Starting phenix.real_space_refine on Tue Aug 26 17:01:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9s_34580/08_2025/8h9s_34580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9s_34580/08_2025/8h9s_34580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h9s_34580/08_2025/8h9s_34580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9s_34580/08_2025/8h9s_34580.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h9s_34580/08_2025/8h9s_34580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9s_34580/08_2025/8h9s_34580.map" } resolution = 2.53 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= 0.003 sd= 1.095 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 5 5.21 5 S 161 5.16 5 C 24846 2.51 5 N 6576 2.21 5 O 7324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 297 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38930 Number of models: 1 Model: "" Number of chains: 36 Chain: "K" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1573 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1259 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3830 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 484} Chain breaks: 1 Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3639 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3714 Classifications: {'peptide': 487} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 468} Chain breaks: 1 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3458 Classifications: {'peptide': 456} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3529 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3562 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 444} Chain: "G" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2103 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 5, 'TRANS': 265} Chain: "J" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1437 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 534 Chain: "3" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 534 Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 422 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 8, 'TRANS': 42} Chain: "R" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 655 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 72 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Time building chain proxies: 7.61, per 1000 atoms: 0.20 Number of scatterers: 38930 At special positions: 0 Unit cell: (143.08, 132.86, 246.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 161 16.00 P 18 15.00 Mg 5 11.99 O 7324 8.00 N 6576 7.00 C 24846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9244 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 22 sheets defined 60.3% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 54 through 121 removed outlier: 3.908A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix removed outlier: 3.528A pdb=" N SER K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 184 removed outlier: 3.513A pdb=" N VAL K 182 " --> pdb=" O GLU K 178 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN K 183 " --> pdb=" O LYS K 179 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER K 184 " --> pdb=" O HIS K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 206 Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.582A pdb=" N GLN L 55 " --> pdb=" O LYS L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 83 removed outlier: 4.079A pdb=" N ARG L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 18 removed outlier: 3.752A pdb=" N ILE M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 43 Processing helix chain 'M' and resid 53 through 58 Processing helix chain 'M' and resid 64 through 75 removed outlier: 3.557A pdb=" N ALA M 75 " --> pdb=" O LYS M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 123 removed outlier: 3.574A pdb=" N VAL M 89 " --> pdb=" O TYR M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 removed outlier: 3.623A pdb=" N LEU M 135 " --> pdb=" O THR M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.570A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing helix chain 'M' and resid 156 through 160 Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.793A pdb=" N LEU A 81 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.511A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.798A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.510A pdb=" N GLY A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 239 through 259 Proline residue: A 247 - end of helix removed outlier: 3.898A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.724A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.593A pdb=" N GLY A 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.632A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 401 removed outlier: 4.144A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 411 through 428 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 457 through 476 removed outlier: 4.422A pdb=" N THR A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 490 through 507 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.582A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.620A pdb=" N LYS B 198 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 239 through 259 Proline residue: B 247 - end of helix removed outlier: 3.945A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.517A pdb=" N GLN B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.760A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'B' and resid 380 through 401 removed outlier: 4.403A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 428 removed outlier: 3.720A pdb=" N LEU B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 460 through 476 Processing helix chain 'B' and resid 476 through 487 Processing helix chain 'B' and resid 490 through 507 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.726A pdb=" N LEU C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.525A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.741A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 194 through 197 removed outlier: 3.679A pdb=" N LYS C 197 " --> pdb=" O ASP C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 239 through 259 Proline residue: C 247 - end of helix removed outlier: 4.033A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.648A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.816A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.556A pdb=" N ALA C 377 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 401 removed outlier: 4.043A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 400 " --> pdb=" O GLN C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 460 through 476 Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 508 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 125 through 129 Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 164 through 180 Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 228 through 249 removed outlier: 4.878A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.599A pdb=" N PHE E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 284 removed outlier: 3.527A pdb=" N TYR E 284 " --> pdb=" O ALA E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 322 through 329 Processing helix chain 'E' and resid 339 through 344 Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 367 through 390 removed outlier: 3.640A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.847A pdb=" N SER E 418 " --> pdb=" O GLN E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 423 No H-bonds generated for 'chain 'E' and resid 421 through 423' Processing helix chain 'E' and resid 424 through 429 Processing helix chain 'E' and resid 436 through 450 Processing helix chain 'E' and resid 456 through 460 removed outlier: 3.541A pdb=" N ALA E 459 " --> pdb=" O PRO E 456 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE E 460 " --> pdb=" O GLU E 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 456 through 460' Processing helix chain 'E' and resid 465 through 475 removed outlier: 3.827A pdb=" N LYS E 475 " --> pdb=" O ALA E 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 125 through 129 Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 164 through 177 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 228 through 249 removed outlier: 4.953A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 273 removed outlier: 3.839A pdb=" N THR F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 287 through 297 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 322 through 329 Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 339 through 345 Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 367 through 394 removed outlier: 4.596A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 399 removed outlier: 3.893A pdb=" N GLU F 398 " --> pdb=" O GLY F 395 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F 399 " --> pdb=" O MET F 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 395 through 399' Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.774A pdb=" N SER F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 450 Processing helix chain 'F' and resid 456 through 461 removed outlier: 3.555A pdb=" N TYR F 461 " --> pdb=" O GLN F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 477 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 164 through 179 Processing helix chain 'D' and resid 192 through 206 Processing helix chain 'D' and resid 228 through 249 removed outlier: 4.859A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 removed outlier: 3.768A pdb=" N THR D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.711A pdb=" N GLY D 283 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 339 through 345 Processing helix chain 'D' and resid 367 through 395 removed outlier: 4.130A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 399 removed outlier: 4.150A pdb=" N LEU D 399 " --> pdb=" O MET D 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 399' Processing helix chain 'D' and resid 400 through 418 removed outlier: 3.648A pdb=" N SER D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 425 removed outlier: 3.552A pdb=" N GLU D 425 " --> pdb=" O GLN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 450 Processing helix chain 'D' and resid 456 through 460 Processing helix chain 'D' and resid 465 through 480 Processing helix chain 'G' and resid 3 through 48 removed outlier: 3.575A pdb=" N ARG G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 80 through 98 Processing helix chain 'G' and resid 109 through 117 removed outlier: 3.829A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 187 through 193 removed outlier: 3.541A pdb=" N SER G 191 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 271 removed outlier: 3.780A pdb=" N THR G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 18 Processing helix chain 'J' and resid 20 through 44 removed outlier: 3.620A pdb=" N ARG J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA J 44 " --> pdb=" O GLU J 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 29 removed outlier: 4.008A pdb=" N GLN O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 48 removed outlier: 3.608A pdb=" N GLU O 48 " --> pdb=" O GLN O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 55 Processing helix chain 'O' and resid 61 through 75 Processing helix chain 'O' and resid 79 through 93 Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'O' and resid 97 through 113 Processing helix chain 'O' and resid 127 through 139 Processing helix chain 'O' and resid 140 through 142 No H-bonds generated for 'chain 'O' and resid 140 through 142' Processing helix chain 'O' and resid 155 through 159 removed outlier: 3.741A pdb=" N ILE O 158 " --> pdb=" O ASP O 155 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU O 159 " --> pdb=" O PRO O 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 155 through 159' Processing helix chain 'O' and resid 174 through 188 removed outlier: 3.549A pdb=" N LYS O 178 " --> pdb=" O SER O 174 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 15 Processing helix chain '1' and resid 17 through 39 removed outlier: 4.318A pdb=" N SER 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 73 Processing helix chain '2' and resid 2 through 16 Processing helix chain '2' and resid 18 through 39 Processing helix chain '2' and resid 42 through 73 removed outlier: 3.614A pdb=" N ALA 2 59 " --> pdb=" O ALA 2 55 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET 2 60 " --> pdb=" O LEU 2 56 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY 2 61 " --> pdb=" O SER 2 57 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 17 removed outlier: 4.009A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 39 Processing helix chain '3' and resid 42 through 73 removed outlier: 3.567A pdb=" N ALA 3 59 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY 3 61 " --> pdb=" O SER 3 57 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 16 Processing helix chain '4' and resid 18 through 39 Processing helix chain '4' and resid 42 through 73 removed outlier: 3.794A pdb=" N CYS 4 64 " --> pdb=" O MET 4 60 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL 4 67 " --> pdb=" O PHE 4 63 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 16 Processing helix chain '5' and resid 18 through 39 Processing helix chain '5' and resid 42 through 73 removed outlier: 3.687A pdb=" N GLU 5 58 " --> pdb=" O PHE 5 54 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA 5 59 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 17 removed outlier: 3.967A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 39 Processing helix chain '6' and resid 42 through 73 Processing helix chain '7' and resid 2 through 16 Processing helix chain '7' and resid 17 through 39 removed outlier: 4.415A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 73 removed outlier: 3.501A pdb=" N PHE 7 73 " --> pdb=" O PHE 7 69 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.997A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 39 Processing helix chain '8' and resid 42 through 73 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.599A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 146 Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 39 removed outlier: 4.340A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 10 removed outlier: 3.639A pdb=" N ILE N 10 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.582A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 68 through 86 Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 Proline residue: N 107 - end of helix removed outlier: 3.626A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 127 Processing helix chain 'N' and resid 134 through 138 removed outlier: 3.625A pdb=" N LEU N 137 " --> pdb=" O PRO N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 181 removed outlier: 3.525A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 3.524A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 224 Processing helix chain 'P' and resid 9 through 19 removed outlier: 3.503A pdb=" N MET P 13 " --> pdb=" O ILE P 9 " (cutoff:3.500A) Proline residue: P 15 - end of helix Processing helix chain 'P' and resid 21 through 41 Processing helix chain 'Q' and resid 1 through 7 removed outlier: 5.476A pdb=" N THR Q 6 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N THR Q 7 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 22 Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 30 removed outlier: 3.605A pdb=" N ASN Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.533A pdb=" N LEU R 30 " --> pdb=" O PRO R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 Processing helix chain 'R' and resid 62 through 80 removed outlier: 4.361A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 85 Processing helix chain 'S' and resid 27 through 34 Processing helix chain 'S' and resid 44 through 61 Processing helix chain 'S' and resid 62 through 67 removed outlier: 3.563A pdb=" N LYS S 65 " --> pdb=" O GLY S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 94 Processing helix chain 'T' and resid 8 through 44 Proline residue: T 35 - end of helix Processing sheet with id=AA1, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.558A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 43 current: chain 'A' and resid 60 through 66 removed outlier: 5.704A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 75 current: chain 'B' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 43 current: chain 'B' and resid 60 through 66 removed outlier: 6.160A pdb=" N GLY B 61 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE B 76 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 76 current: chain 'C' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 43 current: chain 'C' and resid 60 through 66 removed outlier: 5.602A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 75 current: chain 'E' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 23 through 28 current: chain 'E' and resid 49 through 57 removed outlier: 6.775A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 60 through 65 current: chain 'F' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 23 through 28 current: chain 'F' and resid 49 through 57 removed outlier: 6.762A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 60 through 65 current: chain 'D' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 23 through 28 current: chain 'D' and resid 49 through 57 removed outlier: 6.724A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 60 through 65 current: chain 'O' and resid 147 through 151 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 147 through 151 current: chain 'O' and resid 169 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.086A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.499A pdb=" N ALA A 264 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU A 324 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 266 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL A 326 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR A 268 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLU A 328 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.181A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.290A pdb=" N TYR B 200 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE B 267 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 202 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ASP B 269 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 204 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 264 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU B 324 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 266 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL B 326 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR B 268 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N GLU B 328 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.455A pdb=" N ILE B 159 " --> pdb=" O MET B 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.072A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.475A pdb=" N VAL C 108 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA C 264 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LEU C 324 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE C 266 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL C 326 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR C 268 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N GLU C 328 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.460A pdb=" N ILE C 159 " --> pdb=" O MET C 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.225A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.338A pdb=" N MET E 98 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLN E 224 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER E 184 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL E 221 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE E 186 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY E 223 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY E 188 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL E 254 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL E 310 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU E 256 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ALA E 312 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ILE E 258 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE E 155 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS E 154 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR E 336 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLY E 156 " --> pdb=" O THR E 336 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 136 removed outlier: 4.369A pdb=" N TYR E 149 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.234A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 97 through 98 removed outlier: 6.712A pdb=" N SER F 184 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL F 221 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE F 186 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLY F 223 " --> pdb=" O PHE F 186 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY F 188 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE F 155 " --> pdb=" O GLN F 311 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE F 313 " --> pdb=" O ILE F 155 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU F 157 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS F 154 " --> pdb=" O ALA F 334 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR F 336 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY F 156 " --> pdb=" O THR F 336 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.283A pdb=" N TYR F 149 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 86 through 89 removed outlier: 4.250A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.371A pdb=" N MET D 98 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL D 254 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL D 310 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU D 256 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ALA D 312 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE D 258 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N TYR D 314 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU D 157 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE D 158 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.264A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.074A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA G 127 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 17 through 22 removed outlier: 6.472A pdb=" N PHE H 18 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN H 29 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE H 20 " --> pdb=" O PHE H 27 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 43 through 47 current: chain 'H' and resid 72 through 77 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 72 through 77 current: chain 'H' and resid 89 through 93 Processing sheet with id=AC4, first strand: chain 'N' and resid 13 through 14 2243 hydrogen bonds defined for protein. 6496 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: 6.48 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 6504 1.30 - 1.43: 9341 1.43 - 1.56: 23387 1.56 - 1.68: 30 1.68 - 1.81: 303 Bond restraints: 39565 Sorted by residual: bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.461 -0.124 1.10e-02 8.26e+03 1.27e+02 bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.460 -0.123 1.10e-02 8.26e+03 1.25e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.458 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" C4 ATP A 601 " pdb=" N9 ATP A 601 " ideal model delta sigma weight residual 1.374 1.287 0.087 1.00e-02 1.00e+04 7.56e+01 bond pdb=" C8 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.370 1.266 0.104 1.20e-02 6.94e+03 7.55e+01 ... (remaining 39560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 53217 3.39 - 6.77: 247 6.77 - 10.16: 28 10.16 - 13.54: 11 13.54 - 16.93: 3 Bond angle restraints: 53506 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 122.94 16.93 1.00e+00 1.00e+00 2.87e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.70 16.17 1.00e+00 1.00e+00 2.61e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 124.72 15.15 1.00e+00 1.00e+00 2.30e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 125.06 11.77 1.00e+00 1.00e+00 1.38e+02 angle pdb=" N ILE 1 71 " pdb=" CA ILE 1 71 " pdb=" C ILE 1 71 " ideal model delta sigma weight residual 113.71 102.64 11.07 9.50e-01 1.11e+00 1.36e+02 ... (remaining 53501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 23514 35.95 - 71.89: 477 71.89 - 107.84: 48 107.84 - 143.78: 1 143.78 - 179.73: 2 Dihedral angle restraints: 24042 sinusoidal: 9596 harmonic: 14446 Sorted by residual: dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 129.43 170.57 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 83.39 -143.39 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 43.78 -103.78 1 2.00e+01 2.50e-03 2.97e+01 ... (remaining 24039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 5133 0.056 - 0.113: 936 0.113 - 0.169: 138 0.169 - 0.226: 6 0.226 - 0.282: 3 Chirality restraints: 6216 Sorted by residual: chirality pdb=" CA ILE 1 71 " pdb=" N ILE 1 71 " pdb=" C ILE 1 71 " pdb=" CB ILE 1 71 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.43 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.44 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 6213 not shown) Planarity restraints: 6813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 174 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C ASN D 174 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN D 174 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN D 175 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 93 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO N 94 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO N 94 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO N 94 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE 3 54 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C PHE 3 54 " -0.035 2.00e-02 2.50e+03 pdb=" O PHE 3 54 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA 3 55 " 0.012 2.00e-02 2.50e+03 ... (remaining 6810 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 172 2.50 - 3.10: 28803 3.10 - 3.70: 59322 3.70 - 4.30: 92777 4.30 - 4.90: 151526 Nonbonded interactions: 332600 Sorted by model distance: nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 1.895 2.170 nonbonded pdb=" OG1 THR F 166 " pdb="MG MG F 502 " model vdw 1.937 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 1.940 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 2.016 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 2.038 2.170 ... (remaining 332595 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 '1' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '2' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '3' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '4' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '5' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '6' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '7' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '8' and (resid 1 through 37 or resid 39 through 75)) } ncs_group { reference = (chain 'A' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'C' and resid 24 through 602) } ncs_group { reference = (chain 'D' and (resid 12 through 391 or resid 400 through 475)) selection = chain 'E' selection = (chain 'F' and (resid 12 through 391 or resid 400 through 475)) } 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=0.50 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: 8.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 29.590 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.006 0.145 39565 Z= 0.342 Angle : 0.689 16.929 53506 Z= 0.424 Chirality : 0.045 0.282 6216 Planarity : 0.004 0.053 6813 Dihedral : 15.014 179.728 14798 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 0.05 % Allowed : 3.97 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: -2.13 (0.10), residues: 5000 helix: -1.08 (0.09), residues: 2702 sheet: -1.06 (0.20), residues: 578 loop : -1.83 (0.13), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 41 TYR 0.016 0.001 TYR G 193 PHE 0.023 0.002 PHE 8 29 TRP 0.013 0.002 TRP P 10 HIS 0.004 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00638 (39565) covalent geometry : angle 0.68871 (53506) hydrogen bonds : bond 0.14450 ( 2243) hydrogen bonds : angle 6.59964 ( 6496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 669 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LYS cc_start: 0.8125 (mttt) cc_final: 0.7919 (mttm) REVERT: A 488 LYS cc_start: 0.8564 (pttt) cc_final: 0.8354 (ptpt) REVERT: B 195 GLU cc_start: 0.6836 (tp30) cc_final: 0.6391 (tp30) REVERT: N 36 TYR cc_start: 0.6522 (m-10) cc_final: 0.6303 (m-10) REVERT: R 32 ARG cc_start: 0.7817 (mmp-170) cc_final: 0.6529 (mmp-170) outliers start: 1 outliers final: 0 residues processed: 670 average time/residue: 0.7448 time to fit residues: 589.9801 Evaluate side-chains 528 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 0.0770 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 0.0570 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 88 GLN K 115 GLN K 183 GLN L 80 GLN M 23 GLN M 136 ASN A 396 GLN A 416 GLN A 503 ASN B 48 GLN B 70 ASN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN B 503 ASN C 208 GLN C 466 ASN C 503 ASN F 249 GLN F 331 HIS F 364 ASN F 422 GLN F 458 GLN D 180 HIS D 266 GLN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN G 182 ASN O 99 GLN 2 44 GLN H 15 GLN H 85 ASN N 46 GLN N 47 GLN N 61 HIS S 75 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.137253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101281 restraints weight = 74050.140| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.28 r_work: 0.3087 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39565 Z= 0.125 Angle : 0.530 7.410 53506 Z= 0.279 Chirality : 0.041 0.166 6216 Planarity : 0.004 0.060 6813 Dihedral : 8.483 154.121 5695 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.80 % Favored : 98.14 % Rotamer: Outliers : 1.59 % Allowed : 10.56 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: -0.12 (0.12), residues: 5000 helix: 0.79 (0.10), residues: 2675 sheet: -0.62 (0.21), residues: 591 loop : -1.16 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 381 TYR 0.013 0.001 TYR G 44 PHE 0.025 0.001 PHE R 79 TRP 0.024 0.001 TRP R 28 HIS 0.005 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00255 (39565) covalent geometry : angle 0.53019 (53506) hydrogen bonds : bond 0.05069 ( 2243) hydrogen bonds : angle 4.72263 ( 6496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 593 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 104 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7922 (mm) REVERT: K 165 MET cc_start: 0.8521 (tpp) cc_final: 0.8276 (mmm) REVERT: M 55 TYR cc_start: 0.7779 (t80) cc_final: 0.7223 (t80) REVERT: A 8 MET cc_start: 0.5719 (mtm) cc_final: 0.5029 (mmt) REVERT: A 488 LYS cc_start: 0.7976 (pttt) cc_final: 0.7527 (ptpt) REVERT: A 499 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 195 GLU cc_start: 0.6963 (tp30) cc_final: 0.6465 (tp30) REVERT: C 304 ARG cc_start: 0.8379 (ptt180) cc_final: 0.8063 (ptt90) REVERT: E 112 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8248 (mtpt) REVERT: E 249 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: E 260 ASN cc_start: 0.8280 (t0) cc_final: 0.8051 (t0) REVERT: F 27 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: F 252 GLN cc_start: 0.7872 (mm110) cc_final: 0.7343 (mm-40) REVERT: D 132 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: D 170 MET cc_start: 0.7521 (mmm) cc_final: 0.7231 (mmp) REVERT: D 202 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6605 (mp0) REVERT: D 203 MET cc_start: 0.7949 (mtt) cc_final: 0.7671 (mtt) REVERT: D 210 ASN cc_start: 0.8525 (t0) cc_final: 0.8012 (t0) REVERT: D 212 LYS cc_start: 0.7028 (ptmt) cc_final: 0.6268 (ptpp) REVERT: G 33 ARG cc_start: 0.7497 (mtp-110) cc_final: 0.6697 (ttm110) REVERT: G 175 GLU cc_start: 0.8094 (tt0) cc_final: 0.7784 (tt0) REVERT: 6 7 LYS cc_start: 0.7470 (mtmt) cc_final: 0.6996 (mttp) REVERT: 7 45 GLN cc_start: 0.8680 (tp40) cc_final: 0.8478 (tp-100) REVERT: 8 60 MET cc_start: 0.7684 (mmp) cc_final: 0.7382 (mmt) REVERT: I 7 GLN cc_start: 0.7627 (mm110) cc_final: 0.7415 (mt0) REVERT: I 44 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7489 (mtpt) REVERT: N 36 TYR cc_start: 0.8231 (m-10) cc_final: 0.7786 (m-10) REVERT: N 199 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8560 (tt) REVERT: P 2 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6909 (tt) REVERT: Q 30 ASN cc_start: 0.8930 (t0) cc_final: 0.8719 (m-40) REVERT: R 32 ARG cc_start: 0.7768 (mmp-170) cc_final: 0.6143 (mmp-170) REVERT: S 36 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7653 (mt-10) REVERT: S 65 LYS cc_start: 0.8613 (mmtm) cc_final: 0.7830 (mmmt) outliers start: 64 outliers final: 15 residues processed: 619 average time/residue: 0.7130 time to fit residues: 528.8327 Evaluate side-chains 561 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 539 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain 1 residue 21 SER Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain S residue 30 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 384 optimal weight: 4.9990 chunk 488 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 chunk 315 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 292 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 452 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 333 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 158 HIS L 80 GLN A 492 GLN B 78 ASN B 492 GLN C 503 ASN E 445 GLN F 42 GLN F 458 GLN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN N 56 GLN N 172 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099015 restraints weight = 64994.814| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.16 r_work: 0.3095 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 39565 Z= 0.267 Angle : 0.616 9.450 53506 Z= 0.321 Chirality : 0.046 0.182 6216 Planarity : 0.004 0.057 6813 Dihedral : 8.636 151.432 5695 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 2.40 % Allowed : 12.03 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 0.21 (0.12), residues: 5000 helix: 1.07 (0.10), residues: 2679 sheet: -0.53 (0.21), residues: 588 loop : -1.00 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 381 TYR 0.018 0.002 TYR I 12 PHE 0.032 0.002 PHE H 45 TRP 0.016 0.002 TRP R 28 HIS 0.007 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00651 (39565) covalent geometry : angle 0.61616 (53506) hydrogen bonds : bond 0.06129 ( 2243) hydrogen bonds : angle 4.74356 ( 6496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 560 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 165 MET cc_start: 0.8516 (tpp) cc_final: 0.8207 (mmm) REVERT: K 168 LYS cc_start: 0.7928 (tppt) cc_final: 0.7466 (tmtt) REVERT: M 55 TYR cc_start: 0.7849 (t80) cc_final: 0.7419 (t80) REVERT: M 83 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8463 (t0) REVERT: A 8 MET cc_start: 0.5931 (mtm) cc_final: 0.5170 (mmt) REVERT: A 475 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7603 (mt0) REVERT: A 488 LYS cc_start: 0.8144 (pttt) cc_final: 0.7676 (ptpt) REVERT: A 499 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 26 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: B 54 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: B 195 GLU cc_start: 0.7012 (tp30) cc_final: 0.6519 (tp30) REVERT: B 270 ASP cc_start: 0.8984 (p0) cc_final: 0.8745 (p0) REVERT: B 477 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6932 (mp10) REVERT: E 112 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8281 (mtpt) REVERT: E 249 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: F 15 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7956 (ptm-80) REVERT: F 27 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: F 215 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8552 (p) REVERT: F 422 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7377 (mt0) REVERT: D 132 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: D 170 MET cc_start: 0.7627 (mmm) cc_final: 0.7421 (mmp) REVERT: D 202 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6806 (mp0) REVERT: D 203 MET cc_start: 0.8076 (mtt) cc_final: 0.7744 (mtt) REVERT: D 210 ASN cc_start: 0.8525 (t0) cc_final: 0.8101 (t0) REVERT: G 175 GLU cc_start: 0.8215 (tt0) cc_final: 0.7982 (tt0) REVERT: 6 7 LYS cc_start: 0.7607 (mtmt) cc_final: 0.7120 (mttp) REVERT: I 7 GLN cc_start: 0.7729 (mm110) cc_final: 0.7480 (mt0) REVERT: I 44 LYS cc_start: 0.7962 (mmtm) cc_final: 0.7538 (mtpt) REVERT: N 36 TYR cc_start: 0.8286 (m-10) cc_final: 0.7767 (m-10) REVERT: N 163 ASN cc_start: 0.8630 (t0) cc_final: 0.8359 (m110) REVERT: R 32 ARG cc_start: 0.7820 (mmp-170) cc_final: 0.6231 (mmp-170) REVERT: R 91 LYS cc_start: 0.8024 (tmmt) cc_final: 0.7745 (tmmt) REVERT: S 65 LYS cc_start: 0.8680 (mmtm) cc_final: 0.7739 (mmmt) REVERT: T 8 SER cc_start: 0.8066 (m) cc_final: 0.7698 (t) outliers start: 97 outliers final: 32 residues processed: 604 average time/residue: 0.7380 time to fit residues: 532.1264 Evaluate side-chains 579 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 535 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 477 GLN Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 225 MET Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain F residue 15 ARG Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain 1 residue 21 SER Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 30 TRP Chi-restraints excluded: chain T residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 233 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 378 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 353 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 158 HIS L 80 GLN A 492 GLN B 78 ASN B 492 GLN C 503 ASN F 458 GLN D 364 ASN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 45 GLN H 15 GLN N 56 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.101038 restraints weight = 62782.959| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.11 r_work: 0.3126 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39565 Z= 0.181 Angle : 0.557 8.264 53506 Z= 0.289 Chirality : 0.043 0.180 6216 Planarity : 0.004 0.049 6813 Dihedral : 8.270 148.256 5695 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.92 % Rotamer: Outliers : 2.20 % Allowed : 13.74 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 0.60 (0.12), residues: 5000 helix: 1.40 (0.10), residues: 2673 sheet: -0.42 (0.21), residues: 582 loop : -0.81 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 33 TYR 0.019 0.001 TYR T 32 PHE 0.026 0.001 PHE R 79 TRP 0.014 0.001 TRP R 28 HIS 0.008 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00426 (39565) covalent geometry : angle 0.55677 (53506) hydrogen bonds : bond 0.05390 ( 2243) hydrogen bonds : angle 4.60021 ( 6496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 553 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 26 TYR cc_start: 0.8593 (t80) cc_final: 0.8303 (t80) REVERT: K 165 MET cc_start: 0.8525 (tpp) cc_final: 0.8070 (mpp) REVERT: M 55 TYR cc_start: 0.7873 (t80) cc_final: 0.7315 (t80) REVERT: M 83 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8463 (t0) REVERT: A 8 MET cc_start: 0.5788 (mtm) cc_final: 0.5037 (mmt) REVERT: A 381 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.6213 (mtp85) REVERT: A 488 LYS cc_start: 0.8071 (pttt) cc_final: 0.7593 (ptpt) REVERT: A 499 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7904 (tm-30) REVERT: C 304 ARG cc_start: 0.8458 (ptt180) cc_final: 0.8161 (ptt90) REVERT: E 112 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8251 (mtpt) REVERT: E 249 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: F 27 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: F 252 GLN cc_start: 0.7906 (mm110) cc_final: 0.7419 (mm-40) REVERT: F 422 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7317 (mt0) REVERT: D 132 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: D 170 MET cc_start: 0.7586 (mmm) cc_final: 0.7362 (mmp) REVERT: D 202 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6728 (mp0) REVERT: D 203 MET cc_start: 0.8045 (mtt) cc_final: 0.7617 (mtt) REVERT: D 210 ASN cc_start: 0.8509 (t0) cc_final: 0.8050 (t0) REVERT: D 212 LYS cc_start: 0.7052 (ptmt) cc_final: 0.6279 (ptpp) REVERT: D 422 GLN cc_start: 0.7142 (tp40) cc_final: 0.6628 (tp40) REVERT: G 53 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7582 (tm-30) REVERT: G 147 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7367 (mp0) REVERT: G 175 GLU cc_start: 0.8195 (tt0) cc_final: 0.7949 (tt0) REVERT: 4 21 SER cc_start: 0.8754 (m) cc_final: 0.8487 (t) REVERT: 6 7 LYS cc_start: 0.7563 (mtmt) cc_final: 0.7085 (mttp) REVERT: 6 70 LEU cc_start: 0.8010 (tt) cc_final: 0.7791 (tp) REVERT: 8 60 MET cc_start: 0.7719 (mmt) cc_final: 0.7486 (mmt) REVERT: I 7 GLN cc_start: 0.7680 (mm110) cc_final: 0.7439 (mt0) REVERT: I 44 LYS cc_start: 0.7876 (mmtm) cc_final: 0.7415 (mtpt) REVERT: N 36 TYR cc_start: 0.8233 (m-10) cc_final: 0.7691 (m-10) REVERT: N 147 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8474 (mp) REVERT: R 32 ARG cc_start: 0.7748 (mmp-170) cc_final: 0.6228 (mmp-170) REVERT: R 91 LYS cc_start: 0.8120 (tmmt) cc_final: 0.7794 (tmmt) REVERT: S 36 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: S 65 LYS cc_start: 0.8657 (mmtm) cc_final: 0.7677 (mmmt) outliers start: 89 outliers final: 35 residues processed: 596 average time/residue: 0.6861 time to fit residues: 489.8762 Evaluate side-chains 578 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 534 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 30 TRP Chi-restraints excluded: chain S residue 36 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 29 optimal weight: 0.0060 chunk 436 optimal weight: 0.7980 chunk 185 optimal weight: 0.2980 chunk 419 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 482 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 331 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 452 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN A 492 GLN B 78 ASN C 503 ASN E 445 GLN F 458 GLN D 364 ASN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 45 GLN H 15 GLN N 56 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105177 restraints weight = 56688.763| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.02 r_work: 0.3173 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 39565 Z= 0.113 Angle : 0.502 8.914 53506 Z= 0.260 Chirality : 0.041 0.167 6216 Planarity : 0.004 0.048 6813 Dihedral : 7.677 147.988 5695 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.94 % Favored : 98.04 % Rotamer: Outliers : 1.98 % Allowed : 14.87 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 1.05 (0.12), residues: 5000 helix: 1.80 (0.10), residues: 2662 sheet: -0.23 (0.22), residues: 561 loop : -0.65 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 33 TYR 0.018 0.001 TYR S 31 PHE 0.026 0.001 PHE R 79 TRP 0.014 0.001 TRP R 28 HIS 0.010 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00235 (39565) covalent geometry : angle 0.50201 (53506) hydrogen bonds : bond 0.04520 ( 2243) hydrogen bonds : angle 4.38333 ( 6496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 581 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 26 TYR cc_start: 0.8584 (t80) cc_final: 0.8275 (t80) REVERT: K 104 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7324 (pp) REVERT: K 150 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: K 154 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6728 (mmm-85) REVERT: K 165 MET cc_start: 0.8531 (tpp) cc_final: 0.8228 (mmm) REVERT: L 55 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7265 (pm20) REVERT: M 118 MET cc_start: 0.7741 (tpp) cc_final: 0.7425 (tpt) REVERT: M 128 ASP cc_start: 0.8642 (p0) cc_final: 0.8421 (p0) REVERT: A 8 MET cc_start: 0.5774 (mtm) cc_final: 0.5013 (mmt) REVERT: A 347 ASP cc_start: 0.8820 (m-30) cc_final: 0.8509 (m-30) REVERT: A 381 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.6167 (mtp85) REVERT: A 416 GLN cc_start: 0.7362 (tp40) cc_final: 0.7123 (tp-100) REVERT: A 475 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7476 (mt0) REVERT: A 477 GLN cc_start: 0.7705 (tp40) cc_final: 0.7418 (tp40) REVERT: A 488 LYS cc_start: 0.8102 (pttt) cc_final: 0.7621 (ptpt) REVERT: A 499 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 54 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7210 (tm-30) REVERT: B 384 LYS cc_start: 0.6962 (mttt) cc_final: 0.6722 (mttm) REVERT: B 392 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7849 (tm) REVERT: C 304 ARG cc_start: 0.8411 (ptt180) cc_final: 0.8139 (ptt90) REVERT: E 112 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8208 (mtpt) REVERT: E 205 GLU cc_start: 0.8325 (tt0) cc_final: 0.7910 (pp20) REVERT: E 249 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: F 252 GLN cc_start: 0.7815 (mm110) cc_final: 0.7265 (mm-40) REVERT: D 132 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: D 202 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6697 (mp0) REVERT: D 203 MET cc_start: 0.8016 (mtt) cc_final: 0.7597 (mtt) REVERT: D 210 ASN cc_start: 0.8524 (t0) cc_final: 0.7970 (t0) REVERT: D 212 LYS cc_start: 0.7143 (ptmt) cc_final: 0.6324 (ptpp) REVERT: D 362 ASP cc_start: 0.8438 (t0) cc_final: 0.8236 (t0) REVERT: D 422 GLN cc_start: 0.7182 (tp40) cc_final: 0.6786 (tp40) REVERT: G 53 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7528 (tm-30) REVERT: G 175 GLU cc_start: 0.8150 (tt0) cc_final: 0.7863 (tt0) REVERT: G 195 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8424 (m-30) REVERT: 6 7 LYS cc_start: 0.7570 (mtmt) cc_final: 0.7097 (mttp) REVERT: 8 60 MET cc_start: 0.7556 (mmt) cc_final: 0.7305 (mmt) REVERT: 8 69 PHE cc_start: 0.7709 (m-10) cc_final: 0.6909 (t80) REVERT: I 7 GLN cc_start: 0.7637 (mm110) cc_final: 0.7391 (mt0) REVERT: I 44 LYS cc_start: 0.7842 (mmtm) cc_final: 0.7370 (mtpt) REVERT: N 36 TYR cc_start: 0.8155 (m-10) cc_final: 0.7648 (m-10) REVERT: R 32 ARG cc_start: 0.7738 (mmp-170) cc_final: 0.6248 (mmp-170) REVERT: R 91 LYS cc_start: 0.8177 (tmmt) cc_final: 0.7744 (tmmt) REVERT: S 36 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7640 (mt-10) REVERT: S 65 LYS cc_start: 0.8632 (mmtm) cc_final: 0.7640 (mmmt) REVERT: S 92 ILE cc_start: 0.8913 (tt) cc_final: 0.8705 (tt) outliers start: 80 outliers final: 27 residues processed: 626 average time/residue: 0.6799 time to fit residues: 512.8173 Evaluate side-chains 589 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 549 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain 3 residue 65 LEU Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 36 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 219 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 326 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 469 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 380 optimal weight: 2.9990 chunk 376 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN A 492 GLN B 78 ASN C 503 ASN E 260 ASN E 445 GLN F 224 GLN D 260 ASN D 364 ASN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN N 56 GLN S 50 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.135414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098850 restraints weight = 73592.721| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.29 r_work: 0.3077 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 39565 Z= 0.280 Angle : 0.622 9.933 53506 Z= 0.321 Chirality : 0.047 0.187 6216 Planarity : 0.004 0.050 6813 Dihedral : 8.266 148.106 5695 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.40 % Favored : 97.58 % Rotamer: Outliers : 2.55 % Allowed : 15.43 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 0.79 (0.12), residues: 5000 helix: 1.51 (0.10), residues: 2671 sheet: -0.38 (0.21), residues: 587 loop : -0.64 (0.15), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 33 TYR 0.018 0.002 TYR I 12 PHE 0.034 0.002 PHE H 45 TRP 0.012 0.002 TRP R 28 HIS 0.014 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00684 (39565) covalent geometry : angle 0.62175 (53506) hydrogen bonds : bond 0.05967 ( 2243) hydrogen bonds : angle 4.63221 ( 6496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 550 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 26 TYR cc_start: 0.8673 (t80) cc_final: 0.8389 (t80) REVERT: K 154 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6735 (mmm-85) REVERT: K 165 MET cc_start: 0.8495 (tpp) cc_final: 0.8035 (mpp) REVERT: L 55 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: M 55 TYR cc_start: 0.7858 (t80) cc_final: 0.7268 (t80) REVERT: M 85 TYR cc_start: 0.8637 (m-80) cc_final: 0.8394 (m-80) REVERT: A 8 MET cc_start: 0.5843 (mtm) cc_final: 0.5058 (mmt) REVERT: A 381 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6281 (mtp85) REVERT: A 475 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7522 (mt0) REVERT: A 488 LYS cc_start: 0.8149 (pttt) cc_final: 0.7665 (ptpt) REVERT: A 499 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 195 GLU cc_start: 0.6940 (tp30) cc_final: 0.6685 (tp30) REVERT: C 304 ARG cc_start: 0.8522 (ptt180) cc_final: 0.8219 (ptt90) REVERT: E 112 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8254 (mtpt) REVERT: E 249 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: F 27 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: D 132 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: D 202 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6822 (mp0) REVERT: D 203 MET cc_start: 0.8050 (mtt) cc_final: 0.7664 (mtt) REVERT: D 212 LYS cc_start: 0.7062 (ptmt) cc_final: 0.6499 (ptpp) REVERT: D 344 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: G 53 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7560 (tm-30) REVERT: G 56 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: G 166 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7467 (mtp85) REVERT: G 175 GLU cc_start: 0.8241 (tt0) cc_final: 0.8012 (tt0) REVERT: G 195 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8557 (m-30) REVERT: 6 7 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7120 (mttp) REVERT: 8 60 MET cc_start: 0.7756 (mmt) cc_final: 0.7544 (mmt) REVERT: H 74 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8749 (mtmm) REVERT: I 7 GLN cc_start: 0.7657 (mm110) cc_final: 0.7392 (mt0) REVERT: N 36 TYR cc_start: 0.8258 (m-10) cc_final: 0.7670 (m-10) REVERT: R 22 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8322 (tt) REVERT: R 32 ARG cc_start: 0.7700 (mmp-170) cc_final: 0.6076 (mmm160) REVERT: R 91 LYS cc_start: 0.8194 (tmmt) cc_final: 0.7752 (tmmt) REVERT: S 36 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: S 65 LYS cc_start: 0.8633 (mmtm) cc_final: 0.7846 (mmmt) outliers start: 103 outliers final: 37 residues processed: 605 average time/residue: 0.7329 time to fit residues: 529.2037 Evaluate side-chains 581 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 530 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 39 SER Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 36 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 397 optimal weight: 0.8980 chunk 487 optimal weight: 0.9990 chunk 290 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 478 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 475 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN A 416 GLN A 492 GLN B 78 ASN C 503 ASN E 260 ASN E 445 GLN F 458 GLN D 364 ASN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN N 56 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103171 restraints weight = 62533.707| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.12 r_work: 0.3141 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39565 Z= 0.130 Angle : 0.537 11.085 53506 Z= 0.275 Chirality : 0.042 0.158 6216 Planarity : 0.004 0.047 6813 Dihedral : 7.804 147.528 5695 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.06 % Rotamer: Outliers : 2.08 % Allowed : 16.34 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 1.09 (0.12), residues: 5000 helix: 1.80 (0.10), residues: 2661 sheet: -0.27 (0.21), residues: 580 loop : -0.57 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 33 TYR 0.017 0.001 TYR T 32 PHE 0.025 0.001 PHE R 79 TRP 0.013 0.001 TRP R 28 HIS 0.012 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00288 (39565) covalent geometry : angle 0.53735 (53506) hydrogen bonds : bond 0.04819 ( 2243) hydrogen bonds : angle 4.44411 ( 6496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 556 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 26 TYR cc_start: 0.8604 (t80) cc_final: 0.8312 (t80) REVERT: K 154 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6656 (mmm-85) REVERT: K 165 MET cc_start: 0.8509 (tpp) cc_final: 0.8174 (mmm) REVERT: L 55 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: M 85 TYR cc_start: 0.8644 (m-80) cc_final: 0.8335 (m-80) REVERT: A 8 MET cc_start: 0.5748 (mtm) cc_final: 0.4977 (mmt) REVERT: A 381 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.6175 (mtp85) REVERT: A 475 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: A 477 GLN cc_start: 0.7714 (tp40) cc_final: 0.7404 (tp40) REVERT: A 488 LYS cc_start: 0.8095 (pttt) cc_final: 0.7624 (ptpt) REVERT: A 499 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 54 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: B 195 GLU cc_start: 0.6841 (tp30) cc_final: 0.6587 (tp30) REVERT: B 384 LYS cc_start: 0.7045 (mttt) cc_final: 0.6789 (mttm) REVERT: C 54 GLU cc_start: 0.8515 (tt0) cc_final: 0.8193 (tt0) REVERT: C 304 ARG cc_start: 0.8446 (ptt180) cc_final: 0.8216 (ptt180) REVERT: E 112 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8181 (mtpt) REVERT: E 205 GLU cc_start: 0.8318 (tt0) cc_final: 0.8085 (pp20) REVERT: E 249 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7567 (mp10) REVERT: F 27 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: F 252 GLN cc_start: 0.7685 (mm110) cc_final: 0.7267 (tp40) REVERT: D 132 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: D 202 GLU cc_start: 0.7439 (mm-30) cc_final: 0.6737 (mp0) REVERT: D 203 MET cc_start: 0.8002 (mtt) cc_final: 0.7571 (mtt) REVERT: D 210 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8045 (t0) REVERT: D 212 LYS cc_start: 0.7134 (ptmt) cc_final: 0.6351 (ptpp) REVERT: D 422 GLN cc_start: 0.7081 (tp40) cc_final: 0.6781 (tp40) REVERT: G 53 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7586 (tm-30) REVERT: G 147 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7379 (mp0) REVERT: G 166 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7428 (mtp85) REVERT: G 195 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8484 (m-30) REVERT: G 241 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7500 (mm-30) REVERT: G 262 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8144 (tt) REVERT: 4 62 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7728 (mp) REVERT: 6 7 LYS cc_start: 0.7554 (mtmt) cc_final: 0.7084 (mttp) REVERT: 7 75 MET cc_start: 0.7697 (mtm) cc_final: 0.7371 (mtm) REVERT: H 74 LYS cc_start: 0.9017 (mtpt) cc_final: 0.8546 (mtmm) REVERT: H 143 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7913 (mtpt) REVERT: I 7 GLN cc_start: 0.7621 (mm110) cc_final: 0.7357 (mt0) REVERT: N 36 TYR cc_start: 0.8189 (m-10) cc_final: 0.7617 (m-10) REVERT: R 22 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8326 (tt) REVERT: R 32 ARG cc_start: 0.7670 (mmp-170) cc_final: 0.6181 (mmm160) REVERT: R 91 LYS cc_start: 0.8185 (tmmt) cc_final: 0.7854 (tmmt) REVERT: S 36 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: S 65 LYS cc_start: 0.8619 (mmtm) cc_final: 0.7648 (mmmt) outliers start: 84 outliers final: 40 residues processed: 603 average time/residue: 0.6893 time to fit residues: 497.5495 Evaluate side-chains 598 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 542 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 2 residue 58 GLU Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 36 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 343 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 487 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 433 optimal weight: 0.8980 chunk 330 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 363 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN A 492 GLN B 78 ASN C 503 ASN E 260 ASN E 445 GLN F 458 GLN D 364 ASN N 56 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.100500 restraints weight = 65287.564| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.16 r_work: 0.3111 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 39565 Z= 0.220 Angle : 0.593 10.909 53506 Z= 0.305 Chirality : 0.045 0.174 6216 Planarity : 0.004 0.046 6813 Dihedral : 8.041 147.751 5695 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.22 % Favored : 97.76 % Rotamer: Outliers : 2.33 % Allowed : 16.36 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 0.97 (0.12), residues: 5000 helix: 1.67 (0.10), residues: 2667 sheet: -0.34 (0.21), residues: 587 loop : -0.55 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 33 TYR 0.020 0.002 TYR S 31 PHE 0.028 0.002 PHE H 45 TRP 0.011 0.001 TRP R 28 HIS 0.013 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00530 (39565) covalent geometry : angle 0.59321 (53506) hydrogen bonds : bond 0.05540 ( 2243) hydrogen bonds : angle 4.55134 ( 6496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 544 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 26 TYR cc_start: 0.8638 (t80) cc_final: 0.8387 (t80) REVERT: K 154 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6721 (mmm-85) REVERT: K 165 MET cc_start: 0.8503 (tpp) cc_final: 0.8054 (mpp) REVERT: L 55 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7326 (pm20) REVERT: M 85 TYR cc_start: 0.8681 (m-80) cc_final: 0.8451 (m-80) REVERT: M 125 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8014 (tt) REVERT: A 8 MET cc_start: 0.5868 (mtm) cc_final: 0.5062 (mmt) REVERT: A 381 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6247 (mtp85) REVERT: A 475 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7519 (mt0) REVERT: A 477 GLN cc_start: 0.7750 (tp40) cc_final: 0.7378 (tp40) REVERT: A 488 LYS cc_start: 0.8164 (pttt) cc_final: 0.7685 (ptpt) REVERT: A 499 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7887 (tm-30) REVERT: B 195 GLU cc_start: 0.6959 (tp30) cc_final: 0.6692 (tp30) REVERT: C 54 GLU cc_start: 0.8547 (tt0) cc_final: 0.8151 (tt0) REVERT: C 304 ARG cc_start: 0.8498 (ptt180) cc_final: 0.8200 (ptt90) REVERT: E 112 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8214 (mtpt) REVERT: E 205 GLU cc_start: 0.8340 (tt0) cc_final: 0.8121 (pp20) REVERT: E 249 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: F 27 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: F 252 GLN cc_start: 0.7740 (mm110) cc_final: 0.7192 (mm-40) REVERT: D 132 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: D 202 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6796 (mp0) REVERT: D 203 MET cc_start: 0.8036 (mtt) cc_final: 0.7630 (mtt) REVERT: D 212 LYS cc_start: 0.7131 (ptmt) cc_final: 0.6583 (ptpp) REVERT: D 344 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: D 422 GLN cc_start: 0.7174 (tp40) cc_final: 0.6837 (tp40) REVERT: G 53 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7637 (tm-30) REVERT: G 147 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7369 (mp0) REVERT: G 166 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7450 (mtp85) REVERT: G 175 GLU cc_start: 0.8150 (tt0) cc_final: 0.7819 (tt0) REVERT: G 195 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8526 (m-30) REVERT: G 262 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8114 (tt) REVERT: 6 7 LYS cc_start: 0.7596 (mtmt) cc_final: 0.7117 (mttp) REVERT: 7 75 MET cc_start: 0.7838 (mtm) cc_final: 0.7538 (mtm) REVERT: H 74 LYS cc_start: 0.9018 (mtpt) cc_final: 0.8548 (mttm) REVERT: I 7 GLN cc_start: 0.7650 (mm110) cc_final: 0.7393 (mt0) REVERT: N 36 TYR cc_start: 0.8205 (m-10) cc_final: 0.7627 (m-10) REVERT: R 22 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8330 (tt) REVERT: R 32 ARG cc_start: 0.7679 (mmp-170) cc_final: 0.6190 (mmm160) REVERT: R 91 LYS cc_start: 0.8192 (tmmt) cc_final: 0.7920 (tmmt) REVERT: S 36 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: S 65 LYS cc_start: 0.8648 (mmtm) cc_final: 0.7653 (mmmt) outliers start: 94 outliers final: 46 residues processed: 601 average time/residue: 0.7038 time to fit residues: 505.3626 Evaluate side-chains 594 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 533 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 87 MET Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 3 residue 70 LEU Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 36 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 471 optimal weight: 0.7980 chunk 32 optimal weight: 0.0970 chunk 321 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 chunk 414 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 440 optimal weight: 2.9990 chunk 462 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN A 432 GLN A 492 GLN B 78 ASN C 503 ASN E 260 ASN E 445 GLN F 458 GLN D 364 ASN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN N 4 ASN N 56 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.140055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103870 restraints weight = 73185.752| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.32 r_work: 0.3153 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39565 Z= 0.125 Angle : 0.538 12.051 53506 Z= 0.274 Chirality : 0.042 0.225 6216 Planarity : 0.004 0.051 6813 Dihedral : 7.580 147.438 5695 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.82 % Favored : 98.16 % Rotamer: Outliers : 1.52 % Allowed : 17.54 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 1.20 (0.12), residues: 5000 helix: 1.90 (0.10), residues: 2665 sheet: -0.21 (0.22), residues: 568 loop : -0.52 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 33 TYR 0.019 0.001 TYR S 31 PHE 0.026 0.001 PHE R 79 TRP 0.013 0.001 TRP R 28 HIS 0.012 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00278 (39565) covalent geometry : angle 0.53827 (53506) hydrogen bonds : bond 0.04619 ( 2243) hydrogen bonds : angle 4.38987 ( 6496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 566 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 26 TYR cc_start: 0.8607 (t80) cc_final: 0.8290 (t80) REVERT: K 154 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6638 (mmm-85) REVERT: K 165 MET cc_start: 0.8504 (tpp) cc_final: 0.8197 (mmm) REVERT: L 55 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: M 85 TYR cc_start: 0.8694 (m-80) cc_final: 0.8466 (m-80) REVERT: A 8 MET cc_start: 0.5711 (mtm) cc_final: 0.4994 (mmt) REVERT: A 381 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.6152 (mtp85) REVERT: A 475 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: A 477 GLN cc_start: 0.7734 (tp40) cc_final: 0.7363 (tp40) REVERT: A 488 LYS cc_start: 0.8073 (pttt) cc_final: 0.7598 (ptpt) REVERT: A 499 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7826 (tm-30) REVERT: B 80 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8211 (pttt) REVERT: B 195 GLU cc_start: 0.6844 (tp30) cc_final: 0.6557 (tp30) REVERT: B 384 LYS cc_start: 0.6945 (mttt) cc_final: 0.6690 (mttm) REVERT: C 54 GLU cc_start: 0.8510 (tt0) cc_final: 0.8068 (tt0) REVERT: C 304 ARG cc_start: 0.8422 (ptt180) cc_final: 0.8189 (ptt180) REVERT: C 381 ARG cc_start: 0.7167 (mmm-85) cc_final: 0.6523 (tpp-160) REVERT: C 471 HIS cc_start: 0.7677 (t70) cc_final: 0.7396 (t70) REVERT: E 112 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8131 (mtpt) REVERT: E 249 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: F 27 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: F 252 GLN cc_start: 0.7624 (mm110) cc_final: 0.7212 (tp40) REVERT: D 132 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: D 203 MET cc_start: 0.7950 (mtt) cc_final: 0.7569 (mtt) REVERT: D 212 LYS cc_start: 0.7136 (ptmt) cc_final: 0.6596 (ptpp) REVERT: D 422 GLN cc_start: 0.7136 (tp40) cc_final: 0.6801 (tp40) REVERT: G 53 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7571 (tm-30) REVERT: G 147 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7413 (mp0) REVERT: G 166 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7417 (mtp85) REVERT: G 175 GLU cc_start: 0.8095 (tt0) cc_final: 0.7792 (tp30) REVERT: G 262 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8112 (tt) REVERT: 6 7 LYS cc_start: 0.7523 (mtmt) cc_final: 0.7043 (mttp) REVERT: 7 75 MET cc_start: 0.7777 (mtm) cc_final: 0.7534 (mtm) REVERT: H 74 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8535 (mtmm) REVERT: H 143 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7903 (mtpt) REVERT: I 7 GLN cc_start: 0.7607 (mm110) cc_final: 0.7359 (mt0) REVERT: N 36 TYR cc_start: 0.8162 (m-10) cc_final: 0.7585 (m-10) REVERT: R 32 ARG cc_start: 0.7667 (mmp-170) cc_final: 0.6245 (mmm160) REVERT: R 91 LYS cc_start: 0.8208 (tmmt) cc_final: 0.7903 (tmmt) REVERT: S 36 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: S 65 LYS cc_start: 0.8635 (mmtm) cc_final: 0.7655 (mmmt) outliers start: 61 outliers final: 32 residues processed: 603 average time/residue: 0.6938 time to fit residues: 500.6053 Evaluate side-chains 589 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 545 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain S residue 36 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 267 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 453 optimal weight: 0.4980 chunk 297 optimal weight: 3.9990 chunk 383 optimal weight: 0.8980 chunk 401 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 138 optimal weight: 0.1980 chunk 351 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN A 416 GLN A 492 GLN B 78 ASN C 503 ASN E 445 GLN F 458 GLN D 260 ASN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 ASN N 56 GLN R 44 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.105395 restraints weight = 56214.423| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.01 r_work: 0.3175 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39565 Z= 0.119 Angle : 0.540 12.337 53506 Z= 0.273 Chirality : 0.042 0.256 6216 Planarity : 0.004 0.054 6813 Dihedral : 7.314 147.839 5695 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.80 % Favored : 98.18 % Rotamer: Outliers : 1.22 % Allowed : 17.98 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % 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 aren not related in a simple way. whole: 1.36 (0.12), residues: 5000 helix: 2.00 (0.10), residues: 2664 sheet: -0.16 (0.22), residues: 567 loop : -0.39 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 33 TYR 0.014 0.001 TYR P 36 PHE 0.025 0.001 PHE R 79 TRP 0.013 0.001 TRP R 28 HIS 0.012 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00259 (39565) covalent geometry : angle 0.53981 (53506) hydrogen bonds : bond 0.04490 ( 2243) hydrogen bonds : angle 4.31177 ( 6496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 557 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 26 TYR cc_start: 0.8608 (t80) cc_final: 0.8331 (t80) REVERT: K 165 MET cc_start: 0.8526 (tpp) cc_final: 0.8219 (mmm) REVERT: L 80 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: M 85 TYR cc_start: 0.8709 (m-80) cc_final: 0.8480 (m-80) REVERT: A 8 MET cc_start: 0.5688 (mtm) cc_final: 0.4945 (mmt) REVERT: A 347 ASP cc_start: 0.8744 (m-30) cc_final: 0.8356 (m-30) REVERT: A 381 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.6163 (mtp85) REVERT: A 477 GLN cc_start: 0.7743 (tp40) cc_final: 0.7348 (tp40) REVERT: A 488 LYS cc_start: 0.8118 (pttt) cc_final: 0.7640 (ptpt) REVERT: A 491 GLU cc_start: 0.7690 (mm-30) cc_final: 0.6950 (mt-10) REVERT: A 499 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7800 (tm-30) REVERT: B 80 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8239 (pttt) REVERT: B 195 GLU cc_start: 0.6818 (tp30) cc_final: 0.6563 (tp30) REVERT: B 226 MET cc_start: 0.8768 (tpt) cc_final: 0.8258 (tpt) REVERT: C 8 MET cc_start: 0.8530 (ptp) cc_final: 0.8191 (mtm) REVERT: C 54 GLU cc_start: 0.8475 (tt0) cc_final: 0.8045 (tt0) REVERT: C 304 ARG cc_start: 0.8375 (ptt180) cc_final: 0.8149 (ptt180) REVERT: C 381 ARG cc_start: 0.7204 (mmm-85) cc_final: 0.6590 (tpp-160) REVERT: C 471 HIS cc_start: 0.7670 (t70) cc_final: 0.7369 (t70) REVERT: E 249 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: E 415 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.5736 (mpt180) REVERT: F 30 GLU cc_start: 0.7666 (pm20) cc_final: 0.7461 (pt0) REVERT: F 252 GLN cc_start: 0.7601 (mm110) cc_final: 0.7202 (tp40) REVERT: D 132 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: D 202 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6678 (mp0) REVERT: D 203 MET cc_start: 0.7979 (mtt) cc_final: 0.7580 (mtt) REVERT: D 210 ASN cc_start: 0.8592 (t0) cc_final: 0.7983 (t0) REVERT: D 212 LYS cc_start: 0.7164 (ptmt) cc_final: 0.6366 (ptpp) REVERT: D 422 GLN cc_start: 0.7175 (tp40) cc_final: 0.6842 (tp40) REVERT: G 33 ARG cc_start: 0.7529 (mtp-110) cc_final: 0.6902 (ttm110) REVERT: G 53 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7553 (tm-30) REVERT: G 147 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7450 (mp0) REVERT: G 166 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7207 (mtp85) REVERT: G 175 GLU cc_start: 0.8035 (tt0) cc_final: 0.7822 (tp30) REVERT: G 262 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8147 (tt) REVERT: 3 25 ILE cc_start: 0.8866 (mt) cc_final: 0.8658 (mp) REVERT: 6 7 LYS cc_start: 0.7542 (mtmt) cc_final: 0.7069 (mttp) REVERT: 7 75 MET cc_start: 0.7769 (mtm) cc_final: 0.7546 (mtm) REVERT: H 74 LYS cc_start: 0.9018 (mtpt) cc_final: 0.8568 (mtmm) REVERT: H 143 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7960 (mttp) REVERT: I 7 GLN cc_start: 0.7596 (mm110) cc_final: 0.7360 (mt0) REVERT: N 36 TYR cc_start: 0.8110 (m-10) cc_final: 0.7548 (m-10) REVERT: R 32 ARG cc_start: 0.7691 (mmp-170) cc_final: 0.6280 (mmm160) REVERT: S 36 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7522 (mt-10) outliers start: 49 outliers final: 29 residues processed: 588 average time/residue: 0.7034 time to fit residues: 496.3783 Evaluate side-chains 577 residues out of total 4096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 539 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain S residue 36 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 146 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 339 optimal weight: 1.9990 chunk 218 optimal weight: 0.4980 chunk 210 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN A 416 GLN A 492 GLN B 78 ASN C 366 ASN C 503 ASN E 445 GLN F 458 GLN ** G 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN N 4 ASN N 56 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102977 restraints weight = 57963.193| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.04 r_work: 0.3138 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 39565 Z= 0.168 Angle : 0.577 12.761 53506 Z= 0.292 Chirality : 0.043 0.250 6216 Planarity : 0.004 0.052 6813 Dihedral : 7.484 147.599 5695 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.96 % Favored : 98.02 % Rotamer: Outliers : 1.37 % Allowed : 18.15 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.12), residues: 5000 helix: 1.91 (0.10), residues: 2662 sheet: -0.21 (0.21), residues: 574 loop : -0.43 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 33 TYR 0.024 0.001 TYR S 31 PHE 0.025 0.001 PHE R 79 TRP 0.012 0.001 TRP Q 51 HIS 0.011 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00396 (39565) covalent geometry : angle 0.57667 (53506) hydrogen bonds : bond 0.04983 ( 2243) hydrogen bonds : angle 4.39400 ( 6496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21241.19 seconds wall clock time: 359 minutes 34.17 seconds (21574.17 seconds total)