Starting phenix.real_space_refine on Fri Mar 6 14:12:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rw2_24708/03_2026/7rw2_24708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rw2_24708/03_2026/7rw2_24708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rw2_24708/03_2026/7rw2_24708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rw2_24708/03_2026/7rw2_24708.map" model { file = "/net/cci-nas-00/data/ceres_data/7rw2_24708/03_2026/7rw2_24708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rw2_24708/03_2026/7rw2_24708.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.058 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 138 5.16 5 C 20088 2.51 5 N 5184 2.21 5 O 6204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31614 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8406 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 54, 'TRANS': 1022} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 8406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8406 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 54, 'TRANS': 1022} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 8406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8406 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 54, 'TRANS': 1022} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1054 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "G" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1054 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "J" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1054 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 7.43, per 1000 atoms: 0.24 Number of scatterers: 31614 At special positions: 0 Unit cell: (169.06, 172.27, 171.2, 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 138 16.00 O 6204 8.00 N 5184 7.00 C 20088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.05 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 17 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 149 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A1098 " " NAG A1312 " - " ASN A 709 " " NAG A1313 " - " ASN A 717 " " NAG A1314 " - " ASN A1134 " " NAG A1315 " - " ASN A 603 " " NAG A1316 " - " ASN A 331 " " NAG B1301 " - " ASN B 343 " " NAG B1302 " - " ASN B 17 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B1098 " " NAG B1312 " - " ASN B 709 " " NAG B1313 " - " ASN B 717 " " NAG B1314 " - " ASN B1134 " " NAG B1315 " - " ASN B 603 " " NAG B1316 " - " ASN B 331 " " NAG C1301 " - " ASN C 343 " " NAG C1302 " - " ASN C 17 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 149 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C 603 " " NAG C1313 " - " ASN C 717 " " NAG C1314 " - " ASN C1134 " " NAG C1315 " - " ASN C 331 " " NAG C1316 " - " ASN C 709 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 122 " " NAG F 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 122 " Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7368 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 69 sheets defined 21.0% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.521A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.233A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.199A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.421A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.608A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 630 through 638 removed outlier: 4.289A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 748 through 783 removed outlier: 4.521A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.574A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 938 Processing helix chain 'A' and resid 945 through 967 removed outlier: 4.058A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.941A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.246A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A1031 " --> pdb=" O THR A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.910A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.362A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.539A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.678A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.594A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 626 through 629 Processing helix chain 'B' and resid 630 through 638 removed outlier: 3.518A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 748 through 783 removed outlier: 3.610A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N SER B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N PHE B 759 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.546A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 945 through 967 removed outlier: 4.028A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.786A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 5.243A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.326A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.507A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.611A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.608A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.812A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 625 Processing helix chain 'C' and resid 626 through 629 removed outlier: 3.527A pdb=" N LEU C 629 " --> pdb=" O ALA C 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 626 through 629' Processing helix chain 'C' and resid 630 through 638 removed outlier: 3.698A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 748 through 783 removed outlier: 4.052A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE C 759 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.607A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.654A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 967 removed outlier: 4.163A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.894A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1029 removed outlier: 5.197A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.854A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.510A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 100C through 100J removed outlier: 3.620A pdb=" N TRP H 100F" --> pdb=" O SER H 100C" (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU H 100I" --> pdb=" O TRP H 100F" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.037A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.510A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 100C through 100J removed outlier: 3.619A pdb=" N TRP G 100F" --> pdb=" O SER G 100C" (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU G 100I" --> pdb=" O TRP G 100F" (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.036A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.509A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 100C through 100J removed outlier: 3.620A pdb=" N TRP I 100F" --> pdb=" O SER I 100C" (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU I 100I" --> pdb=" O TRP I 100F" (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.036A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.849A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.821A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 160 removed outlier: 5.506A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.558A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.691A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.518A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.518A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.076A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.728A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 552 through 554 removed outlier: 3.503A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 565 through 566 removed outlier: 3.543A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 659 removed outlier: 5.805A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.448A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.448A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A1101 " --> pdb=" O ASN A1098 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.656A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.849A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.834A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 152 through 160 removed outlier: 5.505A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.596A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.573A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 651 " --> pdb=" O VAL B 610 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.552A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.552A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.079A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.773A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 539 through 543 removed outlier: 4.155A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 552 through 554 removed outlier: 4.166A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 659 removed outlier: 5.817A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 693 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 712 through 723 removed outlier: 6.608A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 726 through 727 removed outlier: 3.697A pdb=" N ASN B1098 " --> pdb=" O HIS B1101 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS B1101 " --> pdb=" O ASN B1098 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.235A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.849A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.827A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE4, first strand: chain 'C' and resid 152 through 160 removed outlier: 5.506A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.597A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.514A pdb=" N ALA C 609 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.897A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.532A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.532A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.150A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.653A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 552 through 554 Processing sheet with id=AF4, first strand: chain 'C' and resid 565 through 566 Processing sheet with id=AF5, first strand: chain 'C' and resid 664 through 665 removed outlier: 4.233A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.617A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 712 through 727 removed outlier: 6.617A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN C1098 " --> pdb=" O HIS C1101 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS C1101 " --> pdb=" O ASN C1098 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.153A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.936A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.405A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.598A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.564A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.552A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.936A pdb=" N VAL G 5 " --> pdb=" O LYS G 23 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.405A pdb=" N GLU G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.598A pdb=" N THR J 22 " --> pdb=" O SER J 7 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.564A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.552A pdb=" N TYR J 49 " --> pdb=" O THR J 53 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.935A pdb=" N VAL I 5 " --> pdb=" O LYS I 23 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.404A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.598A pdb=" N THR K 22 " --> pdb=" O SER K 7 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.563A pdb=" N ASP K 105 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.552A pdb=" N TYR K 49 " --> pdb=" O THR K 53 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) 1104 hydrogen bonds defined for protein. 2961 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: 9.28 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5082 1.29 - 1.43: 8750 1.43 - 1.56: 18325 1.56 - 1.69: 9 1.69 - 1.82: 180 Bond restraints: 32346 Sorted by residual: bond pdb=" C PRO C1079 " pdb=" O PRO C1079 " ideal model delta sigma weight residual 1.238 1.164 0.074 1.24e-02 6.50e+03 3.54e+01 bond pdb=" C ASP B 290 " pdb=" N CYS B 291 " ideal model delta sigma weight residual 1.332 1.399 -0.066 1.29e-02 6.01e+03 2.66e+01 bond pdb=" CA ALA C1080 " pdb=" CB ALA C1080 " ideal model delta sigma weight residual 1.537 1.480 0.057 1.45e-02 4.76e+03 1.52e+01 bond pdb=" CA SER B 711 " pdb=" CB SER B 711 " ideal model delta sigma weight residual 1.533 1.467 0.067 1.72e-02 3.38e+03 1.51e+01 bond pdb=" CA ALA C 892 " pdb=" CB ALA C 892 " ideal model delta sigma weight residual 1.536 1.484 0.053 1.46e-02 4.69e+03 1.30e+01 ... (remaining 32341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 42808 2.68 - 5.37: 1056 5.37 - 8.05: 138 8.05 - 10.74: 29 10.74 - 13.42: 6 Bond angle restraints: 44037 Sorted by residual: angle pdb=" N GLY G 100D" pdb=" CA GLY G 100D" pdb=" C GLY G 100D" ideal model delta sigma weight residual 115.34 101.92 13.42 1.67e+00 3.59e-01 6.46e+01 angle pdb=" N GLY H 100D" pdb=" CA GLY H 100D" pdb=" C GLY H 100D" ideal model delta sigma weight residual 115.34 101.94 13.40 1.67e+00 3.59e-01 6.44e+01 angle pdb=" N GLY I 100D" pdb=" CA GLY I 100D" pdb=" C GLY I 100D" ideal model delta sigma weight residual 115.34 102.00 13.34 1.67e+00 3.59e-01 6.38e+01 angle pdb=" N TYR B 707 " pdb=" CA TYR B 707 " pdb=" C TYR B 707 " ideal model delta sigma weight residual 111.28 103.77 7.51 1.09e+00 8.42e-01 4.75e+01 angle pdb=" N GLY H 55 " pdb=" CA GLY H 55 " pdb=" C GLY H 55 " ideal model delta sigma weight residual 115.21 106.31 8.90 1.30e+00 5.92e-01 4.68e+01 ... (remaining 44032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18041 17.98 - 35.95: 1577 35.95 - 53.93: 292 53.93 - 71.90: 59 71.90 - 89.88: 20 Dihedral angle restraints: 19989 sinusoidal: 8493 harmonic: 11496 Sorted by residual: dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual 93.00 172.72 -79.72 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 167.05 -74.05 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -154.55 68.55 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 19986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.292: 5112 0.292 - 0.583: 23 0.583 - 0.874: 0 0.874 - 1.166: 0 1.166 - 1.457: 1 Chirality restraints: 5136 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.11e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.81e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.20e+01 ... (remaining 5133 not shown) Planarity restraints: 5655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.319 2.00e-02 2.50e+03 2.79e-01 9.73e+02 pdb=" C7 NAG F 2 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.095 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.499 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.318 2.00e-02 2.50e+03 2.78e-01 9.69e+02 pdb=" C7 NAG D 2 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.094 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.499 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1316 " 0.138 2.00e-02 2.50e+03 1.14e-01 1.62e+02 pdb=" C7 NAG C1316 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG C1316 " 0.102 2.00e-02 2.50e+03 pdb=" N2 NAG C1316 " -0.184 2.00e-02 2.50e+03 pdb=" O7 NAG C1316 " -0.021 2.00e-02 2.50e+03 ... (remaining 5652 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6697 2.78 - 3.31: 27427 3.31 - 3.84: 51228 3.84 - 4.37: 58307 4.37 - 4.90: 102362 Nonbonded interactions: 246021 Sorted by model distance: nonbonded pdb=" OE1 GLN A 965 " pdb=" OG SER C 758 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR B 739 " pdb=" ND2 ASN C 317 " model vdw 2.264 3.120 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 274 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" OG1 THR A 274 " model vdw 2.269 3.040 ... (remaining 246016 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 33.020 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 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 : 0.005 0.087 32454 Z= 0.325 Angle : 1.029 18.508 44313 Z= 0.586 Chirality : 0.067 1.457 5136 Planarity : 0.009 0.279 5601 Dihedral : 13.472 89.877 12477 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.03 % Allowed : 1.20 % Favored : 98.77 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 3.08 % 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: -1.51 (0.12), residues: 3909 helix: -0.89 (0.18), residues: 696 sheet: -0.08 (0.17), residues: 909 loop : -1.45 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1019 TYR 0.030 0.002 TYR C 707 PHE 0.028 0.002 PHE B 275 TRP 0.029 0.002 TRP C 64 HIS 0.011 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00544 (32346) covalent geometry : angle 0.97123 (44037) SS BOND : bond 0.00559 ( 48) SS BOND : angle 1.41891 ( 96) hydrogen bonds : bond 0.18917 ( 1076) hydrogen bonds : angle 8.69538 ( 2961) link_BETA1-4 : bond 0.00351 ( 6) link_BETA1-4 : angle 2.00124 ( 18) link_NAG-ASN : bond 0.01283 ( 54) link_NAG-ASN : angle 5.61060 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 600 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 THR cc_start: 0.8443 (p) cc_final: 0.7953 (m) REVERT: A 906 PHE cc_start: 0.7049 (m-10) cc_final: 0.6819 (m-80) REVERT: B 114 THR cc_start: 0.8352 (p) cc_final: 0.7856 (m) REVERT: B 900 MET cc_start: 0.6837 (mpp) cc_final: 0.6599 (mtm) REVERT: C 114 THR cc_start: 0.8124 (p) cc_final: 0.7688 (m) REVERT: C 269 TYR cc_start: 0.7939 (m-80) cc_final: 0.7667 (m-10) REVERT: C 1096 VAL cc_start: 0.7112 (t) cc_final: 0.6898 (m) outliers start: 1 outliers final: 0 residues processed: 601 average time/residue: 0.1748 time to fit residues: 173.2429 Evaluate side-chains 316 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 0.0060 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS B 196 ASN B 710 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN J 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.175851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.147255 restraints weight = 54498.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.147433 restraints weight = 68855.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.149224 restraints weight = 56940.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.150169 restraints weight = 36013.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.151893 restraints weight = 31362.552| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 32454 Z= 0.129 Angle : 0.644 12.759 44313 Z= 0.318 Chirality : 0.047 0.388 5136 Planarity : 0.005 0.047 5601 Dihedral : 7.029 59.194 5526 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.23 % Allowed : 9.34 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -1.09 (0.13), residues: 3909 helix: -0.13 (0.19), residues: 711 sheet: -0.08 (0.17), residues: 921 loop : -1.21 (0.12), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 646 TYR 0.024 0.001 TYR C1067 PHE 0.026 0.002 PHE C 133 TRP 0.026 0.002 TRP C 64 HIS 0.008 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00293 (32346) covalent geometry : angle 0.60528 (44037) SS BOND : bond 0.00297 ( 48) SS BOND : angle 1.06998 ( 96) hydrogen bonds : bond 0.04221 ( 1076) hydrogen bonds : angle 6.34959 ( 2961) link_BETA1-4 : bond 0.00463 ( 6) link_BETA1-4 : angle 2.91870 ( 18) link_NAG-ASN : bond 0.00703 ( 54) link_NAG-ASN : angle 3.50751 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 379 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 PHE cc_start: 0.7074 (m-10) cc_final: 0.6692 (m-80) REVERT: A 980 ILE cc_start: 0.8706 (pt) cc_final: 0.8427 (pt) REVERT: A 1096 VAL cc_start: 0.7825 (p) cc_final: 0.7504 (t) REVERT: B 306 PHE cc_start: 0.8011 (m-80) cc_final: 0.7717 (m-80) REVERT: C 269 TYR cc_start: 0.8183 (m-80) cc_final: 0.7886 (m-10) REVERT: H 36 TRP cc_start: 0.6380 (t-100) cc_final: 0.5306 (t-100) REVERT: H 80 MET cc_start: 0.3775 (tmm) cc_final: 0.3298 (tmm) outliers start: 42 outliers final: 32 residues processed: 412 average time/residue: 0.1578 time to fit residues: 113.2133 Evaluate side-chains 337 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 305 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 797 PHE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain K residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 202 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 360 optimal weight: 8.9990 chunk 326 optimal weight: 0.0470 chunk 342 optimal weight: 8.9990 chunk 317 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 196 ASN A 762 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 49 HIS B 99 ASN B 762 GLN B 787 GLN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS C 317 ASN C 913 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 52 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN G 52 ASN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 52 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.168737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.139761 restraints weight = 53615.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.141604 restraints weight = 76985.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.142686 restraints weight = 59890.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.144186 restraints weight = 36862.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.144794 restraints weight = 30467.084| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.194 32454 Z= 0.247 Angle : 0.717 11.755 44313 Z= 0.360 Chirality : 0.049 0.356 5136 Planarity : 0.005 0.052 5601 Dihedral : 6.922 58.899 5526 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.10 % Allowed : 12.38 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -1.13 (0.13), residues: 3909 helix: -0.16 (0.19), residues: 729 sheet: -0.13 (0.16), residues: 972 loop : -1.24 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1000 TYR 0.028 0.002 TYR B 369 PHE 0.026 0.003 PHE C 238 TRP 0.028 0.002 TRP C 64 HIS 0.008 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00593 (32346) covalent geometry : angle 0.68300 (44037) SS BOND : bond 0.00724 ( 48) SS BOND : angle 1.37843 ( 96) hydrogen bonds : bond 0.04466 ( 1076) hydrogen bonds : angle 6.17299 ( 2961) link_BETA1-4 : bond 0.00437 ( 6) link_BETA1-4 : angle 1.93239 ( 18) link_NAG-ASN : bond 0.00641 ( 54) link_NAG-ASN : angle 3.51127 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 338 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7771 (t80) REVERT: A 980 ILE cc_start: 0.8971 (pt) cc_final: 0.8561 (pt) REVERT: B 306 PHE cc_start: 0.8093 (m-80) cc_final: 0.7814 (m-80) REVERT: B 866 THR cc_start: 0.8060 (p) cc_final: 0.7841 (p) REVERT: B 1029 MET cc_start: 0.7955 (tpp) cc_final: 0.7735 (tpp) REVERT: H 80 MET cc_start: 0.4462 (tmm) cc_final: 0.3759 (tmm) REVERT: I 36 TRP cc_start: 0.6248 (t-100) cc_final: 0.5595 (t-100) REVERT: I 80 MET cc_start: 0.4723 (tmm) cc_final: 0.4319 (tmm) outliers start: 106 outliers final: 76 residues processed: 410 average time/residue: 0.1545 time to fit residues: 109.5051 Evaluate side-chains 361 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 284 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 349 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 305 optimal weight: 0.5980 chunk 365 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 142 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 364 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.170905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.142895 restraints weight = 53306.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.144009 restraints weight = 79903.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.145373 restraints weight = 64827.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.146724 restraints weight = 38975.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.147353 restraints weight = 33073.186| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 32454 Z= 0.137 Angle : 0.623 11.962 44313 Z= 0.310 Chirality : 0.046 0.350 5136 Planarity : 0.004 0.049 5601 Dihedral : 6.552 59.862 5526 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.72 % Allowed : 14.81 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.93 (0.13), residues: 3909 helix: 0.17 (0.19), residues: 729 sheet: -0.08 (0.16), residues: 957 loop : -1.13 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.016 0.001 TYR C1067 PHE 0.020 0.001 PHE B 318 TRP 0.021 0.001 TRP C 64 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00327 (32346) covalent geometry : angle 0.58779 (44037) SS BOND : bond 0.00356 ( 48) SS BOND : angle 1.54918 ( 96) hydrogen bonds : bond 0.03797 ( 1076) hydrogen bonds : angle 5.77897 ( 2961) link_BETA1-4 : bond 0.00269 ( 6) link_BETA1-4 : angle 1.92151 ( 18) link_NAG-ASN : bond 0.00633 ( 54) link_NAG-ASN : angle 3.25000 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 326 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8846 (tt) REVERT: A 980 ILE cc_start: 0.8879 (pt) cc_final: 0.8409 (pt) REVERT: B 306 PHE cc_start: 0.7990 (m-80) cc_final: 0.7766 (m-80) REVERT: B 387 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8711 (tt) REVERT: B 1005 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7679 (tm-30) REVERT: B 1029 MET cc_start: 0.7735 (tpp) cc_final: 0.7523 (tpp) REVERT: C 508 TYR cc_start: 0.8070 (m-80) cc_final: 0.7803 (m-80) REVERT: H 80 MET cc_start: 0.4714 (tmm) cc_final: 0.3735 (tmm) REVERT: G 51 ILE cc_start: 0.6568 (OUTLIER) cc_final: 0.6339 (tp) REVERT: I 80 MET cc_start: 0.4324 (tmm) cc_final: 0.2646 (tmm) outliers start: 93 outliers final: 65 residues processed: 399 average time/residue: 0.1627 time to fit residues: 111.2619 Evaluate side-chains 354 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 286 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 14 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 233 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 762 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 955 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.169194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.140880 restraints weight = 53607.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.143986 restraints weight = 76061.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.144551 restraints weight = 50330.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.145520 restraints weight = 33827.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.147391 restraints weight = 28678.990| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 32454 Z= 0.133 Angle : 0.610 11.810 44313 Z= 0.303 Chirality : 0.046 0.345 5136 Planarity : 0.004 0.048 5601 Dihedral : 6.311 58.614 5526 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.99 % Allowed : 15.54 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.80 (0.13), residues: 3909 helix: 0.28 (0.19), residues: 729 sheet: 0.03 (0.17), residues: 960 loop : -1.06 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 94 TYR 0.015 0.001 TYR B1067 PHE 0.019 0.001 PHE B 133 TRP 0.019 0.001 TRP B 64 HIS 0.005 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00319 (32346) covalent geometry : angle 0.57747 (44037) SS BOND : bond 0.00370 ( 48) SS BOND : angle 1.17157 ( 96) hydrogen bonds : bond 0.03668 ( 1076) hydrogen bonds : angle 5.65261 ( 2961) link_BETA1-4 : bond 0.00376 ( 6) link_BETA1-4 : angle 1.85729 ( 18) link_NAG-ASN : bond 0.00630 ( 54) link_NAG-ASN : angle 3.14146 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 311 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7462 (t80) REVERT: A 387 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8896 (tt) REVERT: A 980 ILE cc_start: 0.9028 (pt) cc_final: 0.8568 (pt) REVERT: B 387 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8806 (tt) REVERT: B 1029 MET cc_start: 0.7940 (tpp) cc_final: 0.7542 (tpp) REVERT: C 235 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6891 (tt) REVERT: C 508 TYR cc_start: 0.8265 (m-80) cc_final: 0.7885 (m-80) REVERT: C 1049 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7066 (mt) REVERT: H 80 MET cc_start: 0.4665 (tmm) cc_final: 0.4171 (tmm) REVERT: H 81 GLU cc_start: 0.5454 (mp0) cc_final: 0.5222 (mm-30) REVERT: G 36 TRP cc_start: 0.6229 (t-100) cc_final: 0.5622 (m-90) REVERT: I 80 MET cc_start: 0.4486 (tmm) cc_final: 0.2927 (tmm) outliers start: 102 outliers final: 74 residues processed: 390 average time/residue: 0.1644 time to fit residues: 108.8624 Evaluate side-chains 364 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 285 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 93 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 278 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 274 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.165968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.137090 restraints weight = 53469.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.137640 restraints weight = 74623.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.139406 restraints weight = 56847.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.140303 restraints weight = 35415.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.143335 restraints weight = 30252.940| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.185 32454 Z= 0.244 Angle : 0.707 11.387 44313 Z= 0.355 Chirality : 0.048 0.339 5136 Planarity : 0.005 0.049 5601 Dihedral : 6.749 59.735 5526 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.78 % Allowed : 16.18 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.97 (0.13), residues: 3909 helix: 0.03 (0.19), residues: 714 sheet: -0.06 (0.17), residues: 975 loop : -1.14 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 94 TYR 0.021 0.002 TYR B 369 PHE 0.025 0.002 PHE B 238 TRP 0.022 0.002 TRP C 64 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00594 (32346) covalent geometry : angle 0.67815 (44037) SS BOND : bond 0.00449 ( 48) SS BOND : angle 1.24924 ( 96) hydrogen bonds : bond 0.04225 ( 1076) hydrogen bonds : angle 5.84940 ( 2961) link_BETA1-4 : bond 0.00302 ( 6) link_BETA1-4 : angle 1.86249 ( 18) link_NAG-ASN : bond 0.00636 ( 54) link_NAG-ASN : angle 3.24768 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 318 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7720 (tp) REVERT: A 238 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7927 (t80) REVERT: A 387 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8941 (tt) REVERT: B 200 TYR cc_start: 0.7788 (m-80) cc_final: 0.7548 (m-10) REVERT: B 387 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8857 (tt) REVERT: B 866 THR cc_start: 0.8101 (p) cc_final: 0.7881 (p) REVERT: B 1029 MET cc_start: 0.8043 (tpp) cc_final: 0.7553 (tpp) REVERT: C 417 LYS cc_start: 0.8398 (pttt) cc_final: 0.8140 (pttm) REVERT: C 1049 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7487 (mp) REVERT: H 80 MET cc_start: 0.4726 (tmm) cc_final: 0.3718 (tmm) REVERT: G 34 MET cc_start: 0.7695 (tmm) cc_final: 0.7244 (tmm) REVERT: G 36 TRP cc_start: 0.6393 (t-100) cc_final: 0.5932 (m-90) REVERT: G 52 ASN cc_start: 0.7651 (p0) cc_final: 0.7018 (t0) REVERT: G 100 ASP cc_start: 0.8284 (m-30) cc_final: 0.7984 (m-30) REVERT: I 36 TRP cc_start: 0.6380 (t-100) cc_final: 0.6096 (t-100) REVERT: K 22 THR cc_start: 0.6226 (t) cc_final: 0.5984 (t) outliers start: 129 outliers final: 94 residues processed: 423 average time/residue: 0.1581 time to fit residues: 115.6138 Evaluate side-chains 387 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 288 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 93 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 141 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 269 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 501 ASN B 762 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.167276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.138856 restraints weight = 54194.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.139287 restraints weight = 77515.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.141202 restraints weight = 57673.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.142400 restraints weight = 35823.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.143072 restraints weight = 30930.588| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 32454 Z= 0.179 Angle : 0.654 11.426 44313 Z= 0.327 Chirality : 0.047 0.338 5136 Planarity : 0.004 0.047 5601 Dihedral : 6.537 59.605 5526 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.45 % Allowed : 16.97 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.91 (0.13), residues: 3909 helix: 0.14 (0.19), residues: 714 sheet: -0.02 (0.17), residues: 915 loop : -1.10 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 96 TYR 0.025 0.001 TYR B 707 PHE 0.020 0.002 PHE B 347 TRP 0.020 0.002 TRP C 64 HIS 0.004 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00432 (32346) covalent geometry : angle 0.62306 (44037) SS BOND : bond 0.00489 ( 48) SS BOND : angle 1.51620 ( 96) hydrogen bonds : bond 0.03840 ( 1076) hydrogen bonds : angle 5.70358 ( 2961) link_BETA1-4 : bond 0.00353 ( 6) link_BETA1-4 : angle 1.84273 ( 18) link_NAG-ASN : bond 0.00619 ( 54) link_NAG-ASN : angle 3.12162 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 320 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7210 (t80) REVERT: A 387 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8938 (tt) REVERT: A 1029 MET cc_start: 0.8049 (tpp) cc_final: 0.7775 (mmm) REVERT: A 1077 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7838 (m) REVERT: B 200 TYR cc_start: 0.7764 (m-80) cc_final: 0.7526 (m-10) REVERT: B 306 PHE cc_start: 0.8112 (m-80) cc_final: 0.7852 (m-80) REVERT: B 387 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8834 (tt) REVERT: B 866 THR cc_start: 0.8048 (p) cc_final: 0.7842 (p) REVERT: B 878 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7376 (mt) REVERT: B 900 MET cc_start: 0.7541 (mpp) cc_final: 0.6980 (mtm) REVERT: C 164 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7263 (m-40) REVERT: C 417 LYS cc_start: 0.8393 (pttt) cc_final: 0.8116 (pttm) REVERT: C 1135 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7678 (p0) REVERT: H 29 PHE cc_start: 0.7006 (t80) cc_final: 0.6783 (t80) REVERT: H 80 MET cc_start: 0.4999 (tmm) cc_final: 0.4052 (tmm) REVERT: L 71 PHE cc_start: 0.6176 (m-10) cc_final: 0.5883 (m-10) REVERT: G 29 PHE cc_start: 0.6859 (t80) cc_final: 0.6608 (t80) REVERT: G 34 MET cc_start: 0.7840 (tmm) cc_final: 0.7532 (tmm) REVERT: G 100 ASP cc_start: 0.8299 (m-30) cc_final: 0.7993 (m-30) outliers start: 118 outliers final: 92 residues processed: 416 average time/residue: 0.1587 time to fit residues: 114.3844 Evaluate side-chains 383 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 284 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 93 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 303 optimal weight: 0.0270 chunk 310 optimal weight: 0.5980 chunk 201 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 317 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 197 optimal weight: 0.0980 chunk 329 optimal weight: 2.9990 chunk 289 optimal weight: 0.9990 chunk 333 optimal weight: 20.0000 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.169815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.142634 restraints weight = 53908.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.144860 restraints weight = 81406.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.145686 restraints weight = 57280.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.146566 restraints weight = 38012.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.147702 restraints weight = 32326.226| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 32454 Z= 0.118 Angle : 0.618 11.694 44313 Z= 0.308 Chirality : 0.046 0.337 5136 Planarity : 0.004 0.046 5601 Dihedral : 6.187 57.387 5526 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.58 % Allowed : 18.53 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.78 (0.13), residues: 3909 helix: 0.35 (0.20), residues: 729 sheet: 0.06 (0.17), residues: 936 loop : -1.07 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 96 TYR 0.027 0.001 TYR B 707 PHE 0.024 0.001 PHE J 71 TRP 0.021 0.002 TRP G 36 HIS 0.004 0.001 HIS G 99 Details of bonding type rmsd covalent geometry : bond 0.00274 (32346) covalent geometry : angle 0.58956 (44037) SS BOND : bond 0.00370 ( 48) SS BOND : angle 1.22940 ( 96) hydrogen bonds : bond 0.03583 ( 1076) hydrogen bonds : angle 5.55463 ( 2961) link_BETA1-4 : bond 0.00422 ( 6) link_BETA1-4 : angle 1.79951 ( 18) link_NAG-ASN : bond 0.00636 ( 54) link_NAG-ASN : angle 2.95239 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 314 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7153 (t80) REVERT: A 387 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8855 (tt) REVERT: A 508 TYR cc_start: 0.7751 (m-80) cc_final: 0.7481 (m-80) REVERT: B 200 TYR cc_start: 0.7592 (m-80) cc_final: 0.7334 (m-10) REVERT: B 306 PHE cc_start: 0.7980 (m-80) cc_final: 0.7701 (m-80) REVERT: B 387 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8695 (tt) REVERT: B 417 LYS cc_start: 0.8488 (pttt) cc_final: 0.8246 (ttpt) REVERT: B 900 MET cc_start: 0.7239 (mpp) cc_final: 0.6732 (mtm) REVERT: H 29 PHE cc_start: 0.6965 (t80) cc_final: 0.6741 (t80) REVERT: H 69 MET cc_start: 0.8385 (mmm) cc_final: 0.7931 (mmt) REVERT: H 80 MET cc_start: 0.4861 (tmm) cc_final: 0.3979 (tmm) REVERT: G 29 PHE cc_start: 0.6767 (t80) cc_final: 0.6514 (t80) REVERT: G 34 MET cc_start: 0.7578 (tmm) cc_final: 0.7013 (tmm) REVERT: G 36 TRP cc_start: 0.5478 (OUTLIER) cc_final: 0.5034 (m-90) REVERT: G 100 ASP cc_start: 0.8029 (m-30) cc_final: 0.7752 (m-30) outliers start: 88 outliers final: 76 residues processed: 386 average time/residue: 0.1593 time to fit residues: 105.5860 Evaluate side-chains 373 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 293 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain K residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 123 optimal weight: 0.0980 chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 374 optimal weight: 4.9990 chunk 362 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 368 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.163211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.133340 restraints weight = 54086.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.135008 restraints weight = 73554.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.136210 restraints weight = 56313.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.137356 restraints weight = 34273.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.138648 restraints weight = 29167.997| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.179 32454 Z= 0.258 Angle : 0.723 11.448 44313 Z= 0.364 Chirality : 0.049 0.334 5136 Planarity : 0.005 0.079 5601 Dihedral : 6.769 59.796 5526 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.22 % Allowed : 18.47 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 3909 helix: 0.05 (0.19), residues: 711 sheet: -0.22 (0.16), residues: 966 loop : -1.13 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 96 TYR 0.046 0.002 TYR C 508 PHE 0.029 0.002 PHE L 71 TRP 0.029 0.002 TRP C 886 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00631 (32346) covalent geometry : angle 0.69634 (44037) SS BOND : bond 0.00473 ( 48) SS BOND : angle 1.41878 ( 96) hydrogen bonds : bond 0.04200 ( 1076) hydrogen bonds : angle 5.83372 ( 2961) link_BETA1-4 : bond 0.00372 ( 6) link_BETA1-4 : angle 1.75650 ( 18) link_NAG-ASN : bond 0.00630 ( 54) link_NAG-ASN : angle 3.12253 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 295 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7692 (t80) REVERT: A 387 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8948 (tt) REVERT: A 1031 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7501 (pm20) REVERT: B 387 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8888 (tt) REVERT: B 489 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.7575 (m-80) REVERT: B 866 THR cc_start: 0.8073 (p) cc_final: 0.7854 (p) REVERT: B 900 MET cc_start: 0.7602 (mpp) cc_final: 0.7051 (mtm) REVERT: C 731 MET cc_start: 0.7854 (ttt) cc_final: 0.7595 (ttt) REVERT: H 29 PHE cc_start: 0.7072 (t80) cc_final: 0.6857 (t80) REVERT: G 29 PHE cc_start: 0.6954 (t80) cc_final: 0.6602 (t80) REVERT: G 34 MET cc_start: 0.7581 (tmm) cc_final: 0.6998 (tmm) REVERT: G 36 TRP cc_start: 0.5792 (OUTLIER) cc_final: 0.4753 (m-90) REVERT: G 100 ASP cc_start: 0.8252 (m-30) cc_final: 0.8002 (m-30) REVERT: I 69 MET cc_start: 0.8442 (mmm) cc_final: 0.8119 (mmt) outliers start: 110 outliers final: 88 residues processed: 384 average time/residue: 0.1529 time to fit residues: 102.7459 Evaluate side-chains 374 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 280 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain K residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 143 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 341 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 368 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.166431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.139690 restraints weight = 53937.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.139858 restraints weight = 84766.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.141578 restraints weight = 65287.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.142255 restraints weight = 40386.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.145645 restraints weight = 34373.440| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 32454 Z= 0.141 Angle : 0.646 13.491 44313 Z= 0.323 Chirality : 0.047 0.333 5136 Planarity : 0.004 0.046 5601 Dihedral : 6.368 57.966 5526 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.60 % Allowed : 19.26 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.91 (0.13), residues: 3909 helix: 0.23 (0.19), residues: 729 sheet: -0.20 (0.16), residues: 978 loop : -1.08 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 61 TYR 0.032 0.001 TYR B 707 PHE 0.032 0.001 PHE J 71 TRP 0.021 0.002 TRP C 886 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00335 (32346) covalent geometry : angle 0.61777 (44037) SS BOND : bond 0.00474 ( 48) SS BOND : angle 1.42059 ( 96) hydrogen bonds : bond 0.03708 ( 1076) hydrogen bonds : angle 5.63376 ( 2961) link_BETA1-4 : bond 0.00435 ( 6) link_BETA1-4 : angle 1.75490 ( 18) link_NAG-ASN : bond 0.00634 ( 54) link_NAG-ASN : angle 2.95403 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7818 Ramachandran restraints generated. 3909 Oldfield, 0 Emsley, 3909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 297 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7249 (t80) REVERT: A 387 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8937 (tt) REVERT: A 508 TYR cc_start: 0.7936 (m-80) cc_final: 0.7634 (m-80) REVERT: A 1031 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: B 387 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8768 (tt) REVERT: B 861 LEU cc_start: 0.8271 (mt) cc_final: 0.7932 (mp) REVERT: B 900 MET cc_start: 0.7366 (mpp) cc_final: 0.6825 (mtm) REVERT: C 508 TYR cc_start: 0.8057 (m-80) cc_final: 0.7697 (m-80) REVERT: C 731 MET cc_start: 0.7946 (ttt) cc_final: 0.7745 (ttt) REVERT: C 866 THR cc_start: 0.7391 (p) cc_final: 0.7107 (p) REVERT: H 46 GLU cc_start: 0.7254 (tm-30) cc_final: 0.7008 (tm-30) REVERT: H 69 MET cc_start: 0.8468 (mmm) cc_final: 0.8138 (mmt) REVERT: G 29 PHE cc_start: 0.6781 (t80) cc_final: 0.6568 (t80) REVERT: G 34 MET cc_start: 0.7539 (tmm) cc_final: 0.7066 (tmm) REVERT: G 36 TRP cc_start: 0.5538 (OUTLIER) cc_final: 0.4921 (m-90) REVERT: G 100 ASP cc_start: 0.8186 (m-30) cc_final: 0.7929 (m-30) REVERT: I 69 MET cc_start: 0.8386 (mmm) cc_final: 0.7916 (mmt) outliers start: 89 outliers final: 79 residues processed: 370 average time/residue: 0.1572 time to fit residues: 100.9128 Evaluate side-chains 371 residues out of total 3429 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 287 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 36 TRP Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain K residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 96 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 330 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 387 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.165176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.135456 restraints weight = 54552.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.137071 restraints weight = 73024.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138207 restraints weight = 57839.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.139535 restraints weight = 35217.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.140582 restraints weight = 29980.644| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.162 32454 Z= 0.229 Angle : 0.707 13.085 44313 Z= 0.353 Chirality : 0.048 0.336 5136 Planarity : 0.005 0.049 5601 Dihedral : 6.707 59.434 5526 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.01 % Allowed : 18.96 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.08 (0.13), residues: 3909 helix: 0.09 (0.19), residues: 711 sheet: -0.30 (0.17), residues: 945 loop : -1.17 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 61 TYR 0.038 0.002 TYR C 508 PHE 0.027 0.002 PHE J 71 TRP 0.034 0.002 TRP C 886 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00560 (32346) covalent geometry : angle 0.67927 (44037) SS BOND : bond 0.00489 ( 48) SS BOND : angle 1.63925 ( 96) hydrogen bonds : bond 0.04053 ( 1076) hydrogen bonds : angle 5.80207 ( 2961) link_BETA1-4 : bond 0.00334 ( 6) link_BETA1-4 : angle 1.74514 ( 18) link_NAG-ASN : bond 0.00624 ( 54) link_NAG-ASN : angle 3.04152 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4380.61 seconds wall clock time: 77 minutes 11.24 seconds (4631.24 seconds total)