Starting phenix.real_space_refine on Wed Oct 28 20:59:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sob_25265/10_2026/7sob_25265.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sob_25265/10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sob_25265/10_2026/7sob_25265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sob_25265/10_2026/7sob_25265.map" model { file = "/net/cci-nas-00/data/ceres_data/7sob_25265/10_2026/7sob_25265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sob_25265/10_2026/7sob_25265.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sob_25265/10_2026/7sob_25265.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sob_25265/10_2026/7sob_25265.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/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 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: 9.89, per 1000 atoms: 0.33 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 D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.02 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.08 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.07 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.01 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.04 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.05 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.16 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.12 Simple disulfide: pdb=" SG CYS D 985 " - pdb=" SG CYS K 383 " distance=2.46 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.02 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.00 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 136 " distance=2.04 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.04 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.02 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.02 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.08 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.07 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 488 " distance=2.03 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.01 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.04 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.05 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.16 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.12 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.02 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.00 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.01 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " 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: 2.83 Conformation dependent library (CDL) restraints added in 1.5 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: 1.09 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: 9.98 Time building geometry restraints manager: 3.70 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: 16881 17.80 - 35.61: 371 35.61 - 53.41: 76 53.41 - 71.22: 36 71.22 - 89.02: 6 Dihedral angle restraints: 17370 sinusoidal: 4644 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 17367 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: 0.09 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: 12.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 35.400 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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:8.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 9.265 89.023 8991 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/Z covalent geometry : bond 0.01187 / 0.75 (30117) covalent geometry : angle 1.35682 / 0.93 (41376) SS BOND : bond 0.10561 / 6.59 ( 57) SS BOND : angle 4.22039 / 2.92 ( 114) hydrogen bonds : bond 0.16417 / 10.96 ( 1514) hydrogen bonds : angle 8.56910 / 6.04 ( 4191) link_NAG-ASN : bond 0.02386 / 1.58 ( 51) link_NAG-ASN : angle 3.47029 / 2.54 ( 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 : 0.936 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: 0.6064 time to fit residues: 277.3722 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 : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [432, 197, 388, 215, 20, 132, 261, 248, 207, 401, 424] 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... A 196 ASN A 536 ASN A 607 GLN A1005 GLN A1071 HIS A1088 HIS D 532 ASN D 536 ASN D 901 GLN D 954 GLN D 992 GLN D1002 GLN D1010 GLN D1071 HIS D1088 HIS D1113 GLN K 196 ASN K 532 ASN K 607 GLN K 901 GLN K 954 GLN K1010 GLN K1071 HIS K1088 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.251302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.229157 restraints weight = 27222.540| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 1.39 r_work: 0.4253 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.4207 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30225 Z= 0.152 Angle : 0.590 10.113 41643 Z= 0.311 Chirality : 0.046 0.276 5103 Planarity : 0.004 0.044 5508 Dihedral : 4.443 24.898 4590 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.89 % Allowed : 5.54 % Favored : 92.57 % 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: 1.04 (0.12), residues: 4365 helix: 2.11 (0.21), residues: 633 sheet: 0.94 (0.13), residues: 1386 loop : 0.22 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 995 TYR 0.026 0.002 TYR A1067 PHE 0.022 0.002 PHE A 898 TRP 0.012 0.002 TRP K 886 HIS 0.007 0.002 HIS K1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (30117) covalent geometry : angle 0.56551 / 0.31 (41376) SS BOND : bond 0.00259 / 0.16 ( 57) SS BOND : angle 0.93557 / 0.64 ( 114) hydrogen bonds : bond 0.05169 / 3.48 ( 1514) hydrogen bonds : angle 6.28383 / 4.40 ( 4191) link_NAG-ASN : bond 0.00542 / 0.40 ( 51) link_NAG-ASN : angle 2.73187 / 1.97 ( 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 335 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 294 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 790 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7867 (mmpt) REVERT: A 1029 MET cc_start: 0.9227 (tpp) cc_final: 0.8852 (tpp) REVERT: C 83 MET cc_start: 0.5530 (mtm) cc_final: 0.5302 (mmt) REVERT: D 536 ASN cc_start: 0.6477 (m110) cc_final: 0.5630 (t0) REVERT: D 1010 GLN cc_start: 0.8182 (tt0) cc_final: 0.7936 (pp30) REVERT: F 83 MET cc_start: 0.5246 (mtm) cc_final: 0.4914 (mmt) REVERT: K 223 LEU cc_start: 0.6790 (mp) cc_final: 0.6545 (mp) REVERT: K 697 MET cc_start: 0.8768 (ptm) cc_final: 0.8426 (ptm) outliers start: 41 outliers final: 15 residues processed: 319 average time/residue: 0.5892 time to fit residues: 224.3963 Evaluate side-chains 290 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 274 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 604 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: [96, 140, 19, 350, 293, 85, 424, 392, 138, 65, 414] chunk 96 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 350 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 424 optimal weight: 9.9990 chunk 392 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 414 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 239 GLN A 532 ASN A 751 ASN A 787 GLN A 901 GLN A1002 GLN A1005 GLN A1010 GLN D1002 GLN D1113 GLN K 196 ASN K 532 ASN K 607 GLN K 751 ASN K 787 GLN K 954 GLN K1005 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.246563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.224183 restraints weight = 26836.189| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 1.38 r_work: 0.4198 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.4156 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 30225 Z= 0.316 Angle : 0.738 10.741 41643 Z= 0.389 Chirality : 0.054 0.327 5103 Planarity : 0.006 0.054 5508 Dihedral : 4.876 28.038 4590 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.35 % Allowed : 6.42 % Favored : 91.23 % 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: 0.59 (0.12), residues: 4365 helix: 1.14 (0.20), residues: 669 sheet: 0.98 (0.13), residues: 1341 loop : -0.12 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 905 TYR 0.035 0.003 TYR A1067 PHE 0.040 0.003 PHE D 898 TRP 0.019 0.003 TRP A 886 HIS 0.011 0.003 HIS K1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.32 (30117) covalent geometry : angle 0.71951 / 0.39 (41376) SS BOND : bond 0.00488 / 0.33 ( 57) SS BOND : angle 1.00772 / 0.71 ( 114) hydrogen bonds : bond 0.06490 / 4.35 ( 1514) hydrogen bonds : angle 6.36737 / 4.48 ( 4191) link_NAG-ASN : bond 0.00591 / 0.41 ( 51) link_NAG-ASN : angle 2.73736 / 1.96 ( 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 323 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 272 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7807 (mtt90) REVERT: D 787 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7981 (mm-40) REVERT: F 83 MET cc_start: 0.5463 (mtm) cc_final: 0.5234 (mmt) REVERT: K 223 LEU cc_start: 0.6925 (mp) cc_final: 0.6635 (mp) REVERT: K 858 LEU cc_start: 0.8692 (mp) cc_final: 0.8492 (mp) outliers start: 51 outliers final: 26 residues processed: 298 average time/residue: 0.5905 time to fit residues: 209.9166 Evaluate side-chains 287 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 259 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 604 THR Chi-restraints excluded: chain A residue 615 VAL 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 29 THR Chi-restraints excluded: chain D residue 44 ARG 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 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 94 SER Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 615 VAL Chi-restraints excluded: chain K residue 985 CYS Chi-restraints excluded: chain K residue 1096 VAL Chi-restraints excluded: chain K residue 1111 GLU 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: [308, 108, 270, 26, 358, 266, 141, 152, 196, 22, 335] chunk 308 optimal weight: 7.9990 chunk 108 optimal weight: 50.0000 chunk 270 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 358 optimal weight: 0.6980 chunk 266 optimal weight: 1.9990 chunk 141 optimal weight: 50.0000 chunk 152 optimal weight: 4.9990 chunk 196 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 335 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 239 GLN A 751 ASN A 787 GLN A1005 GLN D 532 ASN D 536 ASN D 954 GLN D1002 GLN D1113 GLN K 532 ASN K 607 GLN K 751 ASN K 954 GLN K 969 ASN K1005 GLN ** K1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.247760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.213064 restraints weight = 27022.061| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 3.10 r_work: 0.3872 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 30225 Z= 0.197 Angle : 0.618 10.800 41643 Z= 0.321 Chirality : 0.049 0.307 5103 Planarity : 0.005 0.047 5508 Dihedral : 4.503 26.145 4590 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.22 % Allowed : 7.85 % Favored : 89.94 % 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 (0.12), residues: 4365 helix: 1.64 (0.21), residues: 636 sheet: 0.87 (0.13), residues: 1362 loop : -0.12 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 995 TYR 0.029 0.002 TYR A1067 PHE 0.030 0.002 PHE K 898 TRP 0.010 0.001 TRP A 886 HIS 0.007 0.002 HIS K1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (30117) covalent geometry : angle 0.59677 / 0.32 (41376) SS BOND : bond 0.00268 / 0.17 ( 57) SS BOND : angle 0.73152 / 0.51 ( 114) hydrogen bonds : bond 0.05354 / 3.59 ( 1514) hydrogen bonds : angle 6.03277 / 4.25 ( 4191) link_NAG-ASN : bond 0.00503 / 0.36 ( 51) link_NAG-ASN : angle 2.68747 / 1.94 ( 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 320 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7853 (p90) REVERT: A 319 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7201 (ttm170) REVERT: D 814 LYS cc_start: 0.6891 (tmtp) cc_final: 0.6117 (tmtm) REVERT: F 83 MET cc_start: 0.5581 (mtm) cc_final: 0.5259 (mmt) REVERT: K 223 LEU cc_start: 0.7108 (mp) cc_final: 0.6764 (mp) REVERT: K 858 LEU cc_start: 0.8712 (mp) cc_final: 0.8494 (mp) outliers start: 48 outliers final: 28 residues processed: 298 average time/residue: 0.5995 time to fit residues: 213.3936 Evaluate side-chains 283 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 319 ARG Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 900 MET 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 302 THR Chi-restraints excluded: chain K residue 780 GLU 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 1111 GLU 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: [338, 432, 283, 304, 431, 365, 93, 104, 405, 374, 409] chunk 338 optimal weight: 4.9990 chunk 432 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 304 optimal weight: 9.9990 chunk 431 optimal weight: 10.0000 chunk 365 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 30.0000 chunk 405 optimal weight: 6.9990 chunk 374 optimal weight: 1.9990 chunk 409 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 239 GLN A 607 GLN A 751 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 787 GLN D1113 GLN K 196 ASN K 239 GLN K 532 ASN K 607 GLN K 751 ASN K 969 ASN K1005 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.245598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.204771 restraints weight = 26785.366| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 3.80 r_work: 0.3727 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.119 30225 Z= 0.370 Angle : 0.800 11.139 41643 Z= 0.418 Chirality : 0.057 0.365 5103 Planarity : 0.006 0.059 5508 Dihedral : 5.083 28.422 4590 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.63 % Allowed : 8.31 % Favored : 89.06 % 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: 0.24 (0.12), residues: 4365 helix: 0.93 (0.20), residues: 654 sheet: 0.63 (0.13), residues: 1329 loop : -0.28 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 905 TYR 0.035 0.003 TYR A1067 PHE 0.045 0.004 PHE D 898 TRP 0.020 0.003 TRP A 886 HIS 0.012 0.004 HIS K1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00854 / 0.37 (30117) covalent geometry : angle 0.77906 / 0.41 (41376) SS BOND : bond 0.00474 / 0.33 ( 57) SS BOND : angle 1.08298 / 0.74 ( 114) hydrogen bonds : bond 0.06731 / 4.51 ( 1514) hydrogen bonds : angle 6.38347 / 4.48 ( 4191) link_NAG-ASN : bond 0.00709 / 0.47 ( 51) link_NAG-ASN : angle 3.03846 / 2.16 ( 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 318 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 1.275 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: symmetry clash REVERT: A 318 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.7900 (p90) REVERT: A 319 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7385 (ttm170) REVERT: F 34 MET cc_start: 0.4996 (OUTLIER) cc_final: 0.4673 (mmm) REVERT: F 83 MET cc_start: 0.5628 (mtm) cc_final: 0.5337 (mmp) REVERT: K 223 LEU cc_start: 0.7087 (mp) cc_final: 0.6740 (mp) REVERT: M 34 MET cc_start: 0.4630 (mmm) cc_final: 0.4425 (mmp) outliers start: 57 outliers final: 37 residues processed: 293 average time/residue: 0.5980 time to fit residues: 209.5458 Evaluate side-chains 285 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 319 ARG Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 29 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 604 THR Chi-restraints excluded: chain D residue 616 ASN 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 34 MET Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 237 ARG Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 616 ASN Chi-restraints excluded: chain K residue 747 THR Chi-restraints excluded: chain K residue 780 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: [400, 16, 285, 353, 7, 351, 246, 320, 39, 60, 63] chunk 400 optimal weight: 50.0000 chunk 16 optimal weight: 0.8980 chunk 285 optimal weight: 40.0000 chunk 353 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 351 optimal weight: 0.9990 chunk 246 optimal weight: 5.9990 chunk 320 optimal weight: 40.0000 chunk 39 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 239 GLN A 607 GLN A1002 GLN A1005 GLN D 239 GLN D 532 ASN D1002 GLN D1113 GLN K 239 GLN K 532 ASN K 607 GLN K 751 ASN ** K 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1005 GLN K1010 GLN M 30 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.248313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.214516 restraints weight = 27055.902| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 3.02 r_work: 0.3895 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30225 Z= 0.134 Angle : 0.563 11.071 41643 Z= 0.290 Chirality : 0.046 0.316 5103 Planarity : 0.004 0.044 5508 Dihedral : 4.295 23.716 4590 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.85 % Allowed : 9.00 % Favored : 89.15 % 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: 0.57 (0.12), residues: 4365 helix: 1.63 (0.20), residues: 672 sheet: 0.79 (0.14), residues: 1335 loop : -0.19 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 995 TYR 0.024 0.002 TYR A1067 PHE 0.022 0.002 PHE K 898 TRP 0.009 0.001 TRP M 47 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (30117) covalent geometry : angle 0.53947 / 0.29 (41376) SS BOND : bond 0.00165 / 0.10 ( 57) SS BOND : angle 0.93984 / 0.60 ( 114) hydrogen bonds : bond 0.04610 / 3.09 ( 1514) hydrogen bonds : angle 5.81420 / 4.09 ( 4191) link_NAG-ASN : bond 0.00472 / 0.36 ( 51) link_NAG-ASN : angle 2.64843 / 1.94 ( 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 304 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 1.207 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: symmetry clash REVERT: A 318 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7821 (p90) REVERT: A 319 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7235 (ttm170) REVERT: A 814 LYS cc_start: 0.6893 (tmtp) cc_final: 0.6446 (tmtm) REVERT: D 318 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8294 (p90) REVERT: D 814 LYS cc_start: 0.6822 (tmtp) cc_final: 0.6229 (tmtm) REVERT: F 83 MET cc_start: 0.5438 (mtm) cc_final: 0.5219 (mmp) REVERT: K 223 LEU cc_start: 0.7065 (mp) cc_final: 0.6796 (mp) outliers start: 40 outliers final: 19 residues processed: 285 average time/residue: 0.5786 time to fit residues: 198.0063 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 : 1.027 ------------------------------------------------------------------------------- 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 319 ARG Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 874 THR 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 29 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 874 THR 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 302 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: [220, 264, 411, 86, 173, 276, 79, 194, 319, 149, 113] chunk 220 optimal weight: 0.0070 chunk 264 optimal weight: 30.0000 chunk 411 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 276 optimal weight: 50.0000 chunk 79 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 319 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1113 GLN D 188 ASN D 239 GLN D 532 ASN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN K 188 ASN K 239 GLN K 607 GLN K 751 ASN K 969 ASN K1005 GLN K1010 GLN M 30 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.244404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.220483 restraints weight = 26711.994| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 1.37 r_work: 0.4156 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.4097 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.142 30225 Z= 0.460 Angle : 0.898 11.663 41643 Z= 0.468 Chirality : 0.063 0.374 5103 Planarity : 0.007 0.068 5508 Dihedral : 5.300 29.552 4590 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.95 % Allowed : 8.91 % Favored : 88.13 % 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: 0.00 (0.12), residues: 4365 helix: 0.73 (0.20), residues: 654 sheet: 0.53 (0.13), residues: 1317 loop : -0.46 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG D 905 TYR 0.038 0.004 TYR A1067 PHE 0.051 0.004 PHE K 898 TRP 0.026 0.003 TRP A 886 HIS 0.014 0.004 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01066 / 0.46 (30117) covalent geometry : angle 0.87545 / 0.46 (41376) SS BOND : bond 0.00633 / 0.44 ( 57) SS BOND : angle 1.49714 / 0.99 ( 114) hydrogen bonds : bond 0.07288 / 4.88 ( 1514) hydrogen bonds : angle 6.47745 / 4.55 ( 4191) link_NAG-ASN : bond 0.00819 / 0.53 ( 51) link_NAG-ASN : angle 3.27814 / 2.31 ( 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 312 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 248 time to evaluate : 1.095 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 202 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6997 (mtmt) REVERT: A 318 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7929 (p90) REVERT: A 319 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7152 (ttm170) REVERT: A 790 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8001 (mmtt) REVERT: D 202 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6640 (mtmt) REVERT: D 318 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8227 (p90) REVERT: K 202 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6740 (mtmt) outliers start: 64 outliers final: 38 residues processed: 290 average time/residue: 0.6161 time to fit residues: 212.3040 Evaluate side-chains 280 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 63 THR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 202 LYS 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 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 1004 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 202 LYS Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 616 ASN Chi-restraints excluded: chain K residue 874 THR Chi-restraints excluded: chain K residue 964 LYS Chi-restraints excluded: chain K residue 985 CYS Chi-restraints excluded: chain K residue 1096 VAL Chi-restraints excluded: chain K residue 1111 GLU 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: [233, 199, 38, 48, 167, 121, 317, 359, 293, 120, 266] chunk 233 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 chunk 38 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 317 optimal weight: 0.8980 chunk 359 optimal weight: 0.6980 chunk 293 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 266 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 607 GLN A 751 ASN A1002 GLN A1113 GLN D 239 GLN D 314 GLN D 954 GLN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 ASN K 239 GLN K 607 GLN K 751 ASN K1005 GLN K1010 GLN M 30 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.247962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.205772 restraints weight = 27144.828| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 4.20 r_work: 0.3713 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30225 Z= 0.127 Angle : 0.582 11.270 41643 Z= 0.297 Chirality : 0.046 0.322 5103 Planarity : 0.004 0.064 5508 Dihedral : 4.368 25.981 4590 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.66 % Allowed : 10.71 % Favored : 87.63 % 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: 0.40 (0.12), residues: 4365 helix: 1.61 (0.20), residues: 672 sheet: 0.62 (0.14), residues: 1344 loop : -0.29 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 995 TYR 0.022 0.001 TYR A1067 PHE 0.019 0.002 PHE A 898 TRP 0.009 0.001 TRP F 47 HIS 0.004 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (30117) covalent geometry : angle 0.55257 / 0.29 (41376) SS BOND : bond 0.00186 / 0.12 ( 57) SS BOND : angle 1.03323 / 0.57 ( 114) hydrogen bonds : bond 0.04605 / 3.08 ( 1514) hydrogen bonds : angle 5.82395 / 4.10 ( 4191) link_NAG-ASN : bond 0.00525 / 0.38 ( 51) link_NAG-ASN : angle 2.99377 / 2.09 ( 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 293 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 257 time to evaluate : 0.918 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: 0.8351 (OUTLIER) cc_final: 0.7796 (p90) REVERT: A 814 LYS cc_start: 0.6845 (tmtp) cc_final: 0.6439 (tmtm) REVERT: D 318 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8209 (p90) REVERT: D 814 LYS cc_start: 0.6805 (tmtp) cc_final: 0.6236 (tmtm) REVERT: K 202 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7123 (mtmt) outliers start: 36 outliers final: 24 residues processed: 283 average time/residue: 0.6183 time to fit residues: 208.8022 Evaluate side-chains 269 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 858 LEU Chi-restraints excluded: chain A residue 874 THR 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 29 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 874 THR Chi-restraints excluded: chain D residue 985 CYS Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1004 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 63 THR Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain K residue 616 ASN Chi-restraints excluded: chain K residue 874 THR Chi-restraints excluded: chain K residue 964 LYS Chi-restraints excluded: chain K residue 985 CYS 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: [337, 117, 112, 197, 187, 83, 69, 429, 412, 297, 38] chunk 337 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 187 optimal weight: 30.0000 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 429 optimal weight: 50.0000 chunk 412 optimal weight: 9.9990 chunk 297 optimal weight: 5.9990 chunk 38 optimal weight: 40.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1113 GLN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 GLN K 532 ASN K 607 GLN K 969 ASN K1005 GLN ** K1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.243938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.203755 restraints weight = 26725.786| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 3.67 r_work: 0.3726 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.151 30225 Z= 0.496 Angle : 0.937 12.533 41643 Z= 0.487 Chirality : 0.066 0.464 5103 Planarity : 0.007 0.084 5508 Dihedral : 5.361 31.371 4590 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.22 % Allowed : 10.34 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: -0.15 (0.12), residues: 4365 helix: 0.60 (0.20), residues: 663 sheet: 0.42 (0.14), residues: 1317 loop : -0.56 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG D 905 TYR 0.038 0.005 TYR A1067 PHE 0.052 0.005 PHE K 898 TRP 0.027 0.004 TRP A 886 HIS 0.015 0.004 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01152 / 0.50 (30117) covalent geometry : angle 0.91406 / 0.48 (41376) SS BOND : bond 0.00711 / 0.50 ( 57) SS BOND : angle 1.50468 / 0.98 ( 114) hydrogen bonds : bond 0.07469 / 5.00 ( 1514) hydrogen bonds : angle 6.51875 / 4.58 ( 4191) link_NAG-ASN : bond 0.00853 / 0.56 ( 51) link_NAG-ASN : angle 3.36818 / 2.36 ( 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 299 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 251 time to evaluate : 1.047 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: 0.8504 (OUTLIER) cc_final: 0.7932 (p90) REVERT: A 814 LYS cc_start: 0.6982 (tmtp) cc_final: 0.6771 (tmtp) REVERT: D 237 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7354 (mtt90) REVERT: D 318 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8299 (p90) REVERT: D 787 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8195 (mm-40) REVERT: F 34 MET cc_start: 0.4363 (mmm) cc_final: 0.4128 (mmp) REVERT: K 202 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.6996 (mtmt) REVERT: K 691 SER cc_start: 0.8082 (p) cc_final: 0.7781 (t) outliers start: 48 outliers final: 35 residues processed: 282 average time/residue: 0.6026 time to fit residues: 202.5467 Evaluate side-chains 281 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 63 THR 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 724 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 874 THR 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 29 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1004 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 202 LYS Chi-restraints excluded: chain K residue 302 THR Chi-restraints excluded: chain K residue 604 THR Chi-restraints excluded: chain K residue 616 ASN Chi-restraints excluded: chain K residue 874 THR Chi-restraints excluded: chain K residue 964 LYS Chi-restraints excluded: chain K residue 985 CYS Chi-restraints excluded: chain K residue 1096 VAL Chi-restraints excluded: chain K residue 1111 GLU 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: [214, 406, 57, 76, 217, 344, 69, 151, 349, 350, 18] chunk 214 optimal weight: 0.5980 chunk 406 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 217 optimal weight: 0.5980 chunk 344 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 349 optimal weight: 0.9990 chunk 350 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 239 GLN A 607 GLN A 751 ASN A1002 GLN A1005 GLN A1010 GLN A1113 GLN D 532 ASN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN K 196 ASN K 239 GLN K 607 GLN K 751 ASN K1005 GLN K1010 GLN M 30 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.247971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.208035 restraints weight = 27074.641| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 3.90 r_work: 0.3756 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30225 Z= 0.121 Angle : 0.587 13.071 41643 Z= 0.297 Chirality : 0.047 0.333 5103 Planarity : 0.004 0.046 5508 Dihedral : 4.358 27.590 4590 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.71 % Allowed : 11.31 % Favored : 86.98 % 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: 0.36 (0.12), residues: 4365 helix: 1.78 (0.20), residues: 654 sheet: 0.59 (0.14), residues: 1344 loop : -0.38 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 995 TYR 0.020 0.001 TYR D1067 PHE 0.022 0.002 PHE D 643 TRP 0.010 0.001 TRP F 47 HIS 0.005 0.001 HIS K1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (30117) covalent geometry : angle 0.55853 / 0.29 (41376) SS BOND : bond 0.00261 / 0.16 ( 57) SS BOND : angle 0.89310 / 0.51 ( 114) hydrogen bonds : bond 0.04508 / 3.02 ( 1514) hydrogen bonds : angle 5.82339 / 4.10 ( 4191) link_NAG-ASN : bond 0.00499 / 0.38 ( 51) link_NAG-ASN : angle 2.96020 / 2.08 ( 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 285 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 248 time to evaluate : 0.686 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: 0.8391 (OUTLIER) cc_final: 0.7823 (p90) REVERT: A 814 LYS cc_start: 0.6844 (tmtp) cc_final: 0.6429 (tmtm) REVERT: D 318 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8196 (p90) REVERT: D 787 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7958 (mm-40) REVERT: D 814 LYS cc_start: 0.6775 (tmtp) cc_final: 0.6210 (tmtm) REVERT: F 34 MET cc_start: 0.4352 (mmm) cc_final: 0.4103 (mmp) REVERT: K 34 ARG cc_start: 0.8051 (mmm160) cc_final: 0.7535 (mmm160) REVERT: M 34 MET cc_start: 0.4378 (mmm) cc_final: 0.4146 (mmp) outliers start: 37 outliers final: 25 residues processed: 271 average time/residue: 0.5997 time to fit residues: 194.0967 Evaluate side-chains 269 residues out of total 3831 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 241 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 63 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 858 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 787 GLN Chi-restraints excluded: chain D residue 874 THR Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1004 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 63 THR Chi-restraints excluded: chain K residue 616 ASN Chi-restraints excluded: chain K residue 964 LYS 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: [229, 89, 143, 352, 176, 286, 303, 300, 184, 72, 261] chunk 229 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 143 optimal weight: 50.0000 chunk 352 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 286 optimal weight: 50.0000 chunk 303 optimal weight: 0.6980 chunk 300 optimal weight: 10.0000 chunk 184 optimal weight: 40.0000 chunk 72 optimal weight: 0.4980 chunk 261 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN A 239 GLN A 607 GLN A1002 GLN A1005 GLN A1010 GLN A1113 GLN D 532 ASN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN K 607 GLN ** K 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1005 GLN K1010 GLN M 30 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.247759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.213757 restraints weight = 27208.863| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 3.07 r_work: 0.3885 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 30225 Z= 0.157 Angle : 0.693 59.200 41643 Z= 0.378 Chirality : 0.050 1.107 5103 Planarity : 0.004 0.074 5508 Dihedral : 4.356 27.461 4590 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.52 % Allowed : 11.59 % Favored : 86.89 % Cbeta Deviations : 0.02 % 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: 0.38 (0.12), residues: 4365 helix: 1.81 (0.20), residues: 654 sheet: 0.60 (0.14), residues: 1344 loop : -0.36 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 995 TYR 0.021 0.002 TYR D1067 PHE 0.023 0.002 PHE D 643 TRP 0.010 0.001 TRP F 47 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (30117) covalent geometry : angle 0.67049 / 0.37 (41376) SS BOND : bond 0.00262 / 0.17 ( 57) SS BOND : angle 0.85679 / 0.50 ( 114) hydrogen bonds : bond 0.04631 / 3.10 ( 1514) hydrogen bonds : angle 5.83092 / 4.11 ( 4191) link_NAG-ASN : bond 0.00492 / 0.38 ( 51) link_NAG-ASN : angle 2.93931 / 2.07 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12187.68 seconds wall clock time: 207 minutes 1.30 seconds (12421.30 seconds total)