Starting phenix.real_space_refine on Sat Mar 7 00:06:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wo5_32639/03_2026/7wo5_32639.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wo5_32639/03_2026/7wo5_32639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wo5_32639/03_2026/7wo5_32639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wo5_32639/03_2026/7wo5_32639.map" model { file = "/net/cci-nas-00/data/ceres_data/7wo5_32639/03_2026/7wo5_32639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wo5_32639/03_2026/7wo5_32639.cif" } resolution = 3.45 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= 0.001 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 150 5.16 5 C 22542 2.51 5 N 5910 2.21 5 O 7002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35604 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "F" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "G" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "H" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "I" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 7.76, per 1000 atoms: 0.22 Number of scatterers: 35604 At special positions: 0 Unit cell: (205.44, 207.58, 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 150 16.00 O 7002 8.00 N 5910 7.00 C 22542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, 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=2.03 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 662 " - pdb=" SG CYS A 671 " 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=2.01 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=2.03 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=2.03 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 D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 140 " - pdb=" SG CYS E 199 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 146 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 801 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A 17 " " NAG A1314 " - " ASN A 122 " " NAG A1315 " - " ASN A 149 " " NAG B1301 " - " ASN B1134 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 282 " " NAG B1310 " - " ASN B 165 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 17 " " NAG B1313 " - " ASN B 149 " " NAG B1314 " - " ASN B 122 " " NAG B1315 " - " ASN B1074 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C 17 " " NAG C1312 " - " ASN C 149 " " NAG C1313 " - " ASN C 61 " " NAG C1314 " - " ASN C 122 " " NAG C1315 " - " ASN C 165 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.4 seconds 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8460 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 82 sheets defined 15.9% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 253 through 257 removed outlier: 4.323A pdb=" N GLY A 257 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.892A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.793A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.544A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.511A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 782 removed outlier: 3.583A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.623A 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 912 through 941 removed outlier: 4.438A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 966 removed outlier: 4.086A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.722A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1034 removed outlier: 3.523A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A1034 " --> pdb=" O SER A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.963A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.711A pdb=" N ASN B 74 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.555A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.808A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.860A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.700A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.725A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.910A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.511A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.725A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.544A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.502A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.123A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 4.054A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 421' Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.684A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.765A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.583A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.617A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.114A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.517A pdb=" N ASP D 90 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 190 through 194 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.553A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 removed outlier: 3.548A pdb=" N ASP G 85 " --> pdb=" O LYS G 82 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 82 through 86' Processing helix chain 'I' and resid 82 through 86 removed outlier: 3.577A pdb=" N GLU I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.833A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.504A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.624A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 145 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.795A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.754A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.802A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.802A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (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 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.247A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.568A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.827A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.827A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.256A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.508A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.752A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.542A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 153 through 157 removed outlier: 6.406A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.581A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.712A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.526A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 394 through 396 removed outlier: 4.098A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.515A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.035A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.734A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.734A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.563A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.751A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.751A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.963A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.746A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.838A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 327 removed outlier: 7.000A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.135A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 394 through 400 removed outlier: 3.608A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.960A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 712 through 713 removed outlier: 4.276A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AF6, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.556A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.313A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.764A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.773A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 71 " --> pdb=" O PHE D 80 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.230A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.948A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP D 33 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR D 108 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 126 through 129 removed outlier: 4.443A pdb=" N ALA D 142 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 126 through 129 removed outlier: 4.443A pdb=" N ALA D 142 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 159 through 160 removed outlier: 4.227A pdb=" N CYS D 202 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS D 215 " --> pdb=" O CYS D 202 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.815A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR E 90 " --> pdb=" O TYR E 37 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER E 93 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL E 102 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.815A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR E 90 " --> pdb=" O TYR E 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 63 through 68 removed outlier: 3.666A pdb=" N SER E 75 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 120 through 121 removed outlier: 5.854A pdb=" N TYR E 178 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER E 181 " --> pdb=" O THR E 168 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.950A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU F 20 " --> pdb=" O LEU F 81 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.511A pdb=" N GLY F 10 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR F 116 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET F 34 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP F 36 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR F 59 " --> pdb=" O ASN F 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.511A pdb=" N GLY F 10 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR F 116 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 97 " --> pdb=" O SER F 35 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.698A pdb=" N SER F 186 " --> pdb=" O CYS F 146 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER F 185 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE F 172 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL F 187 " --> pdb=" O HIS F 170 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 201 through 202 Processing sheet with id=AH6, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AH7, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.094A pdb=" N VAL G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR G 107 " --> pdb=" O TYR G 89 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.094A pdb=" N VAL G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR G 107 " --> pdb=" O TYR G 89 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER G 93 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL G 102 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.717A pdb=" N ILE G 20 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 152 through 155 Processing sheet with id=AI2, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.066A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 46 through 51 removed outlier: 6.687A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA H 97 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AI5, first strand: chain 'H' and resid 148 through 149 Processing sheet with id=AI6, first strand: chain 'H' and resid 159 through 160 removed outlier: 3.728A pdb=" N SER H 159 " --> pdb=" O ASN H 203 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN H 203 " --> pdb=" O SER H 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.183A pdb=" N VAL I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'I' and resid 20 through 23 Processing sheet with id=AI9, first strand: chain 'I' and resid 45 through 50 removed outlier: 7.082A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP I 88 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL I 102 " --> pdb=" O SER I 93 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP I 95 " --> pdb=" O ASN I 100 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN I 100 " --> pdb=" O ASP I 95 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 152 through 155 1013 hydrogen bonds defined for protein. 2700 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: 10.51 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11201 1.34 - 1.46: 6239 1.46 - 1.58: 18809 1.58 - 1.69: 0 1.69 - 1.81: 189 Bond restraints: 36438 Sorted by residual: bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" CA GLN C 613 " pdb=" C GLN C 613 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.35e-02 5.49e+03 4.63e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.68e+00 bond pdb=" CA ASN C 616 " pdb=" C ASN C 616 " ideal model delta sigma weight residual 1.526 1.501 0.025 1.37e-02 5.33e+03 3.43e+00 bond pdb=" C GLN C1142 " pdb=" N PRO C1143 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.30e-02 5.92e+03 3.25e+00 ... (remaining 36433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 48611 1.78 - 3.56: 967 3.56 - 5.34: 70 5.34 - 7.12: 6 7.12 - 8.91: 2 Bond angle restraints: 49656 Sorted by residual: angle pdb=" N GLN C 613 " pdb=" CA GLN C 613 " pdb=" C GLN C 613 " ideal model delta sigma weight residual 109.59 118.50 -8.91 1.47e+00 4.63e-01 3.67e+01 angle pdb=" N VAL A 382 " pdb=" CA VAL A 382 " pdb=" C VAL A 382 " ideal model delta sigma weight residual 113.20 109.66 3.54 9.60e-01 1.09e+00 1.36e+01 angle pdb=" N VAL A 213 " pdb=" CA VAL A 213 " pdb=" C VAL A 213 " ideal model delta sigma weight residual 113.71 110.37 3.34 9.50e-01 1.11e+00 1.24e+01 angle pdb=" C PRO D 153 " pdb=" N GLU D 154 " pdb=" CA GLU D 154 " ideal model delta sigma weight residual 122.28 118.72 3.56 1.02e+00 9.61e-01 1.22e+01 angle pdb=" CA LEU B 141 " pdb=" C LEU B 141 " pdb=" N GLY B 142 " ideal model delta sigma weight residual 116.25 120.62 -4.37 1.30e+00 5.92e-01 1.13e+01 ... (remaining 49651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.09: 21625 23.09 - 46.18: 531 46.18 - 69.27: 64 69.27 - 92.37: 16 92.37 - 115.46: 21 Dihedral angle restraints: 22257 sinusoidal: 9063 harmonic: 13194 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -131.28 45.28 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CA CYS B 617 " pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " ideal model delta sinusoidal sigma weight residual 79.00 7.99 71.01 1 2.00e+01 2.50e-03 1.62e+01 dihedral pdb=" SG CYS B 131 " pdb=" CB CYS B 166 " pdb=" SG CYS B 166 " pdb=" CA CYS B 166 " ideal model delta sinusoidal sigma weight residual -73.00 -3.68 -69.32 1 2.00e+01 2.50e-03 1.55e+01 ... (remaining 22254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 4930 0.059 - 0.118: 787 0.118 - 0.177: 25 0.177 - 0.236: 3 0.236 - 0.295: 3 Chirality restraints: 5748 Sorted by residual: chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA GLN C 613 " pdb=" N GLN C 613 " pdb=" C GLN C 613 " pdb=" CB GLN C 613 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 5745 not shown) Planarity restraints: 6420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 287 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C ASP C 287 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP C 287 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA C 288 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 462 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO B 463 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO C 561 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " 0.025 5.00e-02 4.00e+02 ... (remaining 6417 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3233 2.75 - 3.29: 34020 3.29 - 3.83: 56986 3.83 - 4.36: 63518 4.36 - 4.90: 113529 Nonbonded interactions: 271286 Sorted by model distance: nonbonded pdb=" OG SER D 133 " pdb=" OD2 ASP D 223 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.238 3.040 nonbonded pdb=" OG SER B 155 " pdb=" OE1 GLU B 156 " model vdw 2.243 3.040 nonbonded pdb=" O LYS G 155 " pdb=" OG SER G 198 " model vdw 2.249 3.040 nonbonded pdb=" OE1 GLN F 177 " pdb=" OG SER F 183 " model vdw 2.251 3.040 ... (remaining 271281 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.190 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: 0.050 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.380 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 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 : 0.003 0.050 36535 Z= 0.154 Angle : 0.576 8.905 49895 Z= 0.337 Chirality : 0.041 0.295 5748 Planarity : 0.003 0.051 6375 Dihedral : 10.240 115.457 13641 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.31 % Allowed : 6.24 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.89 (0.11), residues: 4512 helix: 0.78 (0.20), residues: 623 sheet: -2.82 (0.14), residues: 1012 loop : -3.50 (0.09), residues: 2877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C1014 TYR 0.009 0.001 TYR A 145 PHE 0.007 0.001 PHE D 29 TRP 0.006 0.001 TRP F 33 HIS 0.002 0.000 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00273 (36438) covalent geometry : angle 0.57083 (49656) SS BOND : bond 0.00284 ( 52) SS BOND : angle 0.49786 ( 104) hydrogen bonds : bond 0.24140 ( 973) hydrogen bonds : angle 8.72087 ( 2700) link_NAG-ASN : bond 0.00364 ( 45) link_NAG-ASN : angle 1.55076 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 614 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.9369 (OUTLIER) cc_final: 0.9057 (m) REVERT: A 105 ILE cc_start: 0.8661 (pt) cc_final: 0.8351 (pt) REVERT: A 144 TYR cc_start: 0.6112 (t80) cc_final: 0.5876 (t80) REVERT: A 153 MET cc_start: 0.7895 (ptp) cc_final: 0.7198 (ptp) REVERT: A 248 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.5283 (t80) REVERT: A 408 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8060 (ttp80) REVERT: A 410 ILE cc_start: 0.8764 (mm) cc_final: 0.8547 (pt) REVERT: A 697 MET cc_start: 0.8596 (ptm) cc_final: 0.8394 (ptp) REVERT: A 817 PHE cc_start: 0.7030 (t80) cc_final: 0.6767 (t80) REVERT: B 176 LEU cc_start: 0.8384 (tp) cc_final: 0.7925 (pp) REVERT: B 177 MET cc_start: 0.7546 (ttp) cc_final: 0.6785 (tpp) REVERT: B 356 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7869 (tptp) REVERT: B 710 ASN cc_start: 0.7981 (p0) cc_final: 0.7706 (p0) REVERT: B 712 ILE cc_start: 0.8183 (mm) cc_final: 0.7969 (tt) REVERT: B 858 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8469 (pp) REVERT: C 244 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8517 (pt) REVERT: C 265 TYR cc_start: 0.8421 (p90) cc_final: 0.8138 (p90) REVERT: C 423 TYR cc_start: 0.6282 (t80) cc_final: 0.5883 (t80) REVERT: C 515 PHE cc_start: 0.7932 (m-80) cc_final: 0.7384 (m-80) REVERT: C 752 LEU cc_start: 0.9260 (mt) cc_final: 0.8933 (mt) REVERT: C 756 TYR cc_start: 0.8908 (m-80) cc_final: 0.8630 (m-80) REVERT: D 12 VAL cc_start: 0.5975 (m) cc_final: 0.5676 (p) REVERT: E 145 PHE cc_start: 0.6274 (p90) cc_final: 0.5438 (p90) REVERT: E 190 GLN cc_start: 0.5270 (mp10) cc_final: 0.4918 (tp40) REVERT: E 191 TRP cc_start: 0.4426 (OUTLIER) cc_final: 0.3536 (m100) REVERT: F 170 HIS cc_start: 0.4893 (m170) cc_final: 0.4555 (m-70) REVERT: F 172 PHE cc_start: 0.4720 (OUTLIER) cc_final: 0.4222 (p90) REVERT: G 24 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7220 (tpp80) REVERT: G 29 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8145 (tt) REVERT: G 168 THR cc_start: 0.4172 (OUTLIER) cc_final: 0.3802 (p) REVERT: G 192 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.6093 (tptp) REVERT: G 195 ARG cc_start: 0.7054 (mmm160) cc_final: 0.6321 (mpp-170) REVERT: H 74 ASN cc_start: 0.7129 (t0) cc_final: 0.6517 (t0) REVERT: H 80 PHE cc_start: 0.8050 (m-80) cc_final: 0.7532 (m-80) REVERT: H 150 ASP cc_start: 0.7189 (m-30) cc_final: 0.6841 (t0) REVERT: I 4 MET cc_start: 0.7995 (mmm) cc_final: 0.7370 (mmm) REVERT: I 35 GLN cc_start: 0.8196 (mp-120) cc_final: 0.7935 (mm-40) REVERT: I 90 TYR cc_start: 0.8074 (m-80) cc_final: 0.7068 (m-10) outliers start: 168 outliers final: 28 residues processed: 742 average time/residue: 0.2113 time to fit residues: 251.4341 Evaluate side-chains 354 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 314 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain E residue 191 TRP Chi-restraints excluded: chain F residue 146 CYS Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain G residue 194 HIS Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 29 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.0980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 0.5980 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 3.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 23 GLN A 74 ASN A 99 ASN A 183 GLN A 185 ASN A 409 GLN A 439 ASN A 493 GLN A 607 GLN A 655 HIS A 762 GLN A 774 GLN A 787 GLN A 872 GLN A 913 GLN A 957 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1048 HIS A1101 HIS B 23 GLN B 115 GLN B 164 ASN B 183 GLN B 218 GLN B 280 ASN B 409 GLN B 414 GLN B 439 ASN B 460 ASN B 493 GLN B 498 GLN B 536 ASN B 907 ASN B 960 ASN B1011 GLN C 23 GLN C 125 ASN C 183 GLN C 207 HIS C 218 GLN C 394 ASN C 439 ASN C 493 GLN C 580 GLN C 613 GLN C 872 GLN C 914 ASN C 920 GLN C 954 GLN C 965 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN D 161 ASN D 177 GLN D 203 ASN E 32 ASN E 200 GLN F 53 GLN F 77 ASN F 206 HIS G 99 HIS G 100 ASN G 175 ASN G 176 ASN G 200 GLN G 203 HIS H 6 GLN H 39 GLN H 50 ASN H 52 ASN H 84 ASN H 210 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.104739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.080858 restraints weight = 106072.296| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.53 r_work: 0.3272 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36535 Z= 0.113 Angle : 0.570 9.664 49895 Z= 0.288 Chirality : 0.045 0.383 5748 Planarity : 0.004 0.054 6375 Dihedral : 7.252 99.484 5906 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.93 % Allowed : 10.65 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.12), residues: 4512 helix: 1.83 (0.21), residues: 618 sheet: -2.19 (0.15), residues: 1077 loop : -3.01 (0.10), residues: 2817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 408 TYR 0.019 0.001 TYR G 50 PHE 0.017 0.001 PHE A 400 TRP 0.022 0.001 TRP H 160 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00242 (36438) covalent geometry : angle 0.56074 (49656) SS BOND : bond 0.00278 ( 52) SS BOND : angle 0.99667 ( 104) hydrogen bonds : bond 0.04142 ( 973) hydrogen bonds : angle 5.81234 ( 2700) link_NAG-ASN : bond 0.00317 ( 45) link_NAG-ASN : angle 1.90716 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 369 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7923 (ptp) cc_final: 0.7681 (ptp) REVERT: A 248 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.5489 (t80) REVERT: A 408 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8298 (ptp90) REVERT: A 410 ILE cc_start: 0.8772 (mm) cc_final: 0.8515 (pt) REVERT: A 427 ASP cc_start: 0.7180 (m-30) cc_final: 0.6678 (p0) REVERT: A 869 MET cc_start: 0.8702 (mtt) cc_final: 0.8196 (mtt) REVERT: A 1094 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8329 (m) REVERT: B 176 LEU cc_start: 0.8643 (tp) cc_final: 0.8065 (pp) REVERT: B 177 MET cc_start: 0.7425 (ttp) cc_final: 0.6726 (tpp) REVERT: B 356 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8018 (tptp) REVERT: B 492 LEU cc_start: 0.7074 (mm) cc_final: 0.6466 (tp) REVERT: B 858 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8599 (pp) REVERT: B 960 ASN cc_start: 0.8235 (m-40) cc_final: 0.7891 (t0) REVERT: C 244 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8560 (pt) REVERT: C 265 TYR cc_start: 0.8700 (p90) cc_final: 0.8393 (p90) REVERT: C 319 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7613 (mtp85) REVERT: C 453 TYR cc_start: 0.6544 (p90) cc_final: 0.5762 (p90) REVERT: C 515 PHE cc_start: 0.7689 (m-80) cc_final: 0.7370 (m-80) REVERT: C 756 TYR cc_start: 0.9220 (m-80) cc_final: 0.8878 (m-80) REVERT: C 957 GLN cc_start: 0.8257 (tt0) cc_final: 0.7974 (tt0) REVERT: C 1029 MET cc_start: 0.8821 (tpp) cc_final: 0.8068 (ttm) REVERT: D 12 VAL cc_start: 0.6592 (m) cc_final: 0.6380 (p) REVERT: E 32 ASN cc_start: 0.7823 (m110) cc_final: 0.7314 (m-40) REVERT: E 145 PHE cc_start: 0.5963 (p90) cc_final: 0.5260 (p90) REVERT: E 186 LEU cc_start: 0.5267 (OUTLIER) cc_final: 0.4925 (mp) REVERT: E 190 GLN cc_start: 0.5489 (mp10) cc_final: 0.4710 (tp40) REVERT: F 53 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8291 (mm110) REVERT: F 74 ASN cc_start: 0.7740 (m110) cc_final: 0.7526 (m110) REVERT: F 82 GLN cc_start: 0.6676 (tt0) cc_final: 0.6323 (mt0) REVERT: F 123 LYS cc_start: 0.6860 (pttt) cc_final: 0.6139 (mttp) REVERT: F 203 ASN cc_start: 0.4720 (t0) cc_final: 0.4449 (t0) REVERT: G 38 GLN cc_start: 0.8493 (tt0) cc_final: 0.7972 (tt0) REVERT: G 40 ARG cc_start: 0.7654 (tpp80) cc_final: 0.7122 (mpt180) REVERT: G 130 GLU cc_start: 0.3077 (OUTLIER) cc_final: 0.2331 (pt0) REVERT: G 192 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.6157 (tptp) REVERT: G 195 ARG cc_start: 0.7019 (mmm160) cc_final: 0.6206 (mpp-170) REVERT: H 54 ASP cc_start: 0.7033 (t0) cc_final: 0.6638 (t70) REVERT: H 73 ASP cc_start: 0.7099 (t70) cc_final: 0.6830 (t70) REVERT: H 210 ASN cc_start: 0.7991 (t0) cc_final: 0.7715 (t0) REVERT: I 4 MET cc_start: 0.7913 (mmm) cc_final: 0.7188 (mmm) REVERT: I 184 LEU cc_start: 0.6825 (tp) cc_final: 0.6069 (tp) outliers start: 114 outliers final: 48 residues processed: 465 average time/residue: 0.2005 time to fit residues: 153.0498 Evaluate side-chains 326 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 268 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 202 CYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 146 CYS Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain G residue 194 HIS Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 20 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 442 optimal weight: 1.9990 chunk 379 optimal weight: 1.9990 chunk 300 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 372 optimal weight: 4.9990 chunk 417 optimal weight: 0.4980 chunk 297 optimal weight: 1.9990 chunk 105 optimal weight: 0.0040 chunk 436 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A1002 GLN B 125 ASN B 245 HIS C 146 HIS C 787 GLN C 935 GLN C1002 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN G 98 ASN H 205 ASN I 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.110748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.085390 restraints weight = 111644.923| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.34 r_work: 0.3149 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 36535 Z= 0.196 Angle : 0.634 12.610 49895 Z= 0.320 Chirality : 0.047 0.686 5748 Planarity : 0.005 0.060 6375 Dihedral : 6.432 97.170 5877 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.05 % Allowed : 11.34 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.12), residues: 4512 helix: 1.85 (0.21), residues: 621 sheet: -1.85 (0.15), residues: 1119 loop : -2.91 (0.10), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 216 TYR 0.020 0.002 TYR A 145 PHE 0.021 0.002 PHE C 86 TRP 0.021 0.002 TRP D 109 HIS 0.009 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00459 (36438) covalent geometry : angle 0.62150 (49656) SS BOND : bond 0.00680 ( 52) SS BOND : angle 1.36341 ( 104) hydrogen bonds : bond 0.05466 ( 973) hydrogen bonds : angle 5.45356 ( 2700) link_NAG-ASN : bond 0.00915 ( 45) link_NAG-ASN : angle 2.25358 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 287 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.5676 (t80) REVERT: A 408 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8298 (ptp90) REVERT: B 177 MET cc_start: 0.7411 (ttp) cc_final: 0.6703 (tpt) REVERT: B 356 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8305 (tptp) REVERT: B 492 LEU cc_start: 0.7372 (mm) cc_final: 0.6638 (tp) REVERT: B 752 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8802 (mp) REVERT: B 858 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8779 (pp) REVERT: B 1029 MET cc_start: 0.9103 (tpp) cc_final: 0.8825 (ttm) REVERT: C 396 TYR cc_start: 0.7224 (m-10) cc_final: 0.6958 (m-10) REVERT: C 515 PHE cc_start: 0.7712 (m-80) cc_final: 0.7221 (m-80) REVERT: C 775 ASP cc_start: 0.8767 (t0) cc_final: 0.8189 (m-30) REVERT: C 960 ASN cc_start: 0.8364 (m-40) cc_final: 0.8095 (t0) REVERT: C 983 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7819 (tmm-80) REVERT: C 1029 MET cc_start: 0.9006 (tpp) cc_final: 0.8553 (ttm) REVERT: D 12 VAL cc_start: 0.6794 (m) cc_final: 0.6586 (p) REVERT: D 144 LEU cc_start: 0.5879 (tt) cc_final: 0.5213 (mp) REVERT: E 12 GLU cc_start: 0.8014 (tt0) cc_final: 0.7423 (tm-30) REVERT: E 32 ASN cc_start: 0.7949 (m110) cc_final: 0.7549 (m-40) REVERT: E 145 PHE cc_start: 0.6270 (p90) cc_final: 0.5782 (p90) REVERT: E 178 TYR cc_start: 0.6419 (m-80) cc_final: 0.5895 (m-80) REVERT: E 186 LEU cc_start: 0.5174 (OUTLIER) cc_final: 0.4531 (mp) REVERT: E 190 GLN cc_start: 0.5481 (mp10) cc_final: 0.4759 (tp40) REVERT: F 34 MET cc_start: 0.8569 (mmp) cc_final: 0.8226 (mmp) REVERT: F 83 MET cc_start: 0.7278 (pmm) cc_final: 0.6890 (pmm) REVERT: G 33 TYR cc_start: 0.8523 (m-80) cc_final: 0.8283 (m-10) REVERT: G 40 ARG cc_start: 0.7703 (tpp80) cc_final: 0.7111 (mpt180) REVERT: G 192 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.6052 (tptp) REVERT: G 195 ARG cc_start: 0.7142 (mmm160) cc_final: 0.6250 (mpp-170) REVERT: H 46 GLU cc_start: 0.7972 (mp0) cc_final: 0.7760 (mp0) REVERT: H 73 ASP cc_start: 0.7036 (t70) cc_final: 0.6784 (t70) REVERT: H 87 ARG cc_start: 0.7471 (mtp180) cc_final: 0.7261 (mtp-110) REVERT: H 89 GLU cc_start: 0.6517 (pm20) cc_final: 0.6316 (pm20) REVERT: H 160 TRP cc_start: 0.6536 (m100) cc_final: 0.6038 (m-10) REVERT: H 188 VAL cc_start: 0.5767 (p) cc_final: 0.4057 (p) REVERT: I 4 MET cc_start: 0.7910 (mmm) cc_final: 0.7221 (mmm) outliers start: 119 outliers final: 73 residues processed: 393 average time/residue: 0.2041 time to fit residues: 132.4058 Evaluate side-chains 317 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 237 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain G residue 194 HIS Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 172 PHE Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 99 HIS Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 192 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 64 optimal weight: 1.9990 chunk 319 optimal weight: 4.9990 chunk 441 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 405 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 445 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B 81 ASN C 370 ASN C 774 GLN C 955 ASN C1002 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 GLN G 176 ASN H 6 GLN H 177 GLN H 210 ASN I 32 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.105436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.080207 restraints weight = 96286.175| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.62 r_work: 0.3129 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 36535 Z= 0.190 Angle : 0.609 9.606 49895 Z= 0.309 Chirality : 0.046 0.386 5748 Planarity : 0.004 0.059 6375 Dihedral : 6.397 93.116 5870 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 3.64 % Allowed : 11.83 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.65 (0.12), residues: 4512 helix: 1.89 (0.21), residues: 630 sheet: -1.80 (0.15), residues: 1118 loop : -2.80 (0.10), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 319 TYR 0.019 0.001 TYR G 50 PHE 0.019 0.002 PHE E 124 TRP 0.021 0.001 TRP D 109 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00451 (36438) covalent geometry : angle 0.59903 (49656) SS BOND : bond 0.00414 ( 52) SS BOND : angle 1.33296 ( 104) hydrogen bonds : bond 0.05300 ( 973) hydrogen bonds : angle 5.28204 ( 2700) link_NAG-ASN : bond 0.00339 ( 45) link_NAG-ASN : angle 1.96576 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 255 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7910 (ptp) cc_final: 0.7606 (ptp) REVERT: A 239 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7716 (tm-30) REVERT: A 248 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.5745 (t80) REVERT: A 408 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8458 (ttp80) REVERT: B 177 MET cc_start: 0.7419 (ttp) cc_final: 0.6450 (mmt) REVERT: B 214 ARG cc_start: 0.8646 (tpp-160) cc_final: 0.8232 (tpp-160) REVERT: B 347 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6118 (m-80) REVERT: B 492 LEU cc_start: 0.7294 (mm) cc_final: 0.7062 (mm) REVERT: B 752 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8842 (mp) REVERT: B 856 ASN cc_start: 0.9118 (m110) cc_final: 0.8865 (m-40) REVERT: B 858 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 1029 MET cc_start: 0.9152 (tpp) cc_final: 0.8807 (ttm) REVERT: C 244 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8706 (pt) REVERT: C 314 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.7999 (tp40) REVERT: C 515 PHE cc_start: 0.7595 (m-80) cc_final: 0.7158 (m-80) REVERT: C 775 ASP cc_start: 0.8747 (t0) cc_final: 0.8152 (m-30) REVERT: C 949 GLN cc_start: 0.8094 (tp40) cc_final: 0.7752 (tp-100) REVERT: C 960 ASN cc_start: 0.8328 (m-40) cc_final: 0.8083 (t0) REVERT: C 1029 MET cc_start: 0.9051 (tpp) cc_final: 0.8671 (ttm) REVERT: D 144 LEU cc_start: 0.5936 (tt) cc_final: 0.5286 (mp) REVERT: E 142 ILE cc_start: 0.6618 (OUTLIER) cc_final: 0.6255 (mt) REVERT: E 145 PHE cc_start: 0.6400 (p90) cc_final: 0.5887 (p90) REVERT: E 178 TYR cc_start: 0.6353 (m-80) cc_final: 0.5881 (m-80) REVERT: E 186 LEU cc_start: 0.5307 (OUTLIER) cc_final: 0.4757 (mt) REVERT: E 190 GLN cc_start: 0.5577 (mp10) cc_final: 0.4841 (tp40) REVERT: F 53 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8645 (mm110) REVERT: G 33 TYR cc_start: 0.8584 (m-80) cc_final: 0.8358 (m-10) REVERT: G 40 ARG cc_start: 0.7625 (tpp80) cc_final: 0.7050 (mpt180) REVERT: G 130 GLU cc_start: 0.3479 (OUTLIER) cc_final: 0.3276 (pm20) REVERT: G 192 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.5976 (tptp) REVERT: G 195 ARG cc_start: 0.7078 (mmm160) cc_final: 0.6078 (mpp-170) REVERT: G 211 THR cc_start: 0.5025 (OUTLIER) cc_final: 0.4663 (m) REVERT: H 46 GLU cc_start: 0.7945 (mp0) cc_final: 0.7713 (mp0) REVERT: H 73 ASP cc_start: 0.6942 (t70) cc_final: 0.6722 (t70) REVERT: H 83 MET cc_start: 0.8098 (ptt) cc_final: 0.7796 (ttp) REVERT: H 87 ARG cc_start: 0.7438 (mtp180) cc_final: 0.7120 (mtp-110) REVERT: H 160 TRP cc_start: 0.6261 (m100) cc_final: 0.5900 (m-10) REVERT: H 188 VAL cc_start: 0.5648 (p) cc_final: 0.4283 (p) REVERT: H 210 ASN cc_start: 0.8105 (t0) cc_final: 0.7898 (t0) REVERT: I 4 MET cc_start: 0.7828 (mmm) cc_final: 0.7056 (mmm) outliers start: 142 outliers final: 90 residues processed: 378 average time/residue: 0.1974 time to fit residues: 124.5999 Evaluate side-chains 330 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 227 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain G residue 194 HIS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 172 PHE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 192 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 389 optimal weight: 3.9990 chunk 159 optimal weight: 0.5980 chunk 198 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 416 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 345 optimal weight: 6.9990 chunk 82 optimal weight: 0.0070 chunk 176 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN B 907 ASN B1002 GLN C 755 GLN C 774 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 53 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.108791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.083289 restraints weight = 91473.684| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.75 r_work: 0.3145 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 36535 Z= 0.146 Angle : 0.579 9.891 49895 Z= 0.292 Chirality : 0.045 0.333 5748 Planarity : 0.004 0.117 6375 Dihedral : 6.200 92.971 5866 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.23 % Allowed : 12.47 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.12), residues: 4512 helix: 2.10 (0.21), residues: 630 sheet: -1.61 (0.15), residues: 1094 loop : -2.69 (0.11), residues: 2788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 216 TYR 0.017 0.001 TYR A 145 PHE 0.016 0.001 PHE E 124 TRP 0.019 0.001 TRP D 109 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00344 (36438) covalent geometry : angle 0.56975 (49656) SS BOND : bond 0.00347 ( 52) SS BOND : angle 1.10646 ( 104) hydrogen bonds : bond 0.04865 ( 973) hydrogen bonds : angle 5.05252 ( 2700) link_NAG-ASN : bond 0.00308 ( 45) link_NAG-ASN : angle 1.92403 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 251 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4586 (ptp) cc_final: 0.4160 (ptm) REVERT: A 212 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8057 (mt) REVERT: A 239 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7685 (tm-30) REVERT: A 244 LEU cc_start: 0.8246 (tp) cc_final: 0.8019 (tp) REVERT: A 248 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.5780 (t80) REVERT: A 382 VAL cc_start: 0.7836 (OUTLIER) cc_final: 0.7502 (t) REVERT: A 408 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8445 (ttp80) REVERT: B 177 MET cc_start: 0.7394 (ttp) cc_final: 0.6391 (mmt) REVERT: B 214 ARG cc_start: 0.8673 (tpp-160) cc_final: 0.8409 (tpp-160) REVERT: B 347 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6124 (m-80) REVERT: B 752 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8838 (mp) REVERT: B 856 ASN cc_start: 0.9113 (m110) cc_final: 0.8851 (m-40) REVERT: B 858 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8778 (pp) REVERT: B 1029 MET cc_start: 0.9158 (tpp) cc_final: 0.8791 (ttm) REVERT: C 244 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8695 (pt) REVERT: C 515 PHE cc_start: 0.7480 (m-80) cc_final: 0.7076 (m-80) REVERT: C 740 MET cc_start: 0.8830 (mmm) cc_final: 0.8621 (tpp) REVERT: C 775 ASP cc_start: 0.8763 (t0) cc_final: 0.8139 (m-30) REVERT: C 869 MET cc_start: 0.8647 (mtt) cc_final: 0.8428 (mtt) REVERT: C 949 GLN cc_start: 0.8057 (tp40) cc_final: 0.7707 (tp-100) REVERT: C 1029 MET cc_start: 0.9058 (tpp) cc_final: 0.8701 (ttm) REVERT: D 144 LEU cc_start: 0.5854 (tt) cc_final: 0.5594 (mp) REVERT: E 12 GLU cc_start: 0.7795 (tt0) cc_final: 0.7453 (tt0) REVERT: E 142 ILE cc_start: 0.6635 (OUTLIER) cc_final: 0.6329 (mt) REVERT: E 145 PHE cc_start: 0.6395 (p90) cc_final: 0.5928 (p90) REVERT: E 178 TYR cc_start: 0.6570 (m-80) cc_final: 0.6086 (m-80) REVERT: E 186 LEU cc_start: 0.4962 (OUTLIER) cc_final: 0.4493 (mt) REVERT: E 190 GLN cc_start: 0.5544 (mp10) cc_final: 0.4805 (tp40) REVERT: F 53 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8619 (mm-40) REVERT: G 33 TYR cc_start: 0.8577 (m-80) cc_final: 0.8365 (m-10) REVERT: G 40 ARG cc_start: 0.7619 (tpp80) cc_final: 0.6949 (mmt90) REVERT: G 130 GLU cc_start: 0.3685 (OUTLIER) cc_final: 0.3365 (pm20) REVERT: G 192 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6206 (tptp) REVERT: G 195 ARG cc_start: 0.7149 (mmm160) cc_final: 0.6863 (mmm160) REVERT: G 211 THR cc_start: 0.4921 (OUTLIER) cc_final: 0.4571 (m) REVERT: H 73 ASP cc_start: 0.6749 (t70) cc_final: 0.6545 (t70) REVERT: H 83 MET cc_start: 0.8172 (ptt) cc_final: 0.7855 (ttp) REVERT: H 87 ARG cc_start: 0.7555 (mtp180) cc_final: 0.7351 (mtp-110) REVERT: H 160 TRP cc_start: 0.6283 (m100) cc_final: 0.5863 (m-10) REVERT: H 188 VAL cc_start: 0.5546 (p) cc_final: 0.4162 (p) REVERT: H 210 ASN cc_start: 0.8102 (t0) cc_final: 0.7871 (t0) REVERT: I 4 MET cc_start: 0.7832 (mmm) cc_final: 0.7005 (mmm) REVERT: I 36 TRP cc_start: 0.7450 (m100) cc_final: 0.6871 (m100) REVERT: I 81 LEU cc_start: 0.5070 (tp) cc_final: 0.4838 (mp) outliers start: 126 outliers final: 90 residues processed: 360 average time/residue: 0.1884 time to fit residues: 114.3524 Evaluate side-chains 334 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 230 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain G residue 194 HIS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 172 PHE Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 192 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 245 optimal weight: 0.8980 chunk 427 optimal weight: 4.9990 chunk 315 optimal weight: 1.9990 chunk 362 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 390 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 418 optimal weight: 2.9990 chunk 346 optimal weight: 0.0870 chunk 176 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 955 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.107020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.082179 restraints weight = 93480.855| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.65 r_work: 0.3145 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 36535 Z= 0.149 Angle : 0.582 10.246 49895 Z= 0.294 Chirality : 0.044 0.330 5748 Planarity : 0.004 0.056 6375 Dihedral : 6.152 92.767 5864 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.59 % Allowed : 12.80 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.12), residues: 4512 helix: 2.14 (0.21), residues: 630 sheet: -1.61 (0.15), residues: 1138 loop : -2.60 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.020 0.001 TYR C 396 PHE 0.015 0.001 PHE B 86 TRP 0.018 0.001 TRP D 109 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00353 (36438) covalent geometry : angle 0.57235 (49656) SS BOND : bond 0.00304 ( 52) SS BOND : angle 1.07111 ( 104) hydrogen bonds : bond 0.04833 ( 973) hydrogen bonds : angle 4.96230 ( 2700) link_NAG-ASN : bond 0.00301 ( 45) link_NAG-ASN : angle 1.92321 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 245 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7751 (tp) REVERT: A 179 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7176 (mt) REVERT: A 239 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 248 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.5770 (t80) REVERT: A 382 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7402 (t) REVERT: A 408 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8431 (ttp80) REVERT: B 101 ILE cc_start: 0.8901 (mp) cc_final: 0.8550 (tp) REVERT: B 177 MET cc_start: 0.7438 (ttp) cc_final: 0.6379 (mmt) REVERT: B 214 ARG cc_start: 0.8646 (tpp-160) cc_final: 0.8417 (tpp-160) REVERT: B 752 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8827 (mp) REVERT: B 856 ASN cc_start: 0.9111 (m110) cc_final: 0.8879 (m-40) REVERT: B 858 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8752 (pp) REVERT: B 1029 MET cc_start: 0.9140 (tpp) cc_final: 0.8785 (ttm) REVERT: C 152 TRP cc_start: 0.8510 (OUTLIER) cc_final: 0.7912 (m100) REVERT: C 153 MET cc_start: 0.8878 (tpp) cc_final: 0.7407 (mtm) REVERT: C 244 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8683 (pt) REVERT: C 314 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.7908 (tp40) REVERT: C 515 PHE cc_start: 0.7454 (m-80) cc_final: 0.7159 (m-80) REVERT: C 740 MET cc_start: 0.8892 (mmm) cc_final: 0.8688 (tpp) REVERT: C 775 ASP cc_start: 0.8780 (t0) cc_final: 0.8165 (m-30) REVERT: C 949 GLN cc_start: 0.8071 (tp40) cc_final: 0.7748 (tp-100) REVERT: C 1029 MET cc_start: 0.9039 (tpp) cc_final: 0.8734 (ttm) REVERT: D 144 LEU cc_start: 0.5842 (tt) cc_final: 0.5180 (mp) REVERT: E 142 ILE cc_start: 0.6675 (OUTLIER) cc_final: 0.6385 (mt) REVERT: E 145 PHE cc_start: 0.6359 (p90) cc_final: 0.5869 (p90) REVERT: E 178 TYR cc_start: 0.6655 (m-80) cc_final: 0.6204 (m-80) REVERT: E 186 LEU cc_start: 0.4931 (OUTLIER) cc_final: 0.4474 (mt) REVERT: E 190 GLN cc_start: 0.5350 (mp10) cc_final: 0.4616 (tp40) REVERT: F 53 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8555 (mm110) REVERT: G 40 ARG cc_start: 0.7576 (tpp80) cc_final: 0.6920 (mmt90) REVERT: G 130 GLU cc_start: 0.3606 (OUTLIER) cc_final: 0.3312 (pm20) REVERT: G 192 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.6160 (tptp) REVERT: G 195 ARG cc_start: 0.7049 (mmm160) cc_final: 0.6397 (mmm160) REVERT: G 211 THR cc_start: 0.4845 (OUTLIER) cc_final: 0.4532 (m) REVERT: H 73 ASP cc_start: 0.6863 (t70) cc_final: 0.6647 (t70) REVERT: H 87 ARG cc_start: 0.7460 (mtp180) cc_final: 0.7211 (mtp-110) REVERT: H 210 ASN cc_start: 0.8052 (t0) cc_final: 0.7814 (t0) REVERT: I 4 MET cc_start: 0.7823 (mmm) cc_final: 0.6945 (mmm) REVERT: I 36 TRP cc_start: 0.7440 (m100) cc_final: 0.6840 (m100) REVERT: I 81 LEU cc_start: 0.5048 (tp) cc_final: 0.4832 (mp) outliers start: 140 outliers final: 98 residues processed: 368 average time/residue: 0.1912 time to fit residues: 118.2367 Evaluate side-chains 340 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 226 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 53 ASN Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 172 PHE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 192 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 88 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 416 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 439 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A 992 GLN C 115 GLN C 370 ASN C 388 ASN C 481 ASN C 774 GLN C1002 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN E 38 GLN F 53 GLN F 210 ASN I 8 HIS ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.089952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.065135 restraints weight = 112783.662| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.93 r_work: 0.3051 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.143 36535 Z= 0.347 Angle : 0.775 10.948 49895 Z= 0.396 Chirality : 0.050 0.381 5748 Planarity : 0.005 0.057 6375 Dihedral : 7.225 98.050 5862 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer: Outliers : 3.87 % Allowed : 13.42 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.79 (0.12), residues: 4512 helix: 1.24 (0.21), residues: 641 sheet: -1.78 (0.15), residues: 1130 loop : -2.81 (0.11), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 195 TYR 0.035 0.002 TYR C 396 PHE 0.029 0.003 PHE B 429 TRP 0.029 0.002 TRP D 109 HIS 0.014 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00825 (36438) covalent geometry : angle 0.76247 (49656) SS BOND : bond 0.00553 ( 52) SS BOND : angle 1.52668 ( 104) hydrogen bonds : bond 0.07062 ( 973) hydrogen bonds : angle 5.58719 ( 2700) link_NAG-ASN : bond 0.00506 ( 45) link_NAG-ASN : angle 2.51974 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 232 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.7947 (t80) REVERT: A 248 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.5854 (t80) REVERT: A 599 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9031 (p) REVERT: B 101 ILE cc_start: 0.8934 (mp) cc_final: 0.8613 (tp) REVERT: B 177 MET cc_start: 0.7622 (ttp) cc_final: 0.6276 (mmt) REVERT: B 347 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: B 752 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8929 (mt) REVERT: B 775 ASP cc_start: 0.8130 (m-30) cc_final: 0.7850 (m-30) REVERT: B 856 ASN cc_start: 0.9157 (m110) cc_final: 0.8911 (m-40) REVERT: B 858 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8865 (pp) REVERT: B 950 ASP cc_start: 0.8030 (m-30) cc_final: 0.7506 (m-30) REVERT: B 1029 MET cc_start: 0.9097 (tpp) cc_final: 0.8739 (ttm) REVERT: B 1123 SER cc_start: 0.8395 (m) cc_final: 0.7969 (p) REVERT: C 14 GLN cc_start: 0.7182 (mm-40) cc_final: 0.6974 (tp40) REVERT: C 152 TRP cc_start: 0.8631 (OUTLIER) cc_final: 0.8028 (m100) REVERT: C 314 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.7964 (tp40) REVERT: C 515 PHE cc_start: 0.7572 (m-80) cc_final: 0.7030 (m-80) REVERT: C 775 ASP cc_start: 0.8745 (t0) cc_final: 0.8167 (m-30) REVERT: C 1029 MET cc_start: 0.9133 (tpp) cc_final: 0.8842 (ttm) REVERT: D 144 LEU cc_start: 0.6273 (tt) cc_final: 0.5476 (mp) REVERT: E 142 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6494 (mt) REVERT: E 145 PHE cc_start: 0.6647 (p90) cc_final: 0.5918 (p90) REVERT: E 178 TYR cc_start: 0.7068 (m-80) cc_final: 0.6643 (m-80) REVERT: E 186 LEU cc_start: 0.5208 (OUTLIER) cc_final: 0.4687 (mt) REVERT: E 190 GLN cc_start: 0.5375 (mp10) cc_final: 0.4698 (tp40) REVERT: F 53 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8670 (mm110) REVERT: G 16 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6910 (pttm) REVERT: G 40 ARG cc_start: 0.7624 (tpp80) cc_final: 0.6956 (mmt90) REVERT: G 116 LYS cc_start: 0.6843 (tmtt) cc_final: 0.5821 (mmmm) REVERT: G 195 ARG cc_start: 0.7079 (mmm160) cc_final: 0.6381 (mmm160) REVERT: G 211 THR cc_start: 0.4985 (OUTLIER) cc_final: 0.4577 (m) REVERT: H 52 ASN cc_start: 0.7021 (OUTLIER) cc_final: 0.6039 (m-40) REVERT: H 89 GLU cc_start: 0.7188 (pm20) cc_final: 0.6982 (pm20) REVERT: H 210 ASN cc_start: 0.8044 (t0) cc_final: 0.7787 (t0) REVERT: I 4 MET cc_start: 0.8024 (mmm) cc_final: 0.7566 (mmm) outliers start: 151 outliers final: 105 residues processed: 369 average time/residue: 0.1939 time to fit residues: 120.4508 Evaluate side-chains 332 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 213 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 172 PHE Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 169 THR Chi-restraints excluded: chain I residue 192 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 406 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 349 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 401 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 368 optimal weight: 2.9990 chunk 409 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN C 370 ASN C 774 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 GLN ** G 114 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 = 0.3793 r_free = 0.3793 target = 0.106179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081505 restraints weight = 92413.303| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.51 r_work: 0.3111 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 36535 Z= 0.146 Angle : 0.621 11.852 49895 Z= 0.314 Chirality : 0.045 0.337 5748 Planarity : 0.004 0.057 6375 Dihedral : 6.646 98.890 5858 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.05 % Allowed : 14.55 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.47 (0.12), residues: 4512 helix: 1.80 (0.21), residues: 642 sheet: -1.62 (0.15), residues: 1148 loop : -2.66 (0.11), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 765 TYR 0.021 0.001 TYR G 50 PHE 0.019 0.001 PHE B 86 TRP 0.019 0.001 TRP D 109 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00343 (36438) covalent geometry : angle 0.61012 (49656) SS BOND : bond 0.00297 ( 52) SS BOND : angle 1.16761 ( 104) hydrogen bonds : bond 0.05198 ( 973) hydrogen bonds : angle 5.05143 ( 2700) link_NAG-ASN : bond 0.00324 ( 45) link_NAG-ASN : angle 2.11283 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 230 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4552 (pmm) cc_final: 0.4320 (pmm) REVERT: A 179 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7016 (mt) REVERT: A 248 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.5794 (t80) REVERT: A 599 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.8974 (p) REVERT: B 101 ILE cc_start: 0.8914 (mp) cc_final: 0.8660 (tp) REVERT: B 177 MET cc_start: 0.7515 (ttp) cc_final: 0.6167 (mmt) REVERT: B 347 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.5916 (m-80) REVERT: B 752 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8949 (mt) REVERT: B 858 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8791 (pp) REVERT: B 1029 MET cc_start: 0.9105 (tpp) cc_final: 0.8727 (ttm) REVERT: C 14 GLN cc_start: 0.7288 (mm-40) cc_final: 0.7007 (tp40) REVERT: C 152 TRP cc_start: 0.8637 (OUTLIER) cc_final: 0.8037 (m100) REVERT: C 314 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.7918 (tp40) REVERT: C 515 PHE cc_start: 0.7468 (m-80) cc_final: 0.7045 (m-80) REVERT: C 775 ASP cc_start: 0.8710 (t0) cc_final: 0.8128 (m-30) REVERT: C 1029 MET cc_start: 0.9049 (tpp) cc_final: 0.8791 (ttm) REVERT: D 144 LEU cc_start: 0.5961 (tt) cc_final: 0.5243 (mp) REVERT: E 142 ILE cc_start: 0.6861 (OUTLIER) cc_final: 0.6641 (mt) REVERT: E 145 PHE cc_start: 0.6462 (p90) cc_final: 0.5801 (p90) REVERT: E 178 TYR cc_start: 0.6911 (m-80) cc_final: 0.6484 (m-80) REVERT: E 186 LEU cc_start: 0.5002 (OUTLIER) cc_final: 0.4510 (mt) REVERT: E 190 GLN cc_start: 0.5414 (mp10) cc_final: 0.4686 (tp40) REVERT: F 53 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8634 (mm110) REVERT: G 40 ARG cc_start: 0.7570 (tpp80) cc_final: 0.6902 (mmt90) REVERT: G 192 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.5864 (tptp) REVERT: G 195 ARG cc_start: 0.7111 (mmm160) cc_final: 0.6458 (mmm160) REVERT: G 211 THR cc_start: 0.4903 (OUTLIER) cc_final: 0.4546 (m) REVERT: H 210 ASN cc_start: 0.8084 (t0) cc_final: 0.7847 (t0) REVERT: I 4 MET cc_start: 0.7915 (mmm) cc_final: 0.7408 (mmm) REVERT: I 36 TRP cc_start: 0.7618 (m100) cc_final: 0.7127 (m100) REVERT: I 40 ARG cc_start: 0.7610 (tpp80) cc_final: 0.7114 (mmt-90) outliers start: 119 outliers final: 90 residues processed: 333 average time/residue: 0.1925 time to fit residues: 108.0449 Evaluate side-chains 316 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 213 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 172 PHE Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 192 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 80 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 270 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 195 optimal weight: 0.8980 chunk 332 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 774 GLN C 955 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 GLN ** G 114 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 = 0.3804 r_free = 0.3804 target = 0.106147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.080783 restraints weight = 92846.105| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.61 r_work: 0.3127 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36535 Z= 0.135 Angle : 0.598 10.583 49895 Z= 0.302 Chirality : 0.045 0.331 5748 Planarity : 0.004 0.054 6375 Dihedral : 6.342 97.777 5856 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 3.00 % Allowed : 14.68 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.12), residues: 4512 helix: 2.06 (0.21), residues: 642 sheet: -1.46 (0.15), residues: 1131 loop : -2.55 (0.11), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 765 TYR 0.022 0.001 TYR G 50 PHE 0.017 0.001 PHE B 86 TRP 0.017 0.001 TRP D 109 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00318 (36438) covalent geometry : angle 0.58765 (49656) SS BOND : bond 0.00295 ( 52) SS BOND : angle 1.07225 ( 104) hydrogen bonds : bond 0.04771 ( 973) hydrogen bonds : angle 4.86329 ( 2700) link_NAG-ASN : bond 0.00311 ( 45) link_NAG-ASN : angle 2.01035 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 227 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4718 (pmm) cc_final: 0.4506 (pmm) REVERT: A 179 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7125 (mt) REVERT: A 239 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 248 TYR cc_start: 0.7367 (OUTLIER) cc_final: 0.5806 (t80) REVERT: A 599 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8939 (p) REVERT: B 101 ILE cc_start: 0.8922 (mp) cc_final: 0.8649 (tp) REVERT: B 177 MET cc_start: 0.7492 (ttp) cc_final: 0.6179 (mmt) REVERT: B 347 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6000 (m-80) REVERT: B 752 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8814 (mp) REVERT: B 858 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8754 (pp) REVERT: B 1029 MET cc_start: 0.9116 (tpp) cc_final: 0.8730 (ttm) REVERT: C 14 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6931 (tp40) REVERT: C 152 TRP cc_start: 0.8646 (OUTLIER) cc_final: 0.8055 (m100) REVERT: C 153 MET cc_start: 0.9044 (tpp) cc_final: 0.7536 (mtm) REVERT: C 314 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.7878 (tp40) REVERT: C 515 PHE cc_start: 0.7476 (m-80) cc_final: 0.7051 (m-80) REVERT: C 775 ASP cc_start: 0.8766 (t0) cc_final: 0.8103 (m-30) REVERT: C 949 GLN cc_start: 0.8146 (tp40) cc_final: 0.7842 (tp40) REVERT: C 1029 MET cc_start: 0.9046 (tpp) cc_final: 0.8754 (ttm) REVERT: D 144 LEU cc_start: 0.5939 (tt) cc_final: 0.5215 (mp) REVERT: E 145 PHE cc_start: 0.6546 (p90) cc_final: 0.5798 (p90) REVERT: E 178 TYR cc_start: 0.6959 (m-80) cc_final: 0.6468 (m-80) REVERT: E 186 LEU cc_start: 0.5042 (OUTLIER) cc_final: 0.4504 (mt) REVERT: E 190 GLN cc_start: 0.5351 (mp10) cc_final: 0.4582 (tp-100) REVERT: F 53 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8689 (mm110) REVERT: G 40 ARG cc_start: 0.7518 (tpp80) cc_final: 0.6897 (mmt90) REVERT: G 189 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7118 (pp20) REVERT: G 192 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.5960 (tptp) REVERT: G 195 ARG cc_start: 0.7084 (mmm160) cc_final: 0.6475 (mmm160) REVERT: G 211 THR cc_start: 0.4857 (OUTLIER) cc_final: 0.4543 (m) REVERT: H 210 ASN cc_start: 0.8116 (t0) cc_final: 0.7870 (t0) REVERT: I 4 MET cc_start: 0.7824 (mmm) cc_final: 0.7327 (mmm) REVERT: I 36 TRP cc_start: 0.7458 (m100) cc_final: 0.6975 (m100) REVERT: I 40 ARG cc_start: 0.7550 (tpp80) cc_final: 0.7054 (mmt-90) outliers start: 117 outliers final: 90 residues processed: 330 average time/residue: 0.1877 time to fit residues: 104.3169 Evaluate side-chains 316 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 213 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 172 PHE Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 192 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 171 optimal weight: 0.5980 chunk 271 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 275 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN C 370 ASN C 955 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.101955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.077590 restraints weight = 99815.980| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.49 r_work: 0.3126 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 36535 Z= 0.136 Angle : 0.596 10.596 49895 Z= 0.301 Chirality : 0.044 0.329 5748 Planarity : 0.004 0.054 6375 Dihedral : 6.238 96.866 5856 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.67 % Allowed : 14.93 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.12), residues: 4512 helix: 2.07 (0.21), residues: 648 sheet: -1.42 (0.15), residues: 1137 loop : -2.49 (0.11), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 765 TYR 0.034 0.001 TYR C 365 PHE 0.017 0.001 PHE B 86 TRP 0.017 0.001 TRP D 109 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00322 (36438) covalent geometry : angle 0.58512 (49656) SS BOND : bond 0.00292 ( 52) SS BOND : angle 1.32050 ( 104) hydrogen bonds : bond 0.04713 ( 973) hydrogen bonds : angle 4.79878 ( 2700) link_NAG-ASN : bond 0.00304 ( 45) link_NAG-ASN : angle 1.98573 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9024 Ramachandran restraints generated. 4512 Oldfield, 0 Emsley, 4512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 218 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 248 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.5773 (t80) REVERT: A 599 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8936 (p) REVERT: B 101 ILE cc_start: 0.8913 (mp) cc_final: 0.8643 (tp) REVERT: B 177 MET cc_start: 0.7451 (ttp) cc_final: 0.6156 (mmt) REVERT: B 347 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6017 (m-80) REVERT: B 429 PHE cc_start: 0.7310 (t80) cc_final: 0.7096 (t80) REVERT: B 752 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8839 (mp) REVERT: B 858 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8720 (pp) REVERT: B 1029 MET cc_start: 0.9106 (tpp) cc_final: 0.8704 (ttm) REVERT: C 14 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6999 (tp40) REVERT: C 152 TRP cc_start: 0.8642 (OUTLIER) cc_final: 0.8058 (m100) REVERT: C 153 MET cc_start: 0.9048 (tpp) cc_final: 0.7540 (mtm) REVERT: C 314 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7896 (tp40) REVERT: C 515 PHE cc_start: 0.7544 (m-80) cc_final: 0.7099 (m-80) REVERT: C 775 ASP cc_start: 0.8725 (t0) cc_final: 0.8090 (m-30) REVERT: C 949 GLN cc_start: 0.8139 (tp40) cc_final: 0.7819 (tp40) REVERT: C 1029 MET cc_start: 0.9036 (tpp) cc_final: 0.8737 (ttm) REVERT: D 144 LEU cc_start: 0.6050 (tt) cc_final: 0.5296 (mp) REVERT: E 142 ILE cc_start: 0.6834 (mt) cc_final: 0.6584 (mt) REVERT: E 145 PHE cc_start: 0.6657 (p90) cc_final: 0.5851 (p90) REVERT: E 178 TYR cc_start: 0.6924 (m-80) cc_final: 0.6428 (m-80) REVERT: E 190 GLN cc_start: 0.5345 (mp10) cc_final: 0.4578 (tp-100) REVERT: F 53 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8680 (mm110) REVERT: G 40 ARG cc_start: 0.7607 (tpp80) cc_final: 0.7008 (mmt90) REVERT: G 130 GLU cc_start: 0.3799 (OUTLIER) cc_final: 0.3505 (pm20) REVERT: G 189 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7195 (pp20) REVERT: G 192 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.6019 (tptp) REVERT: G 195 ARG cc_start: 0.7164 (mmm160) cc_final: 0.6547 (mmm160) REVERT: G 211 THR cc_start: 0.4854 (OUTLIER) cc_final: 0.4579 (m) REVERT: H 210 ASN cc_start: 0.8088 (t0) cc_final: 0.7842 (t0) REVERT: I 4 MET cc_start: 0.7872 (mmm) cc_final: 0.7350 (mmm) REVERT: I 36 TRP cc_start: 0.7536 (m100) cc_final: 0.7139 (m100) REVERT: I 40 ARG cc_start: 0.7608 (tpp80) cc_final: 0.7175 (mmt-90) outliers start: 104 outliers final: 84 residues processed: 309 average time/residue: 0.1947 time to fit residues: 101.3426 Evaluate side-chains 310 residues out of total 3948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 214 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 449 TYR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1043 CYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain E residue 2 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 144 ASP Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 172 PHE Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 192 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 338 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 448 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 379 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 376 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 ASN C 955 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.103446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.078761 restraints weight = 96469.930| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.55 r_work: 0.3097 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 36535 Z= 0.168 Angle : 0.616 10.673 49895 Z= 0.311 Chirality : 0.045 0.333 5748 Planarity : 0.004 0.054 6375 Dihedral : 6.317 96.683 5856 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 2.69 % Allowed : 14.96 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.12), residues: 4512 helix: 1.96 (0.21), residues: 649 sheet: -1.44 (0.15), residues: 1120 loop : -2.47 (0.11), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 87 TYR 0.021 0.001 TYR G 50 PHE 0.019 0.002 PHE B 429 TRP 0.019 0.001 TRP D 109 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00400 (36438) covalent geometry : angle 0.60467 (49656) SS BOND : bond 0.00336 ( 52) SS BOND : angle 1.35567 ( 104) hydrogen bonds : bond 0.05088 ( 973) hydrogen bonds : angle 4.88859 ( 2700) link_NAG-ASN : bond 0.00310 ( 45) link_NAG-ASN : angle 2.04858 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8616.16 seconds wall clock time: 148 minutes 24.27 seconds (8904.27 seconds total)