Starting phenix.real_space_refine on Sat Mar 7 00:22:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aa2_15291/03_2026/8aa2_15291.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aa2_15291/03_2026/8aa2_15291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aa2_15291/03_2026/8aa2_15291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aa2_15291/03_2026/8aa2_15291.map" model { file = "/net/cci-nas-00/data/ceres_data/8aa2_15291/03_2026/8aa2_15291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aa2_15291/03_2026/8aa2_15291.cif" } resolution = 3.1 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= 0.001 sd= 0.007 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: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 136 5.16 5 C 22700 2.51 5 N 5948 2.21 5 O 7154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35942 Number of models: 1 Model: "" Number of chains: 19 Chain: "E" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3979 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 18, 'TRANS': 478} Chain: "T" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 721 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "G" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3351 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 418} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3979 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 18, 'TRANS': 478} Chain: "B" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4436 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain: "A" Number of atoms: 7267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7267 Classifications: {'peptide': 924} Link IDs: {'PTRANS': 32, 'TRANS': 891} Chain: "J" Number of atoms: 4436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4436 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 18, 'TRANS': 532} Chain: "I" Number of atoms: 7267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7267 Classifications: {'peptide': 924} Link IDs: {'PTRANS': 32, 'TRANS': 891} Chain: "H" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 144 Unusual residues: {'FRU': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'FRU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'FRU': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FRU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'FRU': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'FRU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.22, per 1000 atoms: 0.23 Number of scatterers: 35942 At special positions: 0 Unit cell: (116.085, 189.57, 195.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 Mg 4 11.99 O 7154 8.00 N 5948 7.00 C 22700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 389 " distance=2.03 Simple disulfide: pdb=" SG CYS J 387 " - pdb=" SG CYS J 389 " 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 ALPHA2-1 " FRU C 2 " - " FRU C 7 " ~> Even though FRU is a beta isomer, an alpha linkage is required... " FRU H 6 " - " FRU H 13 " " FRU K 2 " - " FRU K 7 " ALPHA2-6 " FRU C 1 " - " FRU C 2 " " FRU C 2 " - " FRU C 3 " " FRU C 3 " - " FRU C 4 " " FRU C 4 " - " FRU C 5 " " FRU C 5 " - " FRU C 6 " " FRU D 1 " - " FRU D 2 " " FRU D 2 " - " FRU D 3 " " FRU D 3 " - " FRU D 4 " " FRU F 1 " - " FRU F 2 " " FRU F 2 " - " FRU F 3 " " FRU F 3 " - " FRU F 4 " " FRU F 4 " - " FRU F 5 " " FRU H 1 " - " FRU H 2 " " FRU H 2 " - " FRU H 3 " " FRU H 3 " - " FRU H 4 " " FRU H 4 " - " FRU H 5 " " FRU H 5 " - " FRU H 6 " " FRU H 6 " - " FRU H 7 " " FRU H 7 " - " FRU H 8 " " FRU H 8 " - " FRU H 9 " " FRU H 9 " - " FRU H 10 " " FRU H 10 " - " FRU H 11 " " FRU H 11 " - " FRU H 12 " " FRU K 1 " - " FRU K 2 " " FRU K 2 " - " FRU K 3 " " FRU K 3 " - " FRU K 4 " " FRU K 4 " - " FRU K 5 " " FRU K 5 " - " FRU K 6 " " FRU L 1 " - " FRU L 2 " " FRU L 2 " - " FRU L 3 " " FRU L 3 " - " FRU L 4 " " FRU N 1 " - " FRU N 2 " " FRU N 2 " - " FRU N 3 " " FRU N 3 " - " FRU N 4 " " FRU N 4 " - " FRU N 5 " Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.6 seconds 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8152 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 57 sheets defined 21.6% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'E' and resid 159 through 162 Processing helix chain 'E' and resid 254 through 261 Processing helix chain 'E' and resid 303 through 307 removed outlier: 3.738A pdb=" N ASP E 307 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 347 removed outlier: 4.020A pdb=" N TYR E 347 " --> pdb=" O ILE E 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 212 Processing helix chain 'G' and resid 220 through 226 Processing helix chain 'G' and resid 229 through 233 Processing helix chain 'G' and resid 251 through 268 removed outlier: 4.534A pdb=" N GLU G 259 " --> pdb=" O LYS G 255 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS G 260 " --> pdb=" O ALA G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 285 removed outlier: 4.036A pdb=" N ASN G 283 " --> pdb=" O PHE G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 373 Processing helix chain 'G' and resid 422 through 438 removed outlier: 3.900A pdb=" N GLU G 426 " --> pdb=" O HIS G 422 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 162 Processing helix chain 'M' and resid 254 through 261 Processing helix chain 'M' and resid 303 through 307 removed outlier: 3.738A pdb=" N ASP M 307 " --> pdb=" O ALA M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 340 through 347 removed outlier: 4.021A pdb=" N TYR M 347 " --> pdb=" O ILE M 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 removed outlier: 3.933A pdb=" N ALA B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 39 removed outlier: 4.478A pdb=" N TRP B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.816A pdb=" N VAL B 53 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG B 54 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 77 Processing helix chain 'B' and resid 84 through 110 removed outlier: 3.826A pdb=" N GLN B 110 " --> pdb=" O GLN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 141 Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.857A pdb=" N ASN B 158 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 185 removed outlier: 3.878A pdb=" N ASP B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 212 Processing helix chain 'B' and resid 226 through 238 Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.087A pdb=" N MET B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.533A pdb=" N GLU B 262 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 292 removed outlier: 4.382A pdb=" N LEU B 290 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 407 through 422 Processing helix chain 'B' and resid 425 through 443 Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 469 through 485 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 500 through 513 Processing helix chain 'B' and resid 517 through 521 removed outlier: 4.422A pdb=" N ASN B 521 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 542 Processing helix chain 'A' and resid 105 through 112 removed outlier: 3.668A pdb=" N GLN A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.907A pdb=" N GLU A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.385A pdb=" N ALA A 256 " --> pdb=" O ASN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 409 through 418 Processing helix chain 'A' and resid 602 through 608 removed outlier: 5.724A pdb=" N ASN A 605 " --> pdb=" O THR A 602 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE A 606 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 608 " --> pdb=" O ASN A 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 602 through 608' Processing helix chain 'A' and resid 779 through 786 Processing helix chain 'A' and resid 815 through 822 Processing helix chain 'A' and resid 888 through 895 removed outlier: 3.869A pdb=" N LYS A 892 " --> pdb=" O SER A 888 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS A 893 " --> pdb=" O ASP A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 914 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'J' and resid 15 through 20 removed outlier: 3.933A pdb=" N ALA J 20 " --> pdb=" O GLY J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 23 No H-bonds generated for 'chain 'J' and resid 21 through 23' Processing helix chain 'J' and resid 24 through 39 removed outlier: 4.477A pdb=" N TRP J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA J 37 " --> pdb=" O TYR J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 55 removed outlier: 3.816A pdb=" N VAL J 53 " --> pdb=" O ASN J 50 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG J 54 " --> pdb=" O TYR J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 77 Processing helix chain 'J' and resid 84 through 110 removed outlier: 3.825A pdb=" N GLN J 110 " --> pdb=" O GLN J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 141 Processing helix chain 'J' and resid 153 through 160 removed outlier: 3.856A pdb=" N ASN J 158 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 185 removed outlier: 3.878A pdb=" N ASP J 177 " --> pdb=" O LYS J 173 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE J 178 " --> pdb=" O ILE J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 212 Processing helix chain 'J' and resid 226 through 238 Processing helix chain 'J' and resid 238 through 246 removed outlier: 4.088A pdb=" N MET J 242 " --> pdb=" O ASP J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 257 Processing helix chain 'J' and resid 258 through 262 removed outlier: 3.533A pdb=" N GLU J 262 " --> pdb=" O PRO J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 292 removed outlier: 4.381A pdb=" N LEU J 290 " --> pdb=" O GLY J 287 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR J 292 " --> pdb=" O GLY J 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 297 Processing helix chain 'J' and resid 305 through 313 Processing helix chain 'J' and resid 340 through 344 Processing helix chain 'J' and resid 407 through 422 Processing helix chain 'J' and resid 425 through 443 Processing helix chain 'J' and resid 449 through 455 Processing helix chain 'J' and resid 469 through 485 Processing helix chain 'J' and resid 490 through 499 Processing helix chain 'J' and resid 500 through 513 Processing helix chain 'J' and resid 517 through 521 removed outlier: 4.423A pdb=" N ASN J 521 " --> pdb=" O ILE J 518 " (cutoff:3.500A) Processing helix chain 'J' and resid 535 through 542 Processing helix chain 'I' and resid 105 through 112 removed outlier: 3.668A pdb=" N GLN I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 121 Processing helix chain 'I' and resid 167 through 171 removed outlier: 3.906A pdb=" N GLU I 170 " --> pdb=" O GLY I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 190 through 192 No H-bonds generated for 'chain 'I' and resid 190 through 192' Processing helix chain 'I' and resid 233 through 249 Processing helix chain 'I' and resid 251 through 256 removed outlier: 4.385A pdb=" N ALA I 256 " --> pdb=" O ASN I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 300 Processing helix chain 'I' and resid 376 through 384 Processing helix chain 'I' and resid 409 through 418 Processing helix chain 'I' and resid 602 through 608 removed outlier: 5.723A pdb=" N ASN I 605 " --> pdb=" O THR I 602 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE I 606 " --> pdb=" O GLN I 603 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET I 607 " --> pdb=" O GLU I 604 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS I 608 " --> pdb=" O ASN I 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 602 through 608' Processing helix chain 'I' and resid 779 through 786 Processing helix chain 'I' and resid 815 through 822 Processing helix chain 'I' and resid 888 through 895 removed outlier: 3.869A pdb=" N LYS I 892 " --> pdb=" O SER I 888 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS I 893 " --> pdb=" O ASP I 889 " (cutoff:3.500A) Processing helix chain 'I' and resid 908 through 914 Processing helix chain 'I' and resid 939 through 941 No H-bonds generated for 'chain 'I' and resid 939 through 941' Processing helix chain 'I' and resid 961 through 968 Processing sheet with id=AA1, first strand: chain 'E' and resid 39 through 44 removed outlier: 5.539A pdb=" N VAL E 40 " --> pdb=" O ASP E 61 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP E 61 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ALA E 42 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU E 59 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP E 53 " --> pdb=" O ASP E 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 39 through 44 removed outlier: 5.539A pdb=" N VAL E 40 " --> pdb=" O ASP E 61 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP E 61 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ALA E 42 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU E 59 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE E 73 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY E 88 " --> pdb=" O GLY E 75 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA E 77 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER E 86 " --> pdb=" O ALA E 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AA4, first strand: chain 'E' and resid 107 through 111 removed outlier: 3.634A pdb=" N VAL E 137 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 168 through 175 removed outlier: 7.145A pdb=" N PHE E 168 " --> pdb=" O ARG E 188 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ARG E 188 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ASP E 170 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA E 186 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLY E 193 " --> pdb=" O MET E 213 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N MET E 213 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE E 195 " --> pdb=" O THR E 211 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N THR E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU E 197 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 221 through 229 removed outlier: 6.532A pdb=" N ILE E 236 " --> pdb=" O PRO E 224 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL E 226 " --> pdb=" O TYR E 234 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR E 234 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS E 228 " --> pdb=" O TRP E 232 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 283 through 289 removed outlier: 6.072A pdb=" N ALA E 284 " --> pdb=" O TRP E 299 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP E 299 " --> pdb=" O ALA E 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ARG E 294 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 349 through 351 removed outlier: 4.241A pdb=" N VAL E 500 " --> pdb=" O GLN E 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 349 through 351 removed outlier: 4.241A pdb=" N VAL E 500 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL E 498 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER E 389 " --> pdb=" O VAL E 498 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL E 500 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS E 387 " --> pdb=" O VAL E 500 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR E 502 " --> pdb=" O HIS E 385 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N HIS E 385 " --> pdb=" O THR E 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 357 through 358 removed outlier: 3.543A pdb=" N ALA E 357 " --> pdb=" O ILE E 378 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE E 378 " --> pdb=" O ALA E 357 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TRP E 484 " --> pdb=" O PHE E 379 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE E 401 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA E 426 " --> pdb=" O ASP E 440 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASP E 440 " --> pdb=" O ALA E 426 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE E 428 " --> pdb=" O LEU E 438 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 27 through 30 removed outlier: 6.152A pdb=" N ILE T 36 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LYS T 94 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL T 38 " --> pdb=" O LYS T 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 27 through 30 removed outlier: 6.152A pdb=" N ILE T 36 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LYS T 94 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL T 38 " --> pdb=" O LYS T 94 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU I 273 " --> pdb=" O GLY I 264 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY I 264 " --> pdb=" O LEU I 273 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 49 through 50 Processing sheet with id=AB5, first strand: chain 'G' and resid 61 through 62 removed outlier: 4.622A pdb=" N GLY G 39 " --> pdb=" O ALA G 26 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA G 26 " --> pdb=" O GLY G 39 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE G 20 " --> pdb=" O GLY G 27 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL G 29 " --> pdb=" O ASN G 18 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ASN G 18 " --> pdb=" O VAL G 29 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASN G 55 " --> pdb=" O ASN G 18 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE G 20 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU G 53 " --> pdb=" O ILE G 20 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU G 22 " --> pdb=" O VAL G 51 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL G 51 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 61 through 62 removed outlier: 5.272A pdb=" N LEU A 273 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY A 264 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 100 through 104 removed outlier: 3.539A pdb=" N LEU G 133 " --> pdb=" O GLN G 153 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY G 135 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER G 151 " --> pdb=" O GLY G 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 112 through 114 removed outlier: 6.229A pdb=" N ILE G 120 " --> pdb=" O THR G 175 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 215 through 219 removed outlier: 6.367A pdb=" N THR G 184 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE G 218 " --> pdb=" O THR G 184 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE G 186 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE G 236 " --> pdb=" O LEU G 272 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N THR G 274 " --> pdb=" O ILE G 236 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP G 238 " --> pdb=" O THR G 274 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU G 271 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE G 402 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU G 273 " --> pdb=" O ILE G 402 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 215 through 219 removed outlier: 6.367A pdb=" N THR G 184 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE G 218 " --> pdb=" O THR G 184 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE G 186 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE G 236 " --> pdb=" O LEU G 272 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N THR G 274 " --> pdb=" O ILE G 236 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP G 238 " --> pdb=" O THR G 274 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU G 271 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE G 402 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU G 273 " --> pdb=" O ILE G 402 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL G 385 " --> pdb=" O HIS G 379 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N HIS G 379 " --> pdb=" O VAL G 385 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE G 387 " --> pdb=" O LEU G 377 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 306 through 307 removed outlier: 4.452A pdb=" N THR G 307 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR G 344 " --> pdb=" O THR G 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 312 through 314 Processing sheet with id=AC4, first strand: chain 'M' and resid 39 through 44 removed outlier: 5.539A pdb=" N VAL M 40 " --> pdb=" O ASP M 61 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP M 61 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA M 42 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU M 59 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP M 53 " --> pdb=" O ASP M 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 39 through 44 removed outlier: 5.539A pdb=" N VAL M 40 " --> pdb=" O ASP M 61 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP M 61 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA M 42 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU M 59 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE M 73 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY M 88 " --> pdb=" O GLY M 75 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA M 77 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER M 86 " --> pdb=" O ALA M 77 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 102 through 103 Processing sheet with id=AC7, first strand: chain 'M' and resid 107 through 111 removed outlier: 3.635A pdb=" N VAL M 137 " --> pdb=" O LEU M 156 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 168 through 175 removed outlier: 7.146A pdb=" N PHE M 168 " --> pdb=" O ARG M 188 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ARG M 188 " --> pdb=" O PHE M 168 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ASP M 170 " --> pdb=" O ALA M 186 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA M 186 " --> pdb=" O ASP M 170 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLY M 193 " --> pdb=" O MET M 213 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N MET M 213 " --> pdb=" O GLY M 193 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE M 195 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N THR M 211 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU M 197 " --> pdb=" O ALA M 209 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 221 through 229 removed outlier: 6.532A pdb=" N ILE M 236 " --> pdb=" O PRO M 224 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL M 226 " --> pdb=" O TYR M 234 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR M 234 " --> pdb=" O VAL M 226 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LYS M 228 " --> pdb=" O TRP M 232 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP M 232 " --> pdb=" O LYS M 228 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 283 through 289 removed outlier: 6.072A pdb=" N ALA M 284 " --> pdb=" O TRP M 299 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP M 299 " --> pdb=" O ALA M 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ARG M 294 " --> pdb=" O LEU M 327 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 349 through 351 removed outlier: 4.241A pdb=" N VAL M 500 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 349 through 351 removed outlier: 4.241A pdb=" N VAL M 500 " --> pdb=" O GLN M 351 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL M 498 " --> pdb=" O SER M 389 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER M 389 " --> pdb=" O VAL M 498 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL M 500 " --> pdb=" O LYS M 387 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS M 387 " --> pdb=" O VAL M 500 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR M 502 " --> pdb=" O HIS M 385 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N HIS M 385 " --> pdb=" O THR M 502 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 357 through 358 removed outlier: 3.541A pdb=" N ALA M 357 " --> pdb=" O ILE M 378 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE M 378 " --> pdb=" O ALA M 357 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TRP M 484 " --> pdb=" O PHE M 379 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE M 401 " --> pdb=" O VAL M 419 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA M 426 " --> pdb=" O ASP M 440 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASP M 440 " --> pdb=" O ALA M 426 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE M 428 " --> pdb=" O LEU M 438 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 213 through 214 removed outlier: 4.029A pdb=" N GLY B 224 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 267 through 271 removed outlier: 7.433A pdb=" N SER B 267 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ARG B 406 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP B 269 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 345 through 346 Processing sheet with id=AD8, first strand: chain 'B' and resid 390 through 392 Processing sheet with id=AD9, first strand: chain 'A' and resid 101 through 104 removed outlier: 4.135A pdb=" N ILE A 179 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR A 203 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 179 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 201 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL A 181 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 199 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 128 through 131 Processing sheet with id=AE2, first strand: chain 'A' and resid 984 through 986 removed outlier: 3.640A pdb=" N VAL A 304 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG A 421 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 457 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N THR A 591 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLY A 626 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA A 740 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN A 879 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEU A 951 " --> pdb=" O GLN A 879 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL A 881 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU A 949 " --> pdb=" O VAL A 881 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AE4, first strand: chain 'A' and resid 638 through 640 removed outlier: 6.632A pdb=" N ILE A 638 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AE6, first strand: chain 'A' and resid 804 through 806 removed outlier: 6.709A pdb=" N GLN A 804 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.939A pdb=" N ARG A 834 " --> pdb=" O ASP A 810 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AE9, first strand: chain 'J' and resid 213 through 214 removed outlier: 4.030A pdb=" N GLY J 224 " --> pdb=" O ARG J 214 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 267 through 271 removed outlier: 7.433A pdb=" N SER J 267 " --> pdb=" O ARG J 406 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ARG J 406 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP J 269 " --> pdb=" O VAL J 404 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 345 through 346 Processing sheet with id=AF3, first strand: chain 'J' and resid 390 through 392 Processing sheet with id=AF4, first strand: chain 'I' and resid 101 through 104 removed outlier: 4.137A pdb=" N ILE I 179 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR I 203 " --> pdb=" O GLU I 177 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE I 179 " --> pdb=" O ILE I 201 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE I 201 " --> pdb=" O ILE I 179 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL I 181 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL I 199 " --> pdb=" O VAL I 181 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 128 through 131 Processing sheet with id=AF6, first strand: chain 'I' and resid 984 through 986 removed outlier: 3.642A pdb=" N VAL I 304 " --> pdb=" O LEU I 331 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG I 421 " --> pdb=" O ARG I 457 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG I 457 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N THR I 591 " --> pdb=" O GLY I 626 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLY I 626 " --> pdb=" O THR I 591 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA I 740 " --> pdb=" O LEU I 776 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN I 879 " --> pdb=" O LEU I 951 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU I 951 " --> pdb=" O GLN I 879 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL I 881 " --> pdb=" O LEU I 949 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU I 949 " --> pdb=" O VAL I 881 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 464 through 465 Processing sheet with id=AF8, first strand: chain 'I' and resid 638 through 640 removed outlier: 6.633A pdb=" N ILE I 638 " --> pdb=" O ASN I 676 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 719 through 722 Processing sheet with id=AG1, first strand: chain 'I' and resid 804 through 806 removed outlier: 6.709A pdb=" N GLN I 804 " --> pdb=" O ILE I 852 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 809 through 812 removed outlier: 4.940A pdb=" N ARG I 834 " --> pdb=" O ASP I 810 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 885 through 887 1557 hydrogen bonds defined for protein. 4227 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: 10.05 Time building geometry restraints manager: 4.46 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: 11716 1.34 - 1.46: 8739 1.46 - 1.58: 15974 1.58 - 1.70: 135 1.70 - 1.81: 240 Bond restraints: 36804 Sorted by residual: bond pdb=" C2 FRU F 4 " pdb=" O5 FRU F 4 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU H 6 " pdb=" O5 FRU H 6 " ideal model delta sigma weight residual 1.412 1.642 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C2 FRU H 2 " pdb=" O5 FRU H 2 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C2 FRU K 4 " pdb=" O5 FRU K 4 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C2 FRU N 4 " pdb=" O5 FRU N 4 " ideal model delta sigma weight residual 1.412 1.641 -0.229 2.00e-02 2.50e+03 1.31e+02 ... (remaining 36799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 49773 4.34 - 8.68: 179 8.68 - 13.03: 2 13.03 - 17.37: 0 17.37 - 21.71: 2 Bond angle restraints: 49956 Sorted by residual: angle pdb=" C1 FRU H 13 " pdb=" C2 FRU H 13 " pdb=" C3 FRU H 13 " ideal model delta sigma weight residual 113.36 91.65 21.71 3.00e+00 1.11e-01 5.24e+01 angle pdb=" C1 FRU H 13 " pdb=" C2 FRU H 13 " pdb=" O5 FRU H 13 " ideal model delta sigma weight residual 109.29 87.84 21.45 3.00e+00 1.11e-01 5.11e+01 angle pdb=" C2 FRU H 5 " pdb=" O5 FRU H 5 " pdb=" C5 FRU H 5 " ideal model delta sigma weight residual 112.00 100.68 11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C3 FRU H 13 " pdb=" C2 FRU H 13 " pdb=" O5 FRU H 13 " ideal model delta sigma weight residual 104.71 115.26 -10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C ASP T 45 " pdb=" N ILE T 46 " pdb=" CA ILE T 46 " ideal model delta sigma weight residual 121.97 127.74 -5.77 1.80e+00 3.09e-01 1.03e+01 ... (remaining 49951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 20934 26.44 - 52.89: 1004 52.89 - 79.33: 183 79.33 - 105.77: 25 105.77 - 132.21: 3 Dihedral angle restraints: 22149 sinusoidal: 9254 harmonic: 12895 Sorted by residual: dihedral pdb=" C1 FRU H 13 " pdb=" C2 FRU H 13 " pdb=" O5 FRU H 13 " pdb=" C5 FRU H 13 " ideal model delta sinusoidal sigma weight residual 127.64 -100.15 -132.21 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C1 FRU H 13 " pdb=" C2 FRU H 13 " pdb=" C3 FRU H 13 " pdb=" C4 FRU H 13 " ideal model delta sinusoidal sigma weight residual 213.28 83.35 129.93 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C1 FRU H 13 " pdb=" C2 FRU H 13 " pdb=" C3 FRU H 13 " pdb=" O3 FRU H 13 " ideal model delta sinusoidal sigma weight residual 89.04 -38.08 127.12 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 22146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.178: 5348 1.178 - 2.355: 0 2.355 - 3.533: 0 3.533 - 4.710: 0 4.710 - 5.888: 1 Chirality restraints: 5349 Sorted by residual: chirality pdb=" C2 FRU H 13 " pdb=" O1 FRU H 6 " pdb=" C1 FRU H 13 " pdb=" O5 FRU H 13 " both_signs ideal model delta sigma weight residual False 2.60 -3.29 5.89 2.00e-02 2.50e+03 8.67e+04 chirality pdb=" C2 FRU H 6 " pdb=" O6 FRU H 5 " pdb=" C1 FRU H 6 " pdb=" O5 FRU H 6 " both_signs ideal model delta sigma weight residual False 2.60 2.75 -0.15 2.00e-02 2.50e+03 5.98e+01 chirality pdb=" C2 FRU K 7 " pdb=" O1 FRU K 2 " pdb=" C1 FRU K 7 " pdb=" O5 FRU K 7 " both_signs ideal model delta sigma weight residual False 2.60 2.71 -0.11 2.00e-02 2.50e+03 3.18e+01 ... (remaining 5346 not shown) Planarity restraints: 6448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN M 111 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO M 112 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO M 112 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO M 112 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 111 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO E 112 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 112 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 112 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 359 " 0.013 2.00e-02 2.50e+03 9.54e-03 2.28e+00 pdb=" CG TRP G 359 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP G 359 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP G 359 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 359 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 359 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 359 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 359 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 359 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 359 " 0.000 2.00e-02 2.50e+03 ... (remaining 6445 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 353 2.55 - 3.13: 27605 3.13 - 3.72: 56799 3.72 - 4.31: 83109 4.31 - 4.90: 140797 Nonbonded interactions: 308663 Sorted by model distance: nonbonded pdb=" OD1 ASN A 841 " pdb="MG MG A1101 " model vdw 1.958 2.170 nonbonded pdb=" OD1 ASN I 841 " pdb="MG MG I1101 " model vdw 1.959 2.170 nonbonded pdb=" OD2 ASP A 848 " pdb="MG MG A1101 " model vdw 1.972 2.170 nonbonded pdb=" OD2 ASP I 848 " pdb="MG MG I1101 " model vdw 1.972 2.170 nonbonded pdb=" OD1 ASN A 664 " pdb="MG MG B 601 " model vdw 1.998 2.170 ... (remaining 308658 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } 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: 2.280 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 37.220 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.230 36844 Z= 0.630 Angle : 0.636 24.767 50074 Z= 0.289 Chirality : 0.092 5.888 5349 Planarity : 0.003 0.055 6448 Dihedral : 15.445 132.215 13991 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.13), residues: 4456 helix: 1.75 (0.19), residues: 806 sheet: 0.78 (0.14), residues: 1298 loop : -0.26 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 100 TYR 0.016 0.001 TYR A 350 PHE 0.011 0.001 PHE I 758 TRP 0.026 0.001 TRP G 359 HIS 0.006 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.01238 (36804) covalent geometry : angle 0.60033 (49956) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.59301 ( 4) hydrogen bonds : bond 0.10586 ( 1510) hydrogen bonds : angle 5.36397 ( 4227) glycosidic custom : bond 0.03950 ( 3) glycosidic custom : angle 9.05054 ( 9) link_ALPHA2-6 : bond 0.08291 ( 35) link_ALPHA2-6 : angle 3.77116 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 216 MET cc_start: 0.7665 (tpt) cc_final: 0.7188 (tpt) REVERT: T 31 TYR cc_start: 0.8616 (m-80) cc_final: 0.8155 (m-80) REVERT: M 44 MET cc_start: 0.8892 (mtt) cc_final: 0.8647 (mtp) REVERT: M 216 MET cc_start: 0.6552 (tpt) cc_final: 0.6073 (tpt) REVERT: J 7 ARG cc_start: 0.7758 (ttm170) cc_final: 0.7201 (ttt90) REVERT: I 506 MET cc_start: 0.8753 (ttm) cc_final: 0.8468 (ttp) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2646 time to fit residues: 98.6434 Evaluate side-chains 151 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 ASN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 ASN ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN J 96 GLN I 362 HIS I 512 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.074713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.055151 restraints weight = 90632.860| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.21 r_work: 0.2775 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 36844 Z= 0.155 Angle : 0.560 27.596 50074 Z= 0.279 Chirality : 0.044 0.308 5349 Planarity : 0.003 0.039 6448 Dihedral : 9.872 151.696 5850 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.48 % Favored : 96.45 % Rotamer: Outliers : 0.32 % Allowed : 3.35 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.13), residues: 4456 helix: 1.71 (0.19), residues: 794 sheet: 0.73 (0.14), residues: 1293 loop : -0.27 (0.13), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 475 TYR 0.013 0.001 TYR J 463 PHE 0.010 0.001 PHE B 301 TRP 0.019 0.001 TRP G 359 HIS 0.004 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00340 (36804) covalent geometry : angle 0.54147 (49956) SS BOND : bond 0.00179 ( 2) SS BOND : angle 0.50157 ( 4) hydrogen bonds : bond 0.03527 ( 1510) hydrogen bonds : angle 4.72397 ( 4227) glycosidic custom : bond 0.03066 ( 3) glycosidic custom : angle 4.56559 ( 9) link_ALPHA2-6 : bond 0.01267 ( 35) link_ALPHA2-6 : angle 2.87778 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 216 MET cc_start: 0.7932 (tpt) cc_final: 0.7575 (tpt) REVERT: T 30 ASP cc_start: 0.8220 (t0) cc_final: 0.7954 (t70) REVERT: T 31 TYR cc_start: 0.8512 (m-80) cc_final: 0.8231 (m-80) REVERT: T 96 ASP cc_start: 0.6324 (m-30) cc_final: 0.6003 (m-30) REVERT: M 216 MET cc_start: 0.6415 (tpt) cc_final: 0.6062 (tpt) REVERT: M 244 MET cc_start: 0.8596 (tpp) cc_final: 0.7934 (tpp) REVERT: M 362 MET cc_start: 0.8012 (ppp) cc_final: 0.7715 (ppp) REVERT: J 7 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7463 (ttt90) REVERT: I 506 MET cc_start: 0.8945 (ttm) cc_final: 0.8662 (ttp) outliers start: 12 outliers final: 9 residues processed: 164 average time/residue: 0.2376 time to fit residues: 64.8794 Evaluate side-chains 157 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 430 ASP Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 11 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 390 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 386 optimal weight: 7.9990 chunk 276 optimal weight: 6.9990 chunk 208 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS A 366 ASN A 816 GLN I 366 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.073585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.053919 restraints weight = 90874.980| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.20 r_work: 0.2741 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 36844 Z= 0.164 Angle : 0.531 23.745 50074 Z= 0.269 Chirality : 0.043 0.150 5349 Planarity : 0.003 0.038 6448 Dihedral : 7.694 137.767 5850 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 0.50 % Allowed : 4.70 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.13), residues: 4456 helix: 1.49 (0.19), residues: 806 sheet: 0.60 (0.14), residues: 1345 loop : -0.28 (0.13), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 100 TYR 0.016 0.001 TYR I 350 PHE 0.012 0.001 PHE J 342 TRP 0.017 0.001 TRP G 359 HIS 0.003 0.001 HIS J 132 Details of bonding type rmsd covalent geometry : bond 0.00362 (36804) covalent geometry : angle 0.51207 (49956) SS BOND : bond 0.00571 ( 2) SS BOND : angle 0.60201 ( 4) hydrogen bonds : bond 0.03560 ( 1510) hydrogen bonds : angle 4.62035 ( 4227) glycosidic custom : bond 0.04482 ( 3) glycosidic custom : angle 4.06511 ( 9) link_ALPHA2-6 : bond 0.01212 ( 35) link_ALPHA2-6 : angle 2.88306 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: E 215 MET cc_start: 0.8004 (mtt) cc_final: 0.7654 (mtt) REVERT: E 216 MET cc_start: 0.7932 (tpt) cc_final: 0.7550 (tpt) REVERT: T 30 ASP cc_start: 0.8233 (t0) cc_final: 0.7959 (t70) REVERT: T 87 MET cc_start: 0.8737 (tpp) cc_final: 0.8398 (ttt) REVERT: M 216 MET cc_start: 0.6501 (tpt) cc_final: 0.6097 (tpt) REVERT: M 244 MET cc_start: 0.8601 (tpp) cc_final: 0.7943 (tpp) REVERT: M 362 MET cc_start: 0.8090 (ppp) cc_final: 0.7834 (ppp) REVERT: B 229 ASP cc_start: 0.8877 (m-30) cc_final: 0.8542 (m-30) REVERT: A 970 MET cc_start: 0.7191 (ptp) cc_final: 0.6960 (ptp) REVERT: J 7 ARG cc_start: 0.8184 (ttm170) cc_final: 0.7547 (ttt90) REVERT: I 506 MET cc_start: 0.8887 (ttm) cc_final: 0.8620 (ttp) REVERT: I 608 LYS cc_start: 0.8685 (mmmt) cc_final: 0.8392 (tppt) REVERT: I 970 MET cc_start: 0.7982 (ptp) cc_final: 0.7500 (ptp) outliers start: 19 outliers final: 12 residues processed: 165 average time/residue: 0.2347 time to fit residues: 64.8654 Evaluate side-chains 157 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 341 ASP Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 383 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 438 optimal weight: 0.3980 chunk 290 optimal weight: 6.9990 chunk 58 optimal weight: 0.0770 chunk 78 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 274 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.2944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 HIS G 300 ASN ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN A 211 GLN I 816 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.071584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.051588 restraints weight = 90442.310| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.17 r_work: 0.2674 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 36844 Z= 0.244 Angle : 0.582 23.772 50074 Z= 0.297 Chirality : 0.044 0.145 5349 Planarity : 0.004 0.039 6448 Dihedral : 7.354 136.672 5850 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.96 % Rotamer: Outliers : 0.74 % Allowed : 6.08 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.13), residues: 4456 helix: 1.24 (0.19), residues: 804 sheet: 0.45 (0.14), residues: 1353 loop : -0.40 (0.13), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 100 TYR 0.027 0.001 TYR B 203 PHE 0.016 0.002 PHE J 71 TRP 0.016 0.001 TRP G 359 HIS 0.006 0.001 HIS J 132 Details of bonding type rmsd covalent geometry : bond 0.00556 (36804) covalent geometry : angle 0.56375 (49956) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.85000 ( 4) hydrogen bonds : bond 0.04092 ( 1510) hydrogen bonds : angle 4.84620 ( 4227) glycosidic custom : bond 0.03892 ( 3) glycosidic custom : angle 4.15331 ( 9) link_ALPHA2-6 : bond 0.01115 ( 35) link_ALPHA2-6 : angle 2.94632 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.357 Fit side-chains REVERT: T 19 SER cc_start: 0.8376 (t) cc_final: 0.7773 (t) REVERT: T 30 ASP cc_start: 0.8285 (t0) cc_final: 0.7993 (t70) REVERT: T 53 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7990 (tm-30) REVERT: T 54 MET cc_start: 0.8221 (tpp) cc_final: 0.8005 (tpp) REVERT: T 87 MET cc_start: 0.8868 (tpp) cc_final: 0.8440 (ttt) REVERT: T 89 TYR cc_start: 0.8817 (m-80) cc_final: 0.8289 (m-80) REVERT: M 216 MET cc_start: 0.6568 (tpt) cc_final: 0.6186 (tpt) REVERT: B 229 ASP cc_start: 0.8893 (m-30) cc_final: 0.8588 (m-30) REVERT: A 970 MET cc_start: 0.7249 (ptp) cc_final: 0.7036 (ptp) REVERT: J 7 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7623 (ttt90) REVERT: I 121 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9194 (pp) REVERT: I 346 MET cc_start: 0.9172 (mtm) cc_final: 0.8904 (mtt) REVERT: I 506 MET cc_start: 0.8918 (ttm) cc_final: 0.8641 (ttp) REVERT: I 970 MET cc_start: 0.7956 (ptp) cc_final: 0.7596 (ptp) outliers start: 28 outliers final: 19 residues processed: 173 average time/residue: 0.2329 time to fit residues: 67.5541 Evaluate side-chains 164 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 PHE Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 33 ASN Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 73 SER Chi-restraints excluded: chain T residue 77 SER Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 341 ASP Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 12 optimal weight: 8.9990 chunk 372 optimal weight: 6.9990 chunk 419 optimal weight: 4.9990 chunk 357 optimal weight: 0.8980 chunk 317 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 382 optimal weight: 4.9990 chunk 142 optimal weight: 20.0000 chunk 364 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 467 ASN ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.071474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.051527 restraints weight = 90276.118| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.18 r_work: 0.2671 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 36844 Z= 0.229 Angle : 0.558 23.937 50074 Z= 0.286 Chirality : 0.044 0.147 5349 Planarity : 0.003 0.037 6448 Dihedral : 7.191 134.614 5850 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.54 % Rotamer: Outliers : 0.96 % Allowed : 7.20 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.13), residues: 4456 helix: 1.20 (0.19), residues: 802 sheet: 0.36 (0.14), residues: 1353 loop : -0.45 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 100 TYR 0.025 0.001 TYR B 203 PHE 0.018 0.001 PHE J 342 TRP 0.015 0.001 TRP G 359 HIS 0.005 0.001 HIS J 132 Details of bonding type rmsd covalent geometry : bond 0.00520 (36804) covalent geometry : angle 0.53956 (49956) SS BOND : bond 0.00180 ( 2) SS BOND : angle 0.73666 ( 4) hydrogen bonds : bond 0.03929 ( 1510) hydrogen bonds : angle 4.83421 ( 4227) glycosidic custom : bond 0.04204 ( 3) glycosidic custom : angle 3.98534 ( 9) link_ALPHA2-6 : bond 0.01153 ( 35) link_ALPHA2-6 : angle 2.90925 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.388 Fit side-chains REVERT: T 19 SER cc_start: 0.8217 (t) cc_final: 0.7953 (t) REVERT: T 30 ASP cc_start: 0.8346 (t0) cc_final: 0.8062 (t70) REVERT: T 53 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7902 (tm-30) REVERT: T 87 MET cc_start: 0.8862 (tpp) cc_final: 0.8572 (ttt) REVERT: M 216 MET cc_start: 0.6624 (tpt) cc_final: 0.6197 (tpt) REVERT: B 229 ASP cc_start: 0.8901 (m-30) cc_final: 0.8607 (m-30) REVERT: J 7 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7617 (ttt90) REVERT: I 346 MET cc_start: 0.9180 (mtm) cc_final: 0.8928 (mtt) REVERT: I 506 MET cc_start: 0.8986 (ttm) cc_final: 0.8707 (ttp) REVERT: I 970 MET cc_start: 0.7975 (ptp) cc_final: 0.7600 (ptp) outliers start: 36 outliers final: 25 residues processed: 177 average time/residue: 0.2204 time to fit residues: 65.0754 Evaluate side-chains 169 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 20 ILE Chi-restraints excluded: chain T residue 33 ASN Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 341 ASP Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 212 optimal weight: 0.3980 chunk 204 optimal weight: 7.9990 chunk 301 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 427 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 405 optimal weight: 8.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.071270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.051341 restraints weight = 90123.134| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.17 r_work: 0.2667 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 36844 Z= 0.222 Angle : 0.556 23.918 50074 Z= 0.285 Chirality : 0.044 0.149 5349 Planarity : 0.003 0.038 6448 Dihedral : 7.038 133.481 5850 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 1.01 % Allowed : 8.10 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 4456 helix: 1.15 (0.19), residues: 804 sheet: 0.33 (0.14), residues: 1353 loop : -0.47 (0.13), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 100 TYR 0.025 0.001 TYR B 203 PHE 0.016 0.001 PHE J 342 TRP 0.014 0.001 TRP G 359 HIS 0.004 0.001 HIS J 132 Details of bonding type rmsd covalent geometry : bond 0.00503 (36804) covalent geometry : angle 0.53779 (49956) SS BOND : bond 0.00155 ( 2) SS BOND : angle 0.76571 ( 4) hydrogen bonds : bond 0.03915 ( 1510) hydrogen bonds : angle 4.82680 ( 4227) glycosidic custom : bond 0.04268 ( 3) glycosidic custom : angle 3.89534 ( 9) link_ALPHA2-6 : bond 0.01154 ( 35) link_ALPHA2-6 : angle 2.90911 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 1.416 Fit side-chains REVERT: T 30 ASP cc_start: 0.8380 (t0) cc_final: 0.8088 (t70) REVERT: T 87 MET cc_start: 0.8885 (tpp) cc_final: 0.8585 (ttt) REVERT: T 89 TYR cc_start: 0.8895 (m-80) cc_final: 0.8333 (m-80) REVERT: M 216 MET cc_start: 0.6709 (tpt) cc_final: 0.6347 (tpt) REVERT: B 229 ASP cc_start: 0.8872 (m-30) cc_final: 0.8596 (m-30) REVERT: J 7 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7617 (ttt90) REVERT: I 346 MET cc_start: 0.9186 (mtm) cc_final: 0.8956 (mtt) REVERT: I 506 MET cc_start: 0.8971 (ttm) cc_final: 0.8686 (ttp) REVERT: I 970 MET cc_start: 0.7941 (ptp) cc_final: 0.7532 (ptp) outliers start: 38 outliers final: 26 residues processed: 177 average time/residue: 0.2141 time to fit residues: 64.4597 Evaluate side-chains 171 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 341 ASP Chi-restraints excluded: chain M residue 377 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 607 MET Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 244 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 439 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 189 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 chunk 297 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.070638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.051410 restraints weight = 90336.592| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.21 r_work: 0.2646 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 36844 Z= 0.237 Angle : 0.565 23.668 50074 Z= 0.290 Chirality : 0.044 0.151 5349 Planarity : 0.003 0.037 6448 Dihedral : 6.959 132.411 5850 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 0.93 % Allowed : 8.98 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.13), residues: 4456 helix: 1.21 (0.19), residues: 790 sheet: 0.29 (0.14), residues: 1353 loop : -0.50 (0.13), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 100 TYR 0.026 0.001 TYR B 203 PHE 0.016 0.001 PHE J 342 TRP 0.014 0.001 TRP G 359 HIS 0.004 0.001 HIS J 132 Details of bonding type rmsd covalent geometry : bond 0.00538 (36804) covalent geometry : angle 0.54730 (49956) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.76300 ( 4) hydrogen bonds : bond 0.03986 ( 1510) hydrogen bonds : angle 4.85690 ( 4227) glycosidic custom : bond 0.04167 ( 3) glycosidic custom : angle 3.94679 ( 9) link_ALPHA2-6 : bond 0.01150 ( 35) link_ALPHA2-6 : angle 2.92496 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.383 Fit side-chains REVERT: T 9 LEU cc_start: 0.7221 (mt) cc_final: 0.6875 (mt) REVERT: T 30 ASP cc_start: 0.8430 (t0) cc_final: 0.8152 (t70) REVERT: T 87 MET cc_start: 0.8792 (tpp) cc_final: 0.8564 (ttt) REVERT: T 89 TYR cc_start: 0.8934 (m-80) cc_final: 0.8429 (m-80) REVERT: M 216 MET cc_start: 0.6734 (tpt) cc_final: 0.6368 (tpt) REVERT: B 229 ASP cc_start: 0.8868 (m-30) cc_final: 0.8619 (m-30) REVERT: J 7 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7651 (ttt90) REVERT: I 346 MET cc_start: 0.9216 (mtm) cc_final: 0.9009 (mtt) REVERT: I 506 MET cc_start: 0.8933 (ttm) cc_final: 0.8666 (ttp) REVERT: I 970 MET cc_start: 0.7952 (ptp) cc_final: 0.7580 (ptp) outliers start: 35 outliers final: 27 residues processed: 177 average time/residue: 0.2209 time to fit residues: 67.1550 Evaluate side-chains 170 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 341 ASP Chi-restraints excluded: chain M residue 377 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 203 TYR Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 339 optimal weight: 0.9990 chunk 344 optimal weight: 3.9990 chunk 416 optimal weight: 7.9990 chunk 356 optimal weight: 0.9990 chunk 395 optimal weight: 1.9990 chunk 342 optimal weight: 0.7980 chunk 226 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 338 optimal weight: 0.9990 chunk 329 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.072352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.052974 restraints weight = 89151.335| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.15 r_work: 0.2693 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 36844 Z= 0.122 Angle : 0.508 23.791 50074 Z= 0.261 Chirality : 0.042 0.141 5349 Planarity : 0.003 0.036 6448 Dihedral : 6.633 132.437 5850 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 0.80 % Allowed : 9.27 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.13), residues: 4456 helix: 1.20 (0.19), residues: 816 sheet: 0.37 (0.14), residues: 1367 loop : -0.45 (0.13), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 437 TYR 0.019 0.001 TYR B 203 PHE 0.011 0.001 PHE E 472 TRP 0.015 0.001 TRP G 359 HIS 0.003 0.001 HIS I 482 Details of bonding type rmsd covalent geometry : bond 0.00259 (36804) covalent geometry : angle 0.48887 (49956) SS BOND : bond 0.00231 ( 2) SS BOND : angle 0.55145 ( 4) hydrogen bonds : bond 0.03308 ( 1510) hydrogen bonds : angle 4.60020 ( 4227) glycosidic custom : bond 0.04242 ( 3) glycosidic custom : angle 3.82561 ( 9) link_ALPHA2-6 : bond 0.01282 ( 35) link_ALPHA2-6 : angle 2.82958 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.396 Fit side-chains REVERT: T 30 ASP cc_start: 0.8448 (t0) cc_final: 0.8197 (t70) REVERT: T 53 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7868 (tm-30) REVERT: T 87 MET cc_start: 0.8734 (tpp) cc_final: 0.8415 (ttt) REVERT: T 89 TYR cc_start: 0.8683 (m-80) cc_final: 0.7895 (m-80) REVERT: M 216 MET cc_start: 0.6704 (tpt) cc_final: 0.6282 (tpt) REVERT: B 229 ASP cc_start: 0.8831 (m-30) cc_final: 0.8554 (m-30) REVERT: J 7 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7489 (ttt90) REVERT: I 346 MET cc_start: 0.9185 (mtm) cc_final: 0.8966 (mtt) REVERT: I 506 MET cc_start: 0.8945 (ttm) cc_final: 0.8712 (ttp) REVERT: I 970 MET cc_start: 0.7909 (ptp) cc_final: 0.7599 (ptp) outliers start: 30 outliers final: 27 residues processed: 174 average time/residue: 0.2215 time to fit residues: 65.2933 Evaluate side-chains 172 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 377 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 918 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 294 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 334 optimal weight: 0.7980 chunk 221 optimal weight: 0.0970 chunk 107 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 326 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.071742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.052599 restraints weight = 89418.809| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.21 r_work: 0.2676 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 36844 Z= 0.162 Angle : 0.530 23.729 50074 Z= 0.271 Chirality : 0.042 0.146 5349 Planarity : 0.003 0.036 6448 Dihedral : 6.578 132.006 5850 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.48 % Favored : 96.45 % Rotamer: Outliers : 0.88 % Allowed : 9.22 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.13), residues: 4456 helix: 1.28 (0.19), residues: 804 sheet: 0.34 (0.14), residues: 1365 loop : -0.43 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 100 TYR 0.023 0.001 TYR B 203 PHE 0.013 0.001 PHE J 342 TRP 0.013 0.001 TRP G 359 HIS 0.003 0.001 HIS J 132 Details of bonding type rmsd covalent geometry : bond 0.00361 (36804) covalent geometry : angle 0.51221 (49956) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.67520 ( 4) hydrogen bonds : bond 0.03510 ( 1510) hydrogen bonds : angle 4.63290 ( 4227) glycosidic custom : bond 0.04278 ( 3) glycosidic custom : angle 3.64625 ( 9) link_ALPHA2-6 : bond 0.01209 ( 35) link_ALPHA2-6 : angle 2.86070 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 1.525 Fit side-chains REVERT: T 9 LEU cc_start: 0.7313 (mt) cc_final: 0.6943 (mt) REVERT: T 30 ASP cc_start: 0.8430 (t0) cc_final: 0.8177 (t70) REVERT: T 53 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7743 (tm-30) REVERT: T 87 MET cc_start: 0.8740 (tpp) cc_final: 0.8429 (ttt) REVERT: T 89 TYR cc_start: 0.8783 (m-80) cc_final: 0.7977 (m-80) REVERT: M 216 MET cc_start: 0.6723 (tpt) cc_final: 0.6366 (tpt) REVERT: B 229 ASP cc_start: 0.8845 (m-30) cc_final: 0.8573 (m-30) REVERT: J 7 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7518 (ttt90) REVERT: I 346 MET cc_start: 0.9182 (mtm) cc_final: 0.8971 (mtt) REVERT: I 506 MET cc_start: 0.8931 (ttm) cc_final: 0.8693 (ttp) REVERT: I 970 MET cc_start: 0.7922 (ptp) cc_final: 0.7709 (ptm) outliers start: 33 outliers final: 28 residues processed: 172 average time/residue: 0.2257 time to fit residues: 66.0899 Evaluate side-chains 171 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 377 VAL Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 984 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 72 optimal weight: 0.0670 chunk 29 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 344 optimal weight: 5.9990 chunk 419 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 442 optimal weight: 2.9990 chunk 331 optimal weight: 0.0770 chunk 129 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.072150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.052724 restraints weight = 89391.436| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.16 r_work: 0.2687 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 36844 Z= 0.141 Angle : 0.522 23.715 50074 Z= 0.266 Chirality : 0.042 0.150 5349 Planarity : 0.003 0.036 6448 Dihedral : 6.510 132.292 5850 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 0.85 % Allowed : 9.48 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 4456 helix: 1.21 (0.19), residues: 816 sheet: 0.35 (0.14), residues: 1365 loop : -0.41 (0.13), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 95 TYR 0.019 0.001 TYR B 203 PHE 0.012 0.001 PHE J 342 TRP 0.015 0.001 TRP G 359 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00310 (36804) covalent geometry : angle 0.50400 (49956) SS BOND : bond 0.00201 ( 2) SS BOND : angle 0.63323 ( 4) hydrogen bonds : bond 0.03377 ( 1510) hydrogen bonds : angle 4.58231 ( 4227) glycosidic custom : bond 0.04216 ( 3) glycosidic custom : angle 3.52218 ( 9) link_ALPHA2-6 : bond 0.01233 ( 35) link_ALPHA2-6 : angle 2.82555 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8912 Ramachandran restraints generated. 4456 Oldfield, 0 Emsley, 4456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 1.409 Fit side-chains REVERT: T 9 LEU cc_start: 0.7330 (mt) cc_final: 0.6962 (mt) REVERT: T 30 ASP cc_start: 0.8446 (t0) cc_final: 0.8196 (t70) REVERT: T 53 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7813 (tm-30) REVERT: T 87 MET cc_start: 0.8738 (tpp) cc_final: 0.8443 (ttt) REVERT: T 89 TYR cc_start: 0.8682 (m-80) cc_final: 0.7895 (m-80) REVERT: M 216 MET cc_start: 0.6771 (tpt) cc_final: 0.6365 (tpt) REVERT: B 229 ASP cc_start: 0.8839 (m-30) cc_final: 0.8566 (m-30) REVERT: J 7 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7505 (ttt90) REVERT: I 346 MET cc_start: 0.9176 (mtm) cc_final: 0.8959 (mtt) REVERT: I 506 MET cc_start: 0.8928 (ttm) cc_final: 0.8690 (ttp) outliers start: 32 outliers final: 30 residues processed: 172 average time/residue: 0.2245 time to fit residues: 66.0080 Evaluate side-chains 173 residues out of total 3766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 434 ASP Chi-restraints excluded: chain E residue 479 MET Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 92 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 147 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 377 VAL Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 188 VAL Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain J residue 465 LEU Chi-restraints excluded: chain I residue 121 LEU Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 487 MET Chi-restraints excluded: chain I residue 498 VAL Chi-restraints excluded: chain I residue 876 MET Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 984 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 204 optimal weight: 0.5980 chunk 282 optimal weight: 10.0000 chunk 340 optimal weight: 7.9990 chunk 310 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 426 optimal weight: 8.9990 chunk 435 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.069690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.050482 restraints weight = 89812.201| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.20 r_work: 0.2618 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 36844 Z= 0.337 Angle : 0.633 23.697 50074 Z= 0.324 Chirality : 0.046 0.160 5349 Planarity : 0.004 0.046 6448 Dihedral : 6.920 132.050 5850 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.31 % Favored : 95.62 % Rotamer: Outliers : 0.93 % Allowed : 9.40 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.12), residues: 4456 helix: 1.12 (0.19), residues: 786 sheet: 0.24 (0.14), residues: 1349 loop : -0.56 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 100 TYR 0.033 0.002 TYR B 203 PHE 0.018 0.002 PHE J 342 TRP 0.012 0.002 TRP B 36 HIS 0.007 0.001 HIS J 132 Details of bonding type rmsd covalent geometry : bond 0.00772 (36804) covalent geometry : angle 0.61709 (49956) SS BOND : bond 0.00117 ( 2) SS BOND : angle 1.03722 ( 4) hydrogen bonds : bond 0.04422 ( 1510) hydrogen bonds : angle 4.99239 ( 4227) glycosidic custom : bond 0.04263 ( 3) glycosidic custom : angle 3.35944 ( 9) link_ALPHA2-6 : bond 0.01027 ( 35) link_ALPHA2-6 : angle 2.97915 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9658.14 seconds wall clock time: 166 minutes 28.25 seconds (9988.25 seconds total)