N PRO A 792 " pdb=" CA PRO A 792 " ideal model delta sigma weight residual 119.66 125.90 -6.24 7.20e-01 1.93e+00 7.51e+01 angle pdb=" C THR D 791 " pdb=" N PRO D 792 " pdb=" CA PRO D 792 " ideal model delta sigma weight residual 119.66 125.88 -6.22 7.20e-01 1.93e+00 7.47e+01 ... (remaining 41371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 17934 17.80 - 35.61: 388 35.61 - 53.41: 77 53.41 - 71.22: 36 71.22 - 89.02: 6 Dihedral angle restraints: 18441 sinusoidal: 5715 harmonic: 12726 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 44.73 48.27 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual 93.00 44.74 48.26 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 96 " pdb=" CB CYS M 96 " ideal model delta sinusoidal sigma weight residual 93.00 44.76 48.24 1 1.00e+01 1.00e-02 3.21e+01 ... (remaining 18438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 4748 0.125 - 0.250: 256 0.250 - 0.375: 78 0.375 - 0.500: 9 0.500 - 0.625: 12 Chirality restraints: 5103 Sorted by residual: chirality pdb=" CA CYS K1082 " pdb=" N CYS K1082 " pdb=" C CYS K1082 " pdb=" CB CYS K1082 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.63 2.00e-01 2.50e+01 9.77e+00 chirality pdb=" CA CYS A1082 " pdb=" N CYS A1082 " pdb=" C CYS A1082 " pdb=" CB CYS A1082 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.75e+00 chirality pdb=" CA CYS D1082 " pdb=" N CYS D1082 " pdb=" C CYS D1082 " pdb=" CB CYS D1082 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.72e+00 ... (remaining 5100 not shown) Planarity restraints: 5559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 801 " 0.047 2.00e-02 2.50e+03 4.99e-02 3.11e+01 pdb=" CG ASN D 801 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN D 801 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN D 801 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG D1310 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " -0.047 2.00e-02 2.50e+03 4.97e-02 3.09e+01 pdb=" CG ASN A 801 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " 0.078 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 801 " 0.047 2.00e-02 2.50e+03 4.97e-02 3.09e+01 pdb=" CG ASN K 801 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN K 801 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN K 801 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG K1310 " 0.061 2.00e-02 2.50e+03 ... (remaining 5556 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 10705 2.86 - 3.37: 25462 3.37 - 3.88: 48065 3.88 - 4.39: 53294 4.39 - 4.90: 91505 Nonbonded interactions: 229031 Sorted by model distance: nonbonded pdb=" O ASN K 331 " pdb=" OD1 ASN K 331 " model vdw 2.350 3.040 nonbonded pdb=" O ASN A 331 " pdb=" OD1 ASN A 331 " model vdw 2.350 3.040 nonbonded pdb=" O ASN D 331 " pdb=" OD1 ASN D 331 " model vdw 2.350 3.040 nonbonded pdb=" O SER A 31 " pdb=" OG SER A 31 " model vdw 2.431 3.040 nonbonded pdb=" O SER D 31 " pdb=" OG SER D 31 " model vdw 2.431 3.040 ... (remaining 229026 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.900 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: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 33.750 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:9.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.425 30225 Z= 0.780 Angle : 1.386 19.831 41643 Z= 0.931 Chirality : 0.079 0.625 5103 Planarity : 0.006 0.044 5508 Dihedral : 8.946 89.023 10062 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.12), residues: 4365 helix: 0.36 (0.18), residues: 672 sheet: 1.00 (0.14), residues: 1278 loop : 0.17 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 995 TYR 0.043 0.006 TYR A1067 PHE 0.038 0.005 PHE C 50 TRP 0.026 0.006 TRP A 64 HIS 0.008 0.002 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.01187 (30117) covalent geometry : angle 1.35682 (41376) SS BOND : bond 0.10561 ( 57) SS BOND : angle 4.22039 ( 114) hydrogen bonds : bond 0.16417 ( 1514) hydrogen bonds : angle 8.56910 ( 4191) link_NAG-ASN : bond 0.02386 ( 51) link_NAG-ASN : angle 3.47029 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.9313 (tpp) cc_final: 0.8949 (tpp) REVERT: C 83 MET cc_start: 0.5759 (mtm) cc_final: 0.5461 (mtp) REVERT: D 306 PHE cc_start: 0.8103 (m-80) cc_final: 0.7859 (m-80) REVERT: F 83 MET cc_start: 0.5712 (mtm) cc_final: 0.4884 (mmt) REVERT: K 223 LEU cc_start: 0.6358 (mp) cc_final: 0.6129 (mp) REVERT: M 83 MET cc_start: 0.5773 (mtm) cc_final: 0.5482 (mtp) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.6902 time to fit residues: 312.7289 Evaluate side-chains 268 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 532 ASN A 536 ASN A 607 GLN A1005 GLN A1071 HIS A1088 HIS D 532 ASN D 901 GLN D 954 GLN D 992 GLN D1002 GLN D1010 GLN D1071 HIS D1113 GLN K 196 ASN K 532 ASN K 607 GLN K 901 GLN K 954 GLN K1005 GLN K1010 GLN K1071 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.251316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.229286 restraints weight = 27220.750| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 1.39 r_work: 0.4253 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.4197 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30225 Z= 0.149 Angle : 0.595 10.389 41643 Z= 0.313 Chirality : 0.047 0.296 5103 Planarity : 0.004 0.039 5508 Dihedral : 4.546 26.947 5661 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.89 % Allowed : 5.31 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.12), residues: 4365 helix: 1.92 (0.21), residues: 654 sheet: 0.95 (0.13), residues: 1386 loop : 0.23 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 765 TYR 0.027 0.002 TYR A1067 PHE 0.022 0.002 PHE A 898 TRP 0.011 0.001 TRP A 886 HIS 0.007 0.002 HIS K1048 Details of bonding type rmsd covalent geometry : bond 0.00320 (30117) covalent geometry : angle 0.56879 (41376) SS BOND : bond 0.00291 ( 57) SS BOND : angle 0.93293 ( 114) hydrogen bonds : bond 0.05301 ( 1514) hydrogen bonds : angle 6.37425 ( 4191) link_NAG-ASN : bond 0.00495 ( 51) link_NAG-ASN : angle 2.88748 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 300 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 790 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7873 (mmpt) REVERT: C 83 MET cc_start: 0.5544 (mtm) cc_final: 0.5298 (mmt) REVERT: D 536 ASN cc_start: 0.6507 (m-40) cc_final: 0.5665 (t0) REVERT: F 83 MET cc_start: 0.5245 (mtm) cc_final: 0.4886 (mmt) REVERT: K 223 LEU cc_start: 0.6803 (mp) cc_final: 0.6560 (mp) REVERT: K 697 MET cc_start: 0.8779 (ptm) cc_final: 0.8438 (ptm) outliers start: 41 outliers final: 14 residues processed: 325 average time/residue: 0.6358 time to fit residues: 243.8702 Evaluate side-chains 293 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 278 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 615 VAL Chi-restraints excluded: chain K residue 985 CYS Chi-restraints excluded: chain K residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 96 optimal weight: 1.9990 chunk 140 optimal weight: 50.0000 chunk 19 optimal weight: 4.9990 chunk 350 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 424 optimal weight: 40.0000 chunk 392 optimal weight: 0.0980 chunk 138 optimal weight: 30.0000 chunk 65 optimal weight: 4.9990 chunk 414 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 239 GLN A 532 ASN A 787 GLN A 901 GLN A1005 GLN D 532 ASN D 536 ASN D 787 GLN D1002 GLN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1088 HIS D1113 GLN K 81 ASN K 196 ASN K 532 ASN K 607 GLN K 751 ASN K 787 GLN K1005 GLN ** K1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.247280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.224822 restraints weight = 27184.763| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 1.38 r_work: 0.4200 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.4157 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 30225 Z= 0.273 Angle : 0.690 10.724 41643 Z= 0.364 Chirality : 0.052 0.316 5103 Planarity : 0.005 0.050 5508 Dihedral : 5.003 35.125 5661 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.45 % Allowed : 6.09 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.12), residues: 4365 helix: 1.28 (0.20), residues: 669 sheet: 0.99 (0.13), residues: 1338 loop : -0.08 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 905 TYR 0.033 0.003 TYR A1067 PHE 0.036 0.003 PHE D 898 TRP 0.016 0.002 TRP A 886 HIS 0.010 0.003 HIS K1064 Details of bonding type rmsd covalent geometry : bond 0.00621 (30117) covalent geometry : angle 0.67039 (41376) SS BOND : bond 0.00379 ( 57) SS BOND : angle 0.96011 ( 114) hydrogen bonds : bond 0.06165 ( 1514) hydrogen bonds : angle 6.28380 ( 4191) link_NAG-ASN : bond 0.00531 ( 51) link_NAG-ASN : angle 2.71728 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7876 (p90) REVERT: A 740 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8171 (ttm) REVERT: F 83 MET cc_start: 0.5410 (mtm) cc_final: 0.5110 (mmt) REVERT: K 223 LEU cc_start: 0.6854 (mp) cc_final: 0.6568 (mp) REVERT: K 858 LEU cc_start: 0.8691 (mp) cc_final: 0.8469 (mp) outliers start: 53 outliers final: 25 residues processed: 297 average time/residue: 0.6854 time to fit residues: 240.0088 Evaluate side-chains 288 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 261 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 985 CYS Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 615 VAL Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 985 CYS Chi-restraints excluded: chain K residue 1096 VAL Chi-restraints excluded: chain K residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 308 optimal weight: 10.0000 chunk 108 optimal weight: 50.0000 chunk 270 optimal weight: 0.0570 chunk 26 optimal weight: 3.9990 chunk 358 optimal weight: 0.8980 chunk 266 optimal weight: 0.4980 chunk 141 optimal weight: 0.0020 chunk 152 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 335 optimal weight: 30.0000 overall best weight: 0.4906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 239 GLN A 751 ASN A 787 GLN A1005 GLN D 536 ASN D 787 GLN D1002 GLN D1010 GLN D1071 HIS D1113 GLN K 196 ASN K 532 ASN K 607 GLN K 751 ASN K 954 GLN ** K 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1005 GLN ** K1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1071 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.250057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.213624 restraints weight = 27279.871| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 3.49 r_work: 0.3854 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30225 Z= 0.108 Angle : 0.528 10.760 41643 Z= 0.272 Chirality : 0.045 0.292 5103 Planarity : 0.004 0.043 5508 Dihedral : 4.301 32.634 5661 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.34 % Allowed : 8.03 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.90 (0.12), residues: 4365 helix: 1.89 (0.20), residues: 681 sheet: 1.00 (0.13), residues: 1356 loop : 0.02 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 995 TYR 0.022 0.001 TYR A1067 PHE 0.017 0.001 PHE K 898 TRP 0.007 0.001 TRP M 47 HIS 0.003 0.001 HIS K1088 Details of bonding type rmsd covalent geometry : bond 0.00222 (30117) covalent geometry : angle 0.50612 (41376) SS BOND : bond 0.00160 ( 57) SS BOND : angle 0.63537 ( 114) hydrogen bonds : bond 0.04248 ( 1514) hydrogen bonds : angle 5.70483 ( 4191) link_NAG-ASN : bond 0.00443 ( 51) link_NAG-ASN : angle 2.52511 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 267 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7797 (p90) REVERT: A 740 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8249 (ttm) REVERT: F 83 MET cc_start: 0.5435 (mtm) cc_final: 0.4822 (mmt) REVERT: K 223 LEU cc_start: 0.6990 (mp) cc_final: 0.6679 (mp) REVERT: K 740 MET cc_start: 0.8520 (tpp) cc_final: 0.8273 (tpp) outliers start: 29 outliers final: 9 residues processed: 283 average time/residue: 0.6842 time to fit residues: 229.0706 Evaluate side-chains 261 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 250 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 985 CYS Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain K residue 985 CYS Chi-restraints excluded: chain K residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 338 optimal weight: 7.9990 chunk 432 optimal weight: 3.9990 chunk 283 optimal weight: 0.1980 chunk 304 optimal weight: 4.9990 chunk 431 optimal weight: 20.0000 chunk 365 optimal weight: 0.0570 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 405 optimal weight: 20.0000 chunk 374 optimal weight: 0.6980 chunk 409 optimal weight: 8.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 607 GLN A 751 ASN A 787 GLN A1005 GLN D 607 GLN D1002 GLN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1113 GLN K 607 GLN K 751 ASN K1005 GLN K1088 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.247692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.223119 restraints weight = 27242.420| |-----------------------------------------------------------------------------| r_work (start): 0.4463 rms_B_bonded: 1.41 r_work: 0.4177 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4137 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 30225 Z= 0.216 Angle : 0.629 10.979 41643 Z= 0.327 Chirality : 0.050 0.325 5103 Planarity : 0.005 0.046 5508 Dihedral : 4.662 34.096 5661 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.80 % Allowed : 8.63 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.72 (0.12), residues: 4365 helix: 1.71 (0.20), residues: 654 sheet: 0.84 (0.13), residues: 1392 loop : -0.04 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 995 TYR 0.029 0.002 TYR A1067 PHE 0.033 0.002 PHE D 898 TRP 0.011 0.002 TRP A 886 HIS 0.008 0.002 HIS K1064 Details of bonding type rmsd covalent geometry : bond 0.00490 (30117) covalent geometry : angle 0.60865 (41376) SS BOND : bond 0.00299 ( 57) SS BOND : angle 0.74453 ( 114) hydrogen bonds : bond 0.05573 ( 1514) hydrogen bonds : angle 5.94033 ( 4191) link_NAG-ASN : bond 0.00484 ( 51) link_NAG-ASN : angle 2.66815 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7782 (p90) REVERT: A 740 MET cc_start: 0.8291 (ttm) cc_final: 0.8073 (ttm) REVERT: D 814 LYS cc_start: 0.6861 (tmtp) cc_final: 0.6266 (tmtm) REVERT: D 995 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7689 (mtp85) REVERT: F 83 MET cc_start: 0.5320 (mtm) cc_final: 0.4957 (mmt) REVERT: K 223 LEU cc_start: 0.6941 (mp) cc_final: 0.6626 (mp) outliers start: 39 outliers final: 21 residues processed: 280 average time/residue: 0.6747 time to fit residues: 222.6509 Evaluate side-chains 271 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 985 CYS Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 985 CYS Chi-restraints excluded: chain K residue 1096 VAL Chi-restraints excluded: chain K residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 400 optimal weight: 50.0000 chunk 16 optimal weight: 0.0170 chunk 285 optimal weight: 30.0000 chunk 353 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 351 optimal weight: 0.9990 chunk 246 optimal weight: 0.9980 chunk 320 optimal weight: 40.0000 chunk 39 optimal weight: 50.0000 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 607 GLN A 751 ASN A1005 GLN D 607 GLN D1002 GLN D1010 GLN D1113 GLN K 607 GLN K 751 ASN K1005 GLN ** K1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.249413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.224947 restraints weight = 27418.357| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 1.43 r_work: 0.4204 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4165 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30225 Z= 0.122 Angle : 0.535 11.698 41643 Z= 0.274 Chirality : 0.046 0.311 5103 Planarity : 0.004 0.043 5508 Dihedral : 4.289 36.505 5661 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.80 % Allowed : 8.86 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.13), residues: 4365 helix: 2.14 (0.21), residues: 654 sheet: 0.84 (0.13), residues: 1389 loop : 0.06 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 995 TYR 0.024 0.001 TYR A1067 PHE 0.021 0.001 PHE D 898 TRP 0.008 0.001 TRP M 47 HIS 0.004 0.001 HIS K1064 Details of bonding type rmsd covalent geometry : bond 0.00263 (30117) covalent geometry : angle 0.51347 (41376) SS BOND : bond 0.00150 ( 57) SS BOND : angle 0.55340 ( 114) hydrogen bonds : bond 0.04349 ( 1514) hydrogen bonds : angle 5.59224 ( 4191) link_NAG-ASN : bond 0.00440 ( 51) link_NAG-ASN : angle 2.50824 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 258 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7753 (p90) REVERT: D 237 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6905 (mtt90) REVERT: D 814 LYS cc_start: 0.6507 (OUTLIER) cc_final: 0.6186 (tmtm) REVERT: F 83 MET cc_start: 0.5314 (mtm) cc_final: 0.5112 (mmp) REVERT: K 223 LEU cc_start: 0.6893 (mp) cc_final: 0.6583 (mp) REVERT: K 740 MET cc_start: 0.8244 (tpp) cc_final: 0.7978 (tpp) REVERT: K 814 LYS cc_start: 0.6701 (tmtp) cc_final: 0.6265 (tmtm) outliers start: 39 outliers final: 18 residues processed: 280 average time/residue: 0.6852 time to fit residues: 226.5296 Evaluate side-chains 266 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 985 CYS Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 874 THR Chi-restraints excluded: chain K residue 985 CYS Chi-restraints excluded: chain K residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 220 optimal weight: 0.6980 chunk 264 optimal weight: 20.0000 chunk 411 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 276 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 319 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 113 optimal weight: 30.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 607 GLN A 751 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN D 607 GLN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1113 GLN K 532 ASN K 607 GLN K 751 ASN K1005 GLN K1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.247315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.206433 restraints weight = 26933.174| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 3.92 r_work: 0.3708 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 30225 Z= 0.231 Angle : 0.643 11.266 41643 Z= 0.334 Chirality : 0.050 0.343 5103 Planarity : 0.005 0.049 5508 Dihedral : 4.732 36.576 5661 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.03 % Allowed : 8.77 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.12), residues: 4365 helix: 1.55 (0.20), residues: 669 sheet: 0.86 (0.14), residues: 1350 loop : -0.06 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 995 TYR 0.030 0.002 TYR A1067 PHE 0.035 0.002 PHE D 898 TRP 0.012 0.002 TRP A 886 HIS 0.009 0.002 HIS K1064 Details of bonding type rmsd covalent geometry : bond 0.00526 (30117) covalent geometry : angle 0.62214 (41376) SS BOND : bond 0.00305 ( 57) SS BOND : angle 0.82054 ( 114) hydrogen bonds : bond 0.05646 ( 1514) hydrogen bonds : angle 5.89946 ( 4191) link_NAG-ASN : bond 0.00490 ( 51) link_NAG-ASN : angle 2.73369 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7799 (p90) REVERT: A 780 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8301 (mt-10) REVERT: D 814 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6344 (tmtm) REVERT: F 83 MET cc_start: 0.5516 (mtm) cc_final: 0.5030 (mmp) REVERT: K 223 LEU cc_start: 0.7142 (mp) cc_final: 0.6842 (mp) outliers start: 44 outliers final: 30 residues processed: 274 average time/residue: 0.6709 time to fit residues: 217.1873 Evaluate side-chains 279 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 985 CYS Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 616 ASN Chi-restraints excluded: chain K residue 874 THR Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 985 CYS Chi-restraints excluded: chain K residue 1096 VAL Chi-restraints excluded: chain K residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 233 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 317 optimal weight: 0.9980 chunk 359 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 607 GLN A 751 ASN A1005 GLN D 532 ASN D 607 GLN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN D1010 GLN D1113 GLN K 532 ASN K 607 GLN K1005 GLN K1010 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.247730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.207081 restraints weight = 27034.496| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 3.92 r_work: 0.3746 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30225 Z= 0.192 Angle : 0.608 14.146 41643 Z= 0.312 Chirality : 0.049 0.347 5103 Planarity : 0.004 0.044 5508 Dihedral : 4.589 35.707 5661 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.03 % Allowed : 9.23 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.65 (0.13), residues: 4365 helix: 1.61 (0.20), residues: 669 sheet: 0.79 (0.14), residues: 1371 loop : -0.07 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 995 TYR 0.029 0.002 TYR A1067 PHE 0.030 0.002 PHE D 898 TRP 0.009 0.001 TRP A 886 HIS 0.006 0.002 HIS K1064 Details of bonding type rmsd covalent geometry : bond 0.00435 (30117) covalent geometry : angle 0.58633 (41376) SS BOND : bond 0.00241 ( 57) SS BOND : angle 0.69948 ( 114) hydrogen bonds : bond 0.05124 ( 1514) hydrogen bonds : angle 5.78311 ( 4191) link_NAG-ASN : bond 0.00473 ( 51) link_NAG-ASN : angle 2.66768 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 251 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7808 (p90) REVERT: D 814 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6317 (tmtm) REVERT: F 34 MET cc_start: 0.4429 (mmm) cc_final: 0.4170 (mmp) REVERT: F 83 MET cc_start: 0.5512 (mtm) cc_final: 0.5080 (mmp) REVERT: K 223 LEU cc_start: 0.7086 (mp) cc_final: 0.6791 (mp) REVERT: K 740 MET cc_start: 0.8631 (tpp) cc_final: 0.8331 (tpp) outliers start: 44 outliers final: 30 residues processed: 276 average time/residue: 0.6552 time to fit residues: 214.5626 Evaluate side-chains 275 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 985 CYS Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 616 ASN Chi-restraints excluded: chain K residue 874 THR Chi-restraints excluded: chain K residue 985 CYS Chi-restraints excluded: chain K residue 1096 VAL Chi-restraints excluded: chain K residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 337 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 187 optimal weight: 50.0000 chunk 83 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 429 optimal weight: 20.0000 chunk 412 optimal weight: 0.6980 chunk 297 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 751 ASN A1005 GLN D 607 GLN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN D1010 GLN D1113 GLN K 196 ASN K 607 GLN K1005 GLN K1010 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.246939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.205476 restraints weight = 26860.348| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 3.98 r_work: 0.3719 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 30225 Z= 0.217 Angle : 0.643 13.160 41643 Z= 0.331 Chirality : 0.050 0.362 5103 Planarity : 0.005 0.049 5508 Dihedral : 4.768 41.109 5661 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.17 % Allowed : 9.33 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.58 (0.13), residues: 4365 helix: 1.49 (0.20), residues: 669 sheet: 0.80 (0.14), residues: 1353 loop : -0.13 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 995 TYR 0.030 0.002 TYR A1067 PHE 0.033 0.002 PHE D 898 TRP 0.011 0.002 TRP A 886 HIS 0.008 0.002 HIS K1064 Details of bonding type rmsd covalent geometry : bond 0.00495 (30117) covalent geometry : angle 0.62046 (41376) SS BOND : bond 0.00280 ( 57) SS BOND : angle 0.84469 ( 114) hydrogen bonds : bond 0.05530 ( 1514) hydrogen bonds : angle 5.88806 ( 4191) link_NAG-ASN : bond 0.00501 ( 51) link_NAG-ASN : angle 2.78233 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7825 (p90) REVERT: D 318 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8271 (p90) REVERT: D 814 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6367 (tmtm) REVERT: F 34 MET cc_start: 0.4468 (mmm) cc_final: 0.4189 (mmp) REVERT: F 83 MET cc_start: 0.5485 (mtm) cc_final: 0.5035 (mmp) REVERT: K 223 LEU cc_start: 0.7097 (mp) cc_final: 0.6800 (mp) outliers start: 47 outliers final: 32 residues processed: 274 average time/residue: 0.6345 time to fit residues: 206.4716 Evaluate side-chains 276 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 977 LEU Chi-restraints excluded: chain D residue 985 CYS Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1094 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 616 ASN Chi-restraints excluded: chain K residue 874 THR Chi-restraints excluded: chain K residue 977 LEU Chi-restraints excluded: chain K residue 985 CYS Chi-restraints excluded: chain K residue 1096 VAL Chi-restraints excluded: chain K residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 214 optimal weight: 0.9980 chunk 406 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 217 optimal weight: 0.1980 chunk 344 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 349 optimal weight: 0.3980 chunk 350 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 751 ASN A1002 GLN A1005 GLN D 532 ASN D 607 GLN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN D1010 GLN D1113 GLN K 607 GLN K1005 GLN K1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.249632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.211544 restraints weight = 27210.487| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 3.71 r_work: 0.3797 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30225 Z= 0.102 Angle : 0.528 13.124 41643 Z= 0.268 Chirality : 0.045 0.342 5103 Planarity : 0.004 0.045 5508 Dihedral : 4.145 31.202 5661 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.29 % Allowed : 10.43 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.13), residues: 4365 helix: 2.11 (0.20), residues: 672 sheet: 0.86 (0.14), residues: 1371 loop : -0.00 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 995 TYR 0.019 0.001 TYR D1067 PHE 0.022 0.001 PHE D 643 TRP 0.010 0.001 TRP F 47 HIS 0.003 0.001 HIS K1048 Details of bonding type rmsd covalent geometry : bond 0.00209 (30117) covalent geometry : angle 0.50561 (41376) SS BOND : bond 0.00178 ( 57) SS BOND : angle 0.79030 ( 114) hydrogen bonds : bond 0.03966 ( 1514) hydrogen bonds : angle 5.42864 ( 4191) link_NAG-ASN : bond 0.00458 ( 51) link_NAG-ASN : angle 2.51725 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 251 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7734 (p90) REVERT: A 995 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7809 (mtp85) REVERT: D 814 LYS cc_start: 0.6531 (OUTLIER) cc_final: 0.6139 (tmtm) REVERT: F 83 MET cc_start: 0.5493 (mtm) cc_final: 0.5019 (mmp) REVERT: K 223 LEU cc_start: 0.6979 (mp) cc_final: 0.6722 (mp) REVERT: K 740 MET cc_start: 0.8472 (tpp) cc_final: 0.8227 (tpp) REVERT: K 814 LYS cc_start: 0.6543 (tmtp) cc_final: 0.6226 (tmtm) outliers start: 28 outliers final: 15 residues processed: 264 average time/residue: 0.6846 time to fit residues: 213.0759 Evaluate side-chains 254 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 237 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 985 CYS Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 814 LYS Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1136 THR Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 874 THR Chi-restraints excluded: chain K residue 985 CYS Chi-restraints excluded: chain K residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 229 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 352 optimal weight: 0.7980 chunk 176 optimal weight: 8.9990 chunk 286 optimal weight: 50.0000 chunk 303 optimal weight: 0.0670 chunk 300 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A 751 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1005 GLN A1010 GLN A1113 GLN D 239 GLN D 607 GLN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN D1010 GLN D1113 GLN K 607 GLN K1005 GLN ** K1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.248937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.206312 restraints weight = 27228.644| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 4.36 r_work: 0.3694 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30225 Z= 0.124 Angle : 0.561 13.382 41643 Z= 0.282 Chirality : 0.049 0.824 5103 Planarity : 0.004 0.043 5508 Dihedral : 4.240 41.276 5661 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.20 % Allowed : 10.53 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.13), residues: 4365 helix: 2.18 (0.21), residues: 654 sheet: 0.86 (0.14), residues: 1374 loop : 0.02 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 995 TYR 0.024 0.002 TYR A1067 PHE 0.023 0.001 PHE D 643 TRP 0.011 0.001 TRP F 47 HIS 0.004 0.001 HIS K1064 Details of bonding type rmsd covalent geometry : bond 0.00264 (30117) covalent geometry : angle 0.52911 (41376) SS BOND : bond 0.00215 ( 57) SS BOND : angle 0.75695 ( 114) hydrogen bonds : bond 0.04349 ( 1514) hydrogen bonds : angle 5.46980 ( 4191) link_NAG-ASN : bond 0.00589 ( 51) link_NAG-ASN : angle 3.06473 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12885.92 seconds wall clock time: 218 minutes 57.73 seconds (13137.73 seconds total)