Starting phenix.real_space_refine on Fri Sep 19 01:23:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9az6_44013/09_2025/9az6_44013.cif Found real_map, /net/cci-nas-00/data/ceres_data/9az6_44013/09_2025/9az6_44013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9az6_44013/09_2025/9az6_44013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9az6_44013/09_2025/9az6_44013.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9az6_44013/09_2025/9az6_44013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9az6_44013/09_2025/9az6_44013.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 10 5.49 5 Mg 5 5.21 5 S 133 5.16 5 C 13667 2.51 5 N 3798 2.21 5 O 4218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21831 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2916 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2916 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2916 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2916 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2916 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1422 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 1, 'TRANS': 190} Chain: "G" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 364 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "H" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1422 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 1, 'TRANS': 190} Chain: "I" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 353 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "J" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1422 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 1, 'TRANS': 190} Chain: "K" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 353 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "L" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1422 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 1, 'TRANS': 190} Chain: "M" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 353 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "A" 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: "B" 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: "C" 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: "E" 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} Time building chain proxies: 5.14, per 1000 atoms: 0.24 Number of scatterers: 21831 At special positions: 0 Unit cell: (112.05, 145.25, 192.56, 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 133 16.00 P 10 15.00 Mg 5 11.99 O 4218 8.00 N 3798 7.00 C 13667 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: 1.71 Conformation dependent library (CDL) restraints added in 979.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5252 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 30 sheets defined 61.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.701A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.502A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.614A pdb=" N CYS A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.615A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.704A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.021A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.508A pdb=" N CYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.586A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.775A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.537A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.704A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.511A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.684A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.549A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.180A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.574A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.721A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.225A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.514A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.650A pdb=" N CYS E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 2342 through 2373 Processing helix chain 'F' and resid 2392 through 2416 removed outlier: 4.177A pdb=" N ALA F2396 " --> pdb=" O GLY F2392 " (cutoff:3.500A) Processing helix chain 'F' and resid 2420 through 2446 removed outlier: 3.723A pdb=" N LYS F2445 " --> pdb=" O ALA F2441 " (cutoff:3.500A) Processing helix chain 'F' and resid 2450 through 2478 Processing helix chain 'F' and resid 2479 through 2483 removed outlier: 4.494A pdb=" N ASP F2482 " --> pdb=" O ALA F2479 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN F2483 " --> pdb=" O PHE F2480 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2479 through 2483' Processing helix chain 'F' and resid 2493 through 2530 removed outlier: 3.735A pdb=" N GLU F2507 " --> pdb=" O ALA F2503 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU F2516 " --> pdb=" O GLU F2512 " (cutoff:3.500A) Processing helix chain 'G' and resid 2496 through 2528 removed outlier: 3.635A pdb=" N GLN G2528 " --> pdb=" O GLN G2524 " (cutoff:3.500A) Processing helix chain 'H' and resid 2342 through 2374 Processing helix chain 'H' and resid 2392 through 2416 removed outlier: 3.790A pdb=" N ALA H2396 " --> pdb=" O GLY H2392 " (cutoff:3.500A) Processing helix chain 'H' and resid 2420 through 2445 Processing helix chain 'H' and resid 2450 through 2478 Processing helix chain 'H' and resid 2493 through 2530 removed outlier: 4.069A pdb=" N TYR H2530 " --> pdb=" O ARG H2526 " (cutoff:3.500A) Processing helix chain 'I' and resid 2498 through 2528 Processing helix chain 'J' and resid 2342 through 2373 Processing helix chain 'J' and resid 2392 through 2416 removed outlier: 3.977A pdb=" N ALA J2396 " --> pdb=" O GLY J2392 " (cutoff:3.500A) Processing helix chain 'J' and resid 2420 through 2446 removed outlier: 3.652A pdb=" N LEU J2424 " --> pdb=" O SER J2420 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS J2445 " --> pdb=" O ALA J2441 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA J2446 " --> pdb=" O CYS J2442 " (cutoff:3.500A) Processing helix chain 'J' and resid 2450 through 2478 Processing helix chain 'J' and resid 2493 through 2531 removed outlier: 4.295A pdb=" N TYR J2530 " --> pdb=" O ARG J2526 " (cutoff:3.500A) Processing helix chain 'K' and resid 2498 through 2528 removed outlier: 4.016A pdb=" N GLN K2528 " --> pdb=" O GLN K2524 " (cutoff:3.500A) Processing helix chain 'K' and resid 2534 through 2538 Processing helix chain 'L' and resid 2342 through 2373 Processing helix chain 'L' and resid 2392 through 2415 removed outlier: 3.878A pdb=" N ALA L2396 " --> pdb=" O GLY L2392 " (cutoff:3.500A) Processing helix chain 'L' and resid 2420 through 2446 Processing helix chain 'L' and resid 2450 through 2478 Processing helix chain 'L' and resid 2493 through 2530 Processing helix chain 'M' and resid 2498 through 2528 removed outlier: 3.655A pdb=" N GLN M2528 " --> pdb=" O GLN M2524 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.606A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.512A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.216A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.566A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.497A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.086A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.571A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.468A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 4.113A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.571A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.507A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.606A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.554A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 1385 hydrogen bonds defined for protein. 3795 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: 3.83 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7069 1.34 - 1.46: 3233 1.46 - 1.58: 11637 1.58 - 1.70: 15 1.70 - 1.82: 233 Bond restraints: 22187 Sorted by residual: bond pdb=" CD LYS K2511 " pdb=" CE LYS K2511 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.22e+00 bond pdb=" CB GLU K2516 " pdb=" CG GLU K2516 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.21e+00 bond pdb=" CB GLU G2516 " pdb=" CG GLU G2516 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.08e+00 bond pdb=" CB LYS I2511 " pdb=" CG LYS I2511 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.56e+00 ... (remaining 22182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 29591 2.53 - 5.06: 308 5.06 - 7.59: 66 7.59 - 10.12: 13 10.12 - 12.65: 3 Bond angle restraints: 29981 Sorted by residual: angle pdb=" CB MET A 325 " pdb=" CG MET A 325 " pdb=" SD MET A 325 " ideal model delta sigma weight residual 112.70 100.05 12.65 3.00e+00 1.11e-01 1.78e+01 angle pdb=" N MET D 47 " pdb=" CA MET D 47 " pdb=" C MET D 47 " ideal model delta sigma weight residual 108.45 113.34 -4.89 1.26e+00 6.30e-01 1.51e+01 angle pdb=" CA MET H2508 " pdb=" CB MET H2508 " pdb=" CG MET H2508 " ideal model delta sigma weight residual 114.10 121.62 -7.52 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CB MET E 283 " pdb=" CG MET E 283 " pdb=" SD MET E 283 " ideal model delta sigma weight residual 112.70 123.64 -10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" CA ILE L2425 " pdb=" CB ILE L2425 " pdb=" CG1 ILE L2425 " ideal model delta sigma weight residual 110.40 116.52 -6.12 1.70e+00 3.46e-01 1.30e+01 ... (remaining 29976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 12295 17.97 - 35.94: 947 35.94 - 53.91: 213 53.91 - 71.88: 114 71.88 - 89.85: 37 Dihedral angle restraints: 13606 sinusoidal: 5476 harmonic: 8130 Sorted by residual: dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 7.85 -67.85 1 2.00e+01 2.50e-03 1.50e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 5.64 -65.64 1 2.00e+01 2.50e-03 1.41e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 3.57 -63.57 1 2.00e+01 2.50e-03 1.33e+01 ... (remaining 13603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2293 0.038 - 0.076: 763 0.076 - 0.114: 279 0.114 - 0.152: 31 0.152 - 0.190: 1 Chirality restraints: 3367 Sorted by residual: chirality pdb=" CB ILE F2394 " pdb=" CA ILE F2394 " pdb=" CG1 ILE F2394 " pdb=" CG2 ILE F2394 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CG LEU F2515 " pdb=" CB LEU F2515 " pdb=" CD1 LEU F2515 " pdb=" CD2 LEU F2515 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA MET A 325 " pdb=" N MET A 325 " pdb=" C MET A 325 " pdb=" CB MET A 325 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 3364 not shown) Planarity restraints: 3880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F2508 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C MET F2508 " -0.032 2.00e-02 2.50e+03 pdb=" O MET F2508 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU F2509 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F2516 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C GLU F2516 " 0.031 2.00e-02 2.50e+03 pdb=" O GLU F2516 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU F2517 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F2530 " -0.011 2.00e-02 2.50e+03 1.17e-02 2.74e+00 pdb=" CG TYR F2530 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR F2530 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR F2530 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR F2530 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F2530 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F2530 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F2530 " -0.000 2.00e-02 2.50e+03 ... (remaining 3877 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 74 2.49 - 3.09: 16286 3.09 - 3.69: 34677 3.69 - 4.30: 51169 4.30 - 4.90: 83251 Nonbonded interactions: 185457 Sorted by model distance: nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.887 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.903 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 1.912 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.917 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.917 2.170 ... (remaining 185452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = (chain 'G' and resid 2497 through 2538) selection = chain 'I' selection = chain 'K' selection = chain 'M' } 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=0.05 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.940 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.004 0.045 22187 Z= 0.187 Angle : 0.680 12.654 29981 Z= 0.341 Chirality : 0.042 0.190 3367 Planarity : 0.004 0.063 3880 Dihedral : 15.391 89.853 8354 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.75 % Allowed : 16.61 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.16), residues: 2762 helix: 1.17 (0.14), residues: 1475 sheet: -0.19 (0.27), residues: 325 loop : 0.77 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F2368 TYR 0.029 0.001 TYR F2530 PHE 0.023 0.001 PHE F2341 TRP 0.016 0.002 TRP C 79 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00406 (22187) covalent geometry : angle 0.68029 (29981) hydrogen bonds : bond 0.13357 ( 1369) hydrogen bonds : angle 6.04361 ( 3795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 286 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9390 (mmm) cc_final: 0.7645 (pmt) REVERT: B 72 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7708 (pp20) REVERT: B 355 MET cc_start: 0.9120 (mmp) cc_final: 0.8623 (mmm) REVERT: C 123 MET cc_start: 0.9517 (mmt) cc_final: 0.9304 (mmm) REVERT: D 82 MET cc_start: 0.9262 (tpt) cc_final: 0.8953 (tpt) REVERT: D 355 MET cc_start: 0.9289 (mmp) cc_final: 0.9079 (mmm) REVERT: E 176 MET cc_start: 0.9204 (mmm) cc_final: 0.8932 (mmp) REVERT: F 2453 MET cc_start: 0.8874 (tmm) cc_final: 0.8626 (tmm) REVERT: F 2461 ASN cc_start: 0.8729 (m110) cc_final: 0.8352 (m110) REVERT: F 2465 ARG cc_start: 0.8486 (ptp-110) cc_final: 0.8266 (ptp90) REVERT: G 2520 LYS cc_start: 0.8759 (tmmt) cc_final: 0.8508 (tmtt) REVERT: G 2536 GLU cc_start: -0.1346 (pt0) cc_final: -0.1713 (tt0) REVERT: I 2529 GLN cc_start: 0.8783 (tm130) cc_final: 0.8371 (tm-30) REVERT: J 2405 ASN cc_start: 0.9019 (t0) cc_final: 0.8743 (t0) REVERT: J 2453 MET cc_start: 0.8885 (tpp) cc_final: 0.7614 (tpt) REVERT: J 2456 LEU cc_start: 0.9493 (mm) cc_final: 0.9175 (pp) REVERT: J 2461 ASN cc_start: 0.9042 (m110) cc_final: 0.8732 (m-40) REVERT: K 2507 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8554 (mm-30) REVERT: K 2516 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8041 (tm-30) REVERT: L 2356 THR cc_start: 0.9685 (p) cc_final: 0.9187 (t) REVERT: L 2456 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9178 (pp) REVERT: M 2520 LYS cc_start: 0.8828 (mtpp) cc_final: 0.8597 (mtpp) REVERT: M 2529 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8364 (pp30) REVERT: M 2533 LEU cc_start: 0.8860 (mp) cc_final: 0.8564 (mp) outliers start: 17 outliers final: 6 residues processed: 296 average time/residue: 0.8488 time to fit residues: 275.4508 Evaluate side-chains 282 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 274 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain F residue 2488 VAL Chi-restraints excluded: chain G residue 2502 ILE Chi-restraints excluded: chain H residue 2431 VAL Chi-restraints excluded: chain J residue 2490 VAL Chi-restraints excluded: chain J residue 2501 ILE Chi-restraints excluded: chain L residue 2456 LEU Chi-restraints excluded: chain M residue 2529 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN F2406 ASN F2475 GLN F2505 GLN ** G2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2391 GLN H2485 ASN H2529 GLN J2469 ASN K2505 GLN ** K2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2388 GLN L2405 ASN L2406 ASN ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.088616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.059676 restraints weight = 63381.220| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.31 r_work: 0.2592 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22187 Z= 0.207 Angle : 0.642 13.361 29981 Z= 0.315 Chirality : 0.043 0.163 3367 Planarity : 0.004 0.100 3880 Dihedral : 6.041 83.000 3095 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.16 % Allowed : 15.47 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.16), residues: 2762 helix: 1.58 (0.14), residues: 1473 sheet: -0.12 (0.27), residues: 335 loop : 0.83 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I2538 TYR 0.016 0.001 TYR K2530 PHE 0.023 0.001 PHE M2532 TRP 0.043 0.003 TRP H2389 HIS 0.008 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00467 (22187) covalent geometry : angle 0.64184 (29981) hydrogen bonds : bond 0.04149 ( 1369) hydrogen bonds : angle 4.62907 ( 3795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 282 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9447 (mmm) cc_final: 0.7722 (pmt) REVERT: B 355 MET cc_start: 0.9191 (mmp) cc_final: 0.8668 (mtp) REVERT: C 123 MET cc_start: 0.9565 (mmt) cc_final: 0.9338 (mmm) REVERT: E 176 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8807 (mmp) REVERT: E 355 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.8835 (mpp) REVERT: F 2398 ARG cc_start: 0.9406 (mtp-110) cc_final: 0.9188 (ttp80) REVERT: F 2461 ASN cc_start: 0.9012 (m110) cc_final: 0.8512 (m110) REVERT: G 2510 ARG cc_start: 0.9253 (ptm160) cc_final: 0.8716 (ptp90) REVERT: G 2512 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8500 (mm-30) REVERT: G 2520 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8493 (tmmt) REVERT: G 2524 GLN cc_start: 0.7998 (pp30) cc_final: 0.7322 (pp30) REVERT: G 2536 GLU cc_start: -0.1766 (pt0) cc_final: -0.2270 (tt0) REVERT: H 2399 MET cc_start: 0.9016 (ttm) cc_final: 0.8537 (mtm) REVERT: I 2529 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: J 2405 ASN cc_start: 0.9007 (t0) cc_final: 0.8800 (t0) REVERT: J 2453 MET cc_start: 0.8679 (tpp) cc_final: 0.7670 (tpt) REVERT: J 2456 LEU cc_start: 0.9589 (mm) cc_final: 0.9049 (pp) REVERT: J 2465 ARG cc_start: 0.8958 (ptp-110) cc_final: 0.8740 (ptp-110) REVERT: J 2510 ARG cc_start: 0.8050 (ttm-80) cc_final: 0.7422 (ttm-80) REVERT: K 2514 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8056 (mm-30) REVERT: K 2526 ARG cc_start: 0.8560 (mmm160) cc_final: 0.8340 (mmm-85) REVERT: L 2398 ARG cc_start: 0.9347 (ttm-80) cc_final: 0.9058 (ttp80) REVERT: L 2456 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9447 (tp) REVERT: L 2510 ARG cc_start: 0.8159 (tmm-80) cc_final: 0.7835 (tmm-80) REVERT: M 2510 ARG cc_start: 0.6875 (mmp-170) cc_final: 0.6656 (mmp-170) REVERT: M 2513 ARG cc_start: 0.8839 (ttp-110) cc_final: 0.8416 (ttp80) REVERT: M 2516 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8087 (tm-30) REVERT: M 2529 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7485 (pp30) outliers start: 72 outliers final: 14 residues processed: 310 average time/residue: 0.8573 time to fit residues: 292.7175 Evaluate side-chains 290 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 2442 CYS Chi-restraints excluded: chain G residue 2520 LYS Chi-restraints excluded: chain H residue 2376 VAL Chi-restraints excluded: chain H residue 2425 ILE Chi-restraints excluded: chain H residue 2431 VAL Chi-restraints excluded: chain H residue 2490 VAL Chi-restraints excluded: chain I residue 2529 GLN Chi-restraints excluded: chain J residue 2501 ILE Chi-restraints excluded: chain K residue 2498 ILE Chi-restraints excluded: chain K residue 2533 LEU Chi-restraints excluded: chain L residue 2456 LEU Chi-restraints excluded: chain L residue 2501 ILE Chi-restraints excluded: chain M residue 2502 ILE Chi-restraints excluded: chain M residue 2529 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 126 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 127 optimal weight: 4.9990 chunk 233 optimal weight: 20.0000 chunk 144 optimal weight: 0.2980 chunk 232 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 188 optimal weight: 30.0000 chunk 158 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2406 ASN F2469 ASN J2469 ASN K2505 GLN ** K2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2406 ASN M2528 GLN M2529 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.087759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.059431 restraints weight = 64862.454| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.26 r_work: 0.2617 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22187 Z= 0.143 Angle : 0.601 13.305 29981 Z= 0.290 Chirality : 0.041 0.142 3367 Planarity : 0.004 0.046 3880 Dihedral : 5.894 82.782 3088 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.59 % Allowed : 16.26 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.16), residues: 2762 helix: 1.74 (0.14), residues: 1473 sheet: -0.00 (0.27), residues: 335 loop : 0.82 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I2526 TYR 0.020 0.001 TYR J2530 PHE 0.020 0.001 PHE G2532 TRP 0.021 0.002 TRP H2389 HIS 0.006 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00321 (22187) covalent geometry : angle 0.60075 (29981) hydrogen bonds : bond 0.03787 ( 1369) hydrogen bonds : angle 4.41986 ( 3795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 279 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9456 (mmm) cc_final: 0.7698 (pmt) REVERT: B 72 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7737 (pp20) REVERT: B 355 MET cc_start: 0.9146 (mmp) cc_final: 0.8571 (mtp) REVERT: C 72 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7835 (pp20) REVERT: E 176 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8704 (mmp) REVERT: E 355 MET cc_start: 0.9316 (mmm) cc_final: 0.8857 (mpp) REVERT: F 2398 ARG cc_start: 0.9378 (mtp-110) cc_final: 0.9176 (ttp80) REVERT: F 2461 ASN cc_start: 0.9057 (m110) cc_final: 0.8540 (m110) REVERT: F 2465 ARG cc_start: 0.8686 (ptp-110) cc_final: 0.8463 (ptp90) REVERT: F 2526 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7915 (mtt180) REVERT: G 2500 GLN cc_start: 0.9239 (mp10) cc_final: 0.9008 (mm-40) REVERT: G 2510 ARG cc_start: 0.9204 (ptm160) cc_final: 0.8985 (ptp90) REVERT: G 2512 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8595 (mm-30) REVERT: G 2520 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8471 (tmtt) REVERT: G 2522 LEU cc_start: 0.8861 (tm) cc_final: 0.8449 (tm) REVERT: G 2524 GLN cc_start: 0.7488 (pp30) cc_final: 0.7149 (pp30) REVERT: G 2526 ARG cc_start: 0.9185 (tpp80) cc_final: 0.8811 (mmm-85) REVERT: G 2536 GLU cc_start: -0.2211 (pt0) cc_final: -0.2593 (tt0) REVERT: H 2399 MET cc_start: 0.9033 (ttm) cc_final: 0.8535 (mtm) REVERT: I 2520 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8477 (tptp) REVERT: I 2529 GLN cc_start: 0.8153 (tm130) cc_final: 0.7663 (tm-30) REVERT: J 2368 ARG cc_start: 0.9241 (mmt-90) cc_final: 0.8964 (mmt90) REVERT: J 2398 ARG cc_start: 0.9259 (ttm-80) cc_final: 0.8758 (ttp80) REVERT: J 2453 MET cc_start: 0.8703 (tpp) cc_final: 0.7770 (tpt) REVERT: J 2456 LEU cc_start: 0.9557 (mm) cc_final: 0.9002 (pp) REVERT: J 2465 ARG cc_start: 0.8923 (ptp-110) cc_final: 0.8702 (ptp-110) REVERT: J 2494 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8070 (tmm) REVERT: K 2507 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8754 (mm-30) REVERT: K 2510 ARG cc_start: 0.8287 (ptp90) cc_final: 0.8017 (ptp90) REVERT: K 2516 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8037 (tm-30) REVERT: L 2398 ARG cc_start: 0.9335 (ttm-80) cc_final: 0.9022 (ttp80) REVERT: M 2511 LYS cc_start: 0.8303 (ttmm) cc_final: 0.7373 (tttm) REVERT: M 2512 GLU cc_start: 0.8847 (tp30) cc_final: 0.8647 (mm-30) REVERT: M 2513 ARG cc_start: 0.8816 (ttp-110) cc_final: 0.8447 (ttp-110) REVERT: M 2516 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8100 (tm-30) REVERT: M 2517 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8552 (mm-30) REVERT: M 2529 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7224 (pp30) outliers start: 59 outliers final: 13 residues processed: 304 average time/residue: 0.8067 time to fit residues: 270.6225 Evaluate side-chains 289 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain F residue 2442 CYS Chi-restraints excluded: chain F residue 2526 ARG Chi-restraints excluded: chain G residue 2520 LYS Chi-restraints excluded: chain H residue 2425 ILE Chi-restraints excluded: chain H residue 2431 VAL Chi-restraints excluded: chain H residue 2490 VAL Chi-restraints excluded: chain I residue 2520 LYS Chi-restraints excluded: chain J residue 2494 MET Chi-restraints excluded: chain J residue 2501 ILE Chi-restraints excluded: chain J residue 2505 GLN Chi-restraints excluded: chain K residue 2498 ILE Chi-restraints excluded: chain K residue 2511 LYS Chi-restraints excluded: chain M residue 2502 ILE Chi-restraints excluded: chain M residue 2529 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 134 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 272 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2388 GLN F2405 ASN F2406 ASN F2469 ASN H2421 GLN L2406 ASN ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.086710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.057916 restraints weight = 64268.285| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.31 r_work: 0.2552 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22187 Z= 0.265 Angle : 0.656 13.273 29981 Z= 0.320 Chirality : 0.044 0.152 3367 Planarity : 0.004 0.047 3880 Dihedral : 6.029 92.770 3086 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.94 % Allowed : 16.70 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.16), residues: 2762 helix: 1.66 (0.14), residues: 1503 sheet: 0.07 (0.27), residues: 335 loop : 0.64 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I2526 TYR 0.010 0.001 TYR K2530 PHE 0.019 0.001 PHE G2532 TRP 0.018 0.002 TRP H2389 HIS 0.005 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00603 (22187) covalent geometry : angle 0.65640 (29981) hydrogen bonds : bond 0.04017 ( 1369) hydrogen bonds : angle 4.43434 ( 3795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 271 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9465 (mmm) cc_final: 0.7703 (pmt) REVERT: B 355 MET cc_start: 0.9198 (mmp) cc_final: 0.8735 (mtp) REVERT: C 72 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7845 (pp20) REVERT: E 72 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7903 (pp20) REVERT: E 176 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8760 (mmp) REVERT: E 355 MET cc_start: 0.9365 (mmm) cc_final: 0.9035 (mpp) REVERT: F 2398 ARG cc_start: 0.9382 (mtp-110) cc_final: 0.9178 (ttp80) REVERT: F 2461 ASN cc_start: 0.9102 (m110) cc_final: 0.8658 (m110) REVERT: F 2526 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7921 (mtt180) REVERT: G 2500 GLN cc_start: 0.9278 (mp10) cc_final: 0.9046 (mm-40) REVERT: G 2510 ARG cc_start: 0.9240 (ptm160) cc_final: 0.8827 (ptp90) REVERT: G 2512 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8621 (mm-30) REVERT: G 2519 ARG cc_start: 0.8779 (mmm160) cc_final: 0.8262 (mmm160) REVERT: G 2522 LEU cc_start: 0.8452 (tm) cc_final: 0.8246 (tm) REVERT: G 2526 ARG cc_start: 0.9212 (tpp80) cc_final: 0.8945 (mmm160) REVERT: G 2536 GLU cc_start: -0.1775 (pt0) cc_final: -0.2253 (tt0) REVERT: H 2456 LEU cc_start: 0.9553 (mt) cc_final: 0.8961 (pp) REVERT: H 2510 ARG cc_start: 0.8188 (ttp-170) cc_final: 0.7889 (ttp80) REVERT: I 2520 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8530 (tptp) REVERT: I 2529 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: J 2368 ARG cc_start: 0.9270 (mmt-90) cc_final: 0.8907 (mmt90) REVERT: J 2453 MET cc_start: 0.8689 (tpp) cc_final: 0.7677 (tpt) REVERT: J 2456 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9016 (pp) REVERT: J 2461 ASN cc_start: 0.8960 (m110) cc_final: 0.8576 (m110) REVERT: K 2507 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8772 (mm-30) REVERT: K 2510 ARG cc_start: 0.8605 (ptp90) cc_final: 0.7969 (ptp90) REVERT: K 2513 ARG cc_start: 0.8812 (mmm160) cc_final: 0.8446 (mtp-110) REVERT: K 2514 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7983 (mm-30) REVERT: L 2398 ARG cc_start: 0.9387 (ttm-80) cc_final: 0.9094 (ttp80) REVERT: M 2500 GLN cc_start: 0.8858 (mp10) cc_final: 0.8572 (pm20) REVERT: M 2508 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8175 (ttm) REVERT: M 2513 ARG cc_start: 0.8845 (ttp-110) cc_final: 0.8318 (ttp-110) REVERT: M 2516 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7999 (tm-30) REVERT: M 2529 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7249 (pp30) outliers start: 67 outliers final: 17 residues processed: 302 average time/residue: 0.8199 time to fit residues: 272.1027 Evaluate side-chains 291 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 265 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain F residue 2442 CYS Chi-restraints excluded: chain F residue 2501 ILE Chi-restraints excluded: chain F residue 2526 ARG Chi-restraints excluded: chain H residue 2425 ILE Chi-restraints excluded: chain H residue 2431 VAL Chi-restraints excluded: chain H residue 2490 VAL Chi-restraints excluded: chain I residue 2520 LYS Chi-restraints excluded: chain I residue 2529 GLN Chi-restraints excluded: chain J residue 2456 LEU Chi-restraints excluded: chain J residue 2501 ILE Chi-restraints excluded: chain J residue 2505 GLN Chi-restraints excluded: chain K residue 2498 ILE Chi-restraints excluded: chain K residue 2509 LEU Chi-restraints excluded: chain M residue 2498 ILE Chi-restraints excluded: chain M residue 2502 ILE Chi-restraints excluded: chain M residue 2508 MET Chi-restraints excluded: chain M residue 2529 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 261 optimal weight: 0.0030 chunk 157 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 253 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN F2406 ASN ** K2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2344 GLN L2406 ASN ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.089403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.060324 restraints weight = 62706.032| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.29 r_work: 0.2603 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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 : 0.003 0.045 22187 Z= 0.143 Angle : 0.617 13.951 29981 Z= 0.297 Chirality : 0.042 0.173 3367 Planarity : 0.004 0.049 3880 Dihedral : 5.880 86.836 3086 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.46 % Allowed : 17.66 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.16), residues: 2762 helix: 1.73 (0.14), residues: 1503 sheet: 0.15 (0.27), residues: 335 loop : 0.67 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I2526 TYR 0.019 0.001 TYR J2530 PHE 0.021 0.001 PHE G2532 TRP 0.014 0.002 TRP H2389 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00320 (22187) covalent geometry : angle 0.61714 (29981) hydrogen bonds : bond 0.03606 ( 1369) hydrogen bonds : angle 4.31852 ( 3795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 275 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9469 (mmm) cc_final: 0.7693 (pmt) REVERT: B 72 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7755 (pp20) REVERT: B 355 MET cc_start: 0.9176 (mmp) cc_final: 0.8508 (mtp) REVERT: C 72 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7861 (pp20) REVERT: D 47 MET cc_start: 0.8257 (mmt) cc_final: 0.7295 (mmt) REVERT: E 72 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7888 (pp20) REVERT: E 176 MET cc_start: 0.9049 (mmm) cc_final: 0.8735 (mmp) REVERT: E 355 MET cc_start: 0.9363 (mmm) cc_final: 0.8881 (mpp) REVERT: F 2461 ASN cc_start: 0.9079 (m110) cc_final: 0.8442 (m110) REVERT: F 2465 ARG cc_start: 0.8734 (ptp90) cc_final: 0.8451 (ptp90) REVERT: G 2500 GLN cc_start: 0.9285 (mp10) cc_final: 0.9041 (mm-40) REVERT: G 2512 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8609 (mm-30) REVERT: G 2522 LEU cc_start: 0.8513 (tm) cc_final: 0.8187 (tm) REVERT: G 2526 ARG cc_start: 0.9191 (tpp80) cc_final: 0.8466 (mmm160) REVERT: G 2529 GLN cc_start: 0.8129 (pp30) cc_final: 0.7615 (pm20) REVERT: G 2536 GLU cc_start: -0.2101 (pt0) cc_final: -0.2563 (tt0) REVERT: H 2399 MET cc_start: 0.8914 (ttm) cc_final: 0.8385 (mtm) REVERT: H 2456 LEU cc_start: 0.9560 (mt) cc_final: 0.8998 (pp) REVERT: H 2510 ARG cc_start: 0.8139 (ttp-170) cc_final: 0.7838 (ttp80) REVERT: I 2520 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8561 (tptp) REVERT: I 2529 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: J 2368 ARG cc_start: 0.9255 (mmt-90) cc_final: 0.8852 (mmt90) REVERT: J 2398 ARG cc_start: 0.9304 (ttm-80) cc_final: 0.8856 (ttp80) REVERT: J 2453 MET cc_start: 0.8757 (tpp) cc_final: 0.7857 (tpt) REVERT: J 2456 LEU cc_start: 0.9562 (mm) cc_final: 0.8986 (pp) REVERT: J 2461 ASN cc_start: 0.8933 (m110) cc_final: 0.8489 (m110) REVERT: K 2507 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8770 (mm-30) REVERT: K 2510 ARG cc_start: 0.8533 (ptp90) cc_final: 0.8140 (ptp90) REVERT: K 2513 ARG cc_start: 0.8840 (mmm160) cc_final: 0.8629 (mmm160) REVERT: K 2514 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8165 (mm-30) REVERT: K 2516 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7973 (tm-30) REVERT: K 2520 LYS cc_start: 0.8938 (mmmt) cc_final: 0.8460 (tptp) REVERT: K 2526 ARG cc_start: 0.8833 (tpp80) cc_final: 0.8424 (mmm-85) REVERT: K 2531 LYS cc_start: 0.7729 (pptt) cc_final: 0.7482 (pptt) REVERT: K 2532 PHE cc_start: 0.6631 (p90) cc_final: 0.6424 (p90) REVERT: L 2344 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8211 (mp10) REVERT: L 2398 ARG cc_start: 0.9372 (ttm-80) cc_final: 0.9083 (ttp80) REVERT: L 2456 LEU cc_start: 0.9797 (tp) cc_final: 0.9422 (pp) REVERT: M 2500 GLN cc_start: 0.8804 (mp10) cc_final: 0.8519 (pm20) REVERT: M 2511 LYS cc_start: 0.8364 (tttm) cc_final: 0.7468 (tttm) REVERT: M 2513 ARG cc_start: 0.8768 (ttp-110) cc_final: 0.8454 (ttp-110) REVERT: M 2516 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8124 (tm-30) REVERT: M 2517 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8488 (mm-30) REVERT: M 2520 LYS cc_start: 0.8953 (mtpp) cc_final: 0.8694 (mtpp) REVERT: M 2529 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7195 (pp30) outliers start: 56 outliers final: 16 residues processed: 301 average time/residue: 0.8212 time to fit residues: 271.9892 Evaluate side-chains 289 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 267 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 2442 CYS Chi-restraints excluded: chain F residue 2526 ARG Chi-restraints excluded: chain G residue 2505 GLN Chi-restraints excluded: chain H residue 2425 ILE Chi-restraints excluded: chain H residue 2431 VAL Chi-restraints excluded: chain H residue 2490 VAL Chi-restraints excluded: chain I residue 2520 LYS Chi-restraints excluded: chain I residue 2529 GLN Chi-restraints excluded: chain J residue 2501 ILE Chi-restraints excluded: chain K residue 2498 ILE Chi-restraints excluded: chain K residue 2509 LEU Chi-restraints excluded: chain L residue 2344 GLN Chi-restraints excluded: chain M residue 2502 ILE Chi-restraints excluded: chain M residue 2529 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 211 optimal weight: 0.0980 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2405 ASN F2406 ASN F2469 ASN ** G2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2500 GLN ** K2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2344 GLN L2406 ASN ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.087762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.059053 restraints weight = 63639.872| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.24 r_work: 0.2583 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 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 0.045 22187 Z= 0.208 Angle : 0.640 13.766 29981 Z= 0.311 Chirality : 0.043 0.212 3367 Planarity : 0.004 0.043 3880 Dihedral : 5.906 89.007 3086 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.68 % Allowed : 17.75 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.16), residues: 2762 helix: 1.74 (0.14), residues: 1503 sheet: 0.20 (0.27), residues: 335 loop : 0.61 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I2526 TYR 0.023 0.001 TYR K2530 PHE 0.021 0.001 PHE G2532 TRP 0.013 0.002 TRP C 79 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00474 (22187) covalent geometry : angle 0.64015 (29981) hydrogen bonds : bond 0.03713 ( 1369) hydrogen bonds : angle 4.33798 ( 3795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9459 (mmm) cc_final: 0.7704 (pmt) REVERT: B 355 MET cc_start: 0.9190 (mmp) cc_final: 0.8568 (mtp) REVERT: C 72 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7888 (pp20) REVERT: D 49 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: E 72 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7893 (pp20) REVERT: E 176 MET cc_start: 0.9061 (mmm) cc_final: 0.8755 (mmp) REVERT: E 355 MET cc_start: 0.9383 (mmm) cc_final: 0.8908 (mpp) REVERT: F 2461 ASN cc_start: 0.9123 (m110) cc_final: 0.8466 (m110) REVERT: F 2465 ARG cc_start: 0.8757 (ptp90) cc_final: 0.8474 (ptp90) REVERT: G 2500 GLN cc_start: 0.9307 (mp10) cc_final: 0.9056 (mm-40) REVERT: G 2510 ARG cc_start: 0.9034 (ptp-110) cc_final: 0.8702 (ptp90) REVERT: G 2512 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8599 (mm-30) REVERT: G 2513 ARG cc_start: 0.8747 (tmm-80) cc_final: 0.8527 (ttm-80) REVERT: G 2526 ARG cc_start: 0.9188 (tpp80) cc_final: 0.8606 (mmm160) REVERT: G 2529 GLN cc_start: 0.8203 (pp30) cc_final: 0.7735 (pp30) REVERT: H 2399 MET cc_start: 0.8914 (ttm) cc_final: 0.8383 (mtm) REVERT: H 2456 LEU cc_start: 0.9576 (mt) cc_final: 0.9029 (pp) REVERT: H 2510 ARG cc_start: 0.8178 (ttp-170) cc_final: 0.7854 (ttp80) REVERT: I 2520 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8475 (tptp) REVERT: J 2368 ARG cc_start: 0.9270 (mmt-90) cc_final: 0.8856 (mmt90) REVERT: J 2453 MET cc_start: 0.8773 (tpp) cc_final: 0.7828 (tpt) REVERT: J 2456 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.8994 (pp) REVERT: J 2508 MET cc_start: 0.8817 (ttp) cc_final: 0.8545 (ttp) REVERT: K 2507 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8745 (mm-30) REVERT: K 2510 ARG cc_start: 0.8585 (ptp90) cc_final: 0.8221 (ptp90) REVERT: K 2512 GLU cc_start: 0.9189 (tp30) cc_final: 0.8942 (mm-30) REVERT: K 2513 ARG cc_start: 0.8839 (mmm160) cc_final: 0.8619 (mmm160) REVERT: K 2514 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8217 (mm-30) REVERT: K 2516 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7979 (tm-30) REVERT: L 2344 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8496 (pm20) REVERT: L 2398 ARG cc_start: 0.9363 (ttm-80) cc_final: 0.9067 (ttp80) REVERT: L 2456 LEU cc_start: 0.9804 (tp) cc_final: 0.9416 (pp) REVERT: M 2513 ARG cc_start: 0.8863 (ttp-110) cc_final: 0.8340 (ttp-110) REVERT: M 2516 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8033 (tm-30) REVERT: M 2520 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8685 (mtpp) REVERT: M 2529 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7182 (pp30) REVERT: M 2538 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.6975 (ppp80) outliers start: 61 outliers final: 21 residues processed: 302 average time/residue: 0.8213 time to fit residues: 272.7406 Evaluate side-chains 292 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 263 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain F residue 2442 CYS Chi-restraints excluded: chain F residue 2525 ILE Chi-restraints excluded: chain F residue 2526 ARG Chi-restraints excluded: chain G residue 2505 GLN Chi-restraints excluded: chain H residue 2425 ILE Chi-restraints excluded: chain H residue 2431 VAL Chi-restraints excluded: chain H residue 2490 VAL Chi-restraints excluded: chain I residue 2520 LYS Chi-restraints excluded: chain J residue 2442 CYS Chi-restraints excluded: chain J residue 2456 LEU Chi-restraints excluded: chain J residue 2501 ILE Chi-restraints excluded: chain K residue 2498 ILE Chi-restraints excluded: chain L residue 2344 GLN Chi-restraints excluded: chain M residue 2502 ILE Chi-restraints excluded: chain M residue 2525 ILE Chi-restraints excluded: chain M residue 2529 GLN Chi-restraints excluded: chain M residue 2538 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 257 optimal weight: 0.0170 chunk 208 optimal weight: 40.0000 chunk 170 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 174 optimal weight: 0.4980 chunk 236 optimal weight: 6.9990 chunk 215 optimal weight: 30.0000 overall best weight: 3.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2344 GLN L2406 ASN L2461 ASN ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.087587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.058897 restraints weight = 64057.495| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.23 r_work: 0.2586 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22187 Z= 0.204 Angle : 0.655 13.894 29981 Z= 0.319 Chirality : 0.043 0.210 3367 Planarity : 0.004 0.054 3880 Dihedral : 5.918 89.337 3086 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.24 % Allowed : 18.41 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.16), residues: 2762 helix: 1.75 (0.14), residues: 1503 sheet: 0.24 (0.27), residues: 335 loop : 0.59 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I2526 TYR 0.017 0.001 TYR J2530 PHE 0.022 0.001 PHE G2532 TRP 0.013 0.002 TRP C 79 HIS 0.004 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00466 (22187) covalent geometry : angle 0.65502 (29981) hydrogen bonds : bond 0.03701 ( 1369) hydrogen bonds : angle 4.33661 ( 3795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 271 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9462 (mmm) cc_final: 0.7708 (pmt) REVERT: B 72 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7787 (pp20) REVERT: B 355 MET cc_start: 0.9206 (mmp) cc_final: 0.8595 (mtp) REVERT: C 72 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7808 (pp20) REVERT: D 49 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: E 72 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7879 (pp20) REVERT: E 176 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8744 (mmp) REVERT: E 355 MET cc_start: 0.9380 (mmm) cc_final: 0.8912 (mpp) REVERT: F 2398 ARG cc_start: 0.9142 (ttp80) cc_final: 0.8401 (ttp80) REVERT: F 2461 ASN cc_start: 0.9105 (m110) cc_final: 0.8571 (m110) REVERT: F 2510 ARG cc_start: 0.8959 (ttp80) cc_final: 0.8546 (ttp80) REVERT: G 2500 GLN cc_start: 0.9314 (mp10) cc_final: 0.9046 (mm-40) REVERT: G 2510 ARG cc_start: 0.9064 (ptp-110) cc_final: 0.8819 (ptp90) REVERT: G 2512 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8791 (mm-30) REVERT: G 2526 ARG cc_start: 0.9174 (tpp80) cc_final: 0.8618 (mmm160) REVERT: G 2529 GLN cc_start: 0.8267 (pp30) cc_final: 0.7713 (pp30) REVERT: H 2399 MET cc_start: 0.8922 (ttm) cc_final: 0.8457 (mtm) REVERT: H 2456 LEU cc_start: 0.9577 (mt) cc_final: 0.9055 (pp) REVERT: H 2510 ARG cc_start: 0.8176 (ttp-170) cc_final: 0.7851 (ttp80) REVERT: I 2520 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8493 (tptp) REVERT: I 2529 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7385 (tm-30) REVERT: J 2368 ARG cc_start: 0.9259 (mmt-90) cc_final: 0.8823 (mmt90) REVERT: J 2453 MET cc_start: 0.8778 (tpp) cc_final: 0.7845 (tpt) REVERT: J 2456 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.8995 (pp) REVERT: J 2508 MET cc_start: 0.8793 (ttp) cc_final: 0.8535 (ttp) REVERT: K 2507 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8767 (mm-30) REVERT: K 2510 ARG cc_start: 0.8555 (ptp90) cc_final: 0.8142 (ptp90) REVERT: K 2512 GLU cc_start: 0.9191 (tp30) cc_final: 0.8923 (mm-30) REVERT: K 2516 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8052 (tm-30) REVERT: K 2520 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8441 (tptp) REVERT: K 2526 ARG cc_start: 0.8751 (tpp80) cc_final: 0.8471 (mmm160) REVERT: K 2528 GLN cc_start: 0.7653 (mp10) cc_final: 0.7298 (mt0) REVERT: K 2531 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7736 (pptt) REVERT: L 2344 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8522 (pm20) REVERT: L 2456 LEU cc_start: 0.9808 (tp) cc_final: 0.9403 (pp) REVERT: M 2500 GLN cc_start: 0.8868 (mp10) cc_final: 0.8594 (pm20) REVERT: M 2511 LYS cc_start: 0.8611 (ttmm) cc_final: 0.7738 (ttmm) REVERT: M 2513 ARG cc_start: 0.8758 (ttp-110) cc_final: 0.8468 (ttp-110) REVERT: M 2516 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8197 (tm-30) REVERT: M 2520 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8657 (mtpp) REVERT: M 2529 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7242 (pp30) outliers start: 51 outliers final: 22 residues processed: 301 average time/residue: 0.8044 time to fit residues: 266.6799 Evaluate side-chains 298 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 267 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain F residue 2442 CYS Chi-restraints excluded: chain F residue 2525 ILE Chi-restraints excluded: chain F residue 2526 ARG Chi-restraints excluded: chain F residue 2530 TYR Chi-restraints excluded: chain G residue 2505 GLN Chi-restraints excluded: chain G residue 2508 MET Chi-restraints excluded: chain H residue 2425 ILE Chi-restraints excluded: chain H residue 2431 VAL Chi-restraints excluded: chain H residue 2490 VAL Chi-restraints excluded: chain I residue 2520 LYS Chi-restraints excluded: chain J residue 2442 CYS Chi-restraints excluded: chain J residue 2456 LEU Chi-restraints excluded: chain J residue 2501 ILE Chi-restraints excluded: chain K residue 2498 ILE Chi-restraints excluded: chain K residue 2531 LYS Chi-restraints excluded: chain L residue 2344 GLN Chi-restraints excluded: chain M residue 2502 ILE Chi-restraints excluded: chain M residue 2529 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 204 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 266 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2405 ASN F2469 ASN ** G2524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2528 GLN L2344 GLN L2406 ASN ** M2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.087337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.058302 restraints weight = 63968.669| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.31 r_work: 0.2554 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 22187 Z= 0.264 Angle : 0.701 13.787 29981 Z= 0.341 Chirality : 0.044 0.237 3367 Planarity : 0.004 0.066 3880 Dihedral : 6.048 93.394 3086 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.24 % Allowed : 18.80 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.16), residues: 2762 helix: 1.71 (0.14), residues: 1503 sheet: 0.23 (0.27), residues: 335 loop : 0.55 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K2513 TYR 0.020 0.001 TYR K2530 PHE 0.023 0.001 PHE M2532 TRP 0.013 0.002 TRP C 79 HIS 0.004 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00602 (22187) covalent geometry : angle 0.70136 (29981) hydrogen bonds : bond 0.03881 ( 1369) hydrogen bonds : angle 4.41696 ( 3795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 272 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9460 (mmm) cc_final: 0.7696 (pmt) REVERT: B 355 MET cc_start: 0.9221 (mmp) cc_final: 0.8602 (mtp) REVERT: C 72 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7850 (pp20) REVERT: C 355 MET cc_start: 0.9217 (mtp) cc_final: 0.9011 (mtp) REVERT: E 72 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7897 (pp20) REVERT: E 176 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8754 (mmp) REVERT: F 2453 MET cc_start: 0.8915 (tmm) cc_final: 0.8657 (tmm) REVERT: F 2461 ASN cc_start: 0.9087 (m110) cc_final: 0.8613 (m110) REVERT: G 2500 GLN cc_start: 0.9304 (mp10) cc_final: 0.9043 (mm-40) REVERT: G 2510 ARG cc_start: 0.9060 (ptp-110) cc_final: 0.8652 (ptp90) REVERT: G 2512 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8758 (mm-30) REVERT: G 2513 ARG cc_start: 0.8736 (tmm-80) cc_final: 0.8524 (ttm-80) REVERT: G 2526 ARG cc_start: 0.9145 (tpp80) cc_final: 0.8774 (mmm160) REVERT: G 2529 GLN cc_start: 0.8277 (pp30) cc_final: 0.7689 (pp30) REVERT: H 2399 MET cc_start: 0.8930 (ttm) cc_final: 0.8440 (mtm) REVERT: H 2456 LEU cc_start: 0.9567 (mt) cc_final: 0.9050 (pp) REVERT: H 2510 ARG cc_start: 0.8149 (ttp-170) cc_final: 0.7864 (ttp80) REVERT: I 2520 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8494 (tptp) REVERT: I 2529 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7309 (tm-30) REVERT: J 2368 ARG cc_start: 0.9275 (mmt-90) cc_final: 0.8847 (mmt90) REVERT: J 2453 MET cc_start: 0.8774 (tpp) cc_final: 0.7863 (tpt) REVERT: J 2456 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.8992 (pp) REVERT: J 2508 MET cc_start: 0.8813 (ttp) cc_final: 0.8601 (ttp) REVERT: K 2507 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8742 (mm-30) REVERT: K 2510 ARG cc_start: 0.8545 (ptp90) cc_final: 0.7988 (ptp90) REVERT: K 2512 GLU cc_start: 0.9204 (tp30) cc_final: 0.8931 (mm-30) REVERT: K 2513 ARG cc_start: 0.8794 (mmm160) cc_final: 0.8376 (mtp-110) REVERT: K 2514 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7856 (mm-30) REVERT: K 2526 ARG cc_start: 0.8727 (tpp80) cc_final: 0.8389 (mmm160) REVERT: L 2398 ARG cc_start: 0.9226 (ttm-80) cc_final: 0.8921 (ttm-80) REVERT: L 2456 LEU cc_start: 0.9806 (tp) cc_final: 0.9386 (pp) REVERT: M 2500 GLN cc_start: 0.8831 (mp10) cc_final: 0.8547 (pm20) REVERT: M 2513 ARG cc_start: 0.8822 (ttp-110) cc_final: 0.8379 (ttp80) REVERT: M 2516 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8052 (tm-30) REVERT: M 2517 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8351 (mm-30) REVERT: M 2520 LYS cc_start: 0.8975 (mtpp) cc_final: 0.8691 (mtpp) REVERT: M 2529 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7247 (pp30) outliers start: 51 outliers final: 20 residues processed: 298 average time/residue: 0.7955 time to fit residues: 261.2056 Evaluate side-chains 292 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 266 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain F residue 2442 CYS Chi-restraints excluded: chain F residue 2525 ILE Chi-restraints excluded: chain F residue 2526 ARG Chi-restraints excluded: chain F residue 2530 TYR Chi-restraints excluded: chain H residue 2425 ILE Chi-restraints excluded: chain H residue 2431 VAL Chi-restraints excluded: chain H residue 2490 VAL Chi-restraints excluded: chain I residue 2520 LYS Chi-restraints excluded: chain J residue 2442 CYS Chi-restraints excluded: chain J residue 2456 LEU Chi-restraints excluded: chain J residue 2490 VAL Chi-restraints excluded: chain J residue 2501 ILE Chi-restraints excluded: chain L residue 2344 GLN Chi-restraints excluded: chain L residue 2490 VAL Chi-restraints excluded: chain M residue 2529 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 23 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 237 optimal weight: 9.9990 chunk 214 optimal weight: 20.0000 chunk 230 optimal weight: 30.0000 chunk 210 optimal weight: 30.0000 chunk 219 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2406 ASN ** G2524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2382 ASN K2529 GLN L2406 ASN ** M2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.087622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.058437 restraints weight = 63980.641| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.34 r_work: 0.2546 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 22187 Z= 0.266 Angle : 0.714 13.838 29981 Z= 0.348 Chirality : 0.045 0.276 3367 Planarity : 0.004 0.071 3880 Dihedral : 6.120 95.095 3086 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.71 % Allowed : 19.42 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.16), residues: 2762 helix: 1.69 (0.14), residues: 1504 sheet: 0.22 (0.27), residues: 335 loop : 0.51 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K2513 TYR 0.015 0.001 TYR J2530 PHE 0.026 0.001 PHE G2532 TRP 0.032 0.002 TRP H2389 HIS 0.005 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00608 (22187) covalent geometry : angle 0.71433 (29981) hydrogen bonds : bond 0.03901 ( 1369) hydrogen bonds : angle 4.42804 ( 3795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9465 (mmm) cc_final: 0.7701 (pmt) REVERT: B 355 MET cc_start: 0.9231 (mmp) cc_final: 0.8621 (mtp) REVERT: C 72 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7875 (pp20) REVERT: C 355 MET cc_start: 0.9238 (mtp) cc_final: 0.9021 (mtp) REVERT: D 62 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8736 (mtm-85) REVERT: E 72 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7910 (pp20) REVERT: E 176 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8756 (mmp) REVERT: F 2453 MET cc_start: 0.8927 (tmm) cc_final: 0.8650 (tmm) REVERT: F 2461 ASN cc_start: 0.9041 (m110) cc_final: 0.8619 (m110) REVERT: G 2500 GLN cc_start: 0.9286 (mp10) cc_final: 0.9016 (mm-40) REVERT: G 2512 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8856 (mm-30) REVERT: G 2513 ARG cc_start: 0.8741 (tmm-80) cc_final: 0.8539 (tmm-80) REVERT: G 2519 ARG cc_start: 0.9133 (mmt90) cc_final: 0.8927 (mmm160) REVERT: G 2526 ARG cc_start: 0.9153 (tpp80) cc_final: 0.8760 (mmm160) REVERT: G 2529 GLN cc_start: 0.8257 (pp30) cc_final: 0.7683 (pp30) REVERT: G 2530 TYR cc_start: 0.8818 (p90) cc_final: 0.8609 (p90) REVERT: H 2456 LEU cc_start: 0.9557 (mt) cc_final: 0.9032 (pp) REVERT: H 2510 ARG cc_start: 0.8151 (ttp-170) cc_final: 0.7842 (ttp80) REVERT: I 2520 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8506 (tptp) REVERT: I 2526 ARG cc_start: 0.8630 (tpp80) cc_final: 0.8361 (mmm160) REVERT: I 2529 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7372 (tm-30) REVERT: J 2368 ARG cc_start: 0.9285 (mmt-90) cc_final: 0.8859 (mmt90) REVERT: J 2453 MET cc_start: 0.8781 (tpp) cc_final: 0.7896 (tpt) REVERT: J 2456 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.8989 (pp) REVERT: K 2507 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8747 (mm-30) REVERT: K 2510 ARG cc_start: 0.8553 (ptp90) cc_final: 0.8000 (ptp90) REVERT: K 2512 GLU cc_start: 0.9190 (tp30) cc_final: 0.8918 (mm-30) REVERT: K 2513 ARG cc_start: 0.8808 (mmm160) cc_final: 0.8425 (mtp-110) REVERT: K 2514 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7975 (mm-30) REVERT: K 2526 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8381 (mmm160) REVERT: L 2398 ARG cc_start: 0.9265 (ttm-80) cc_final: 0.8947 (ttm-80) REVERT: L 2456 LEU cc_start: 0.9808 (tp) cc_final: 0.9382 (pp) REVERT: M 2500 GLN cc_start: 0.8805 (mp10) cc_final: 0.8517 (pm20) REVERT: M 2511 LYS cc_start: 0.8224 (tttm) cc_final: 0.7523 (tttm) REVERT: M 2516 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8121 (tm-30) REVERT: M 2520 LYS cc_start: 0.8999 (mtpp) cc_final: 0.8704 (mtpp) outliers start: 39 outliers final: 18 residues processed: 288 average time/residue: 0.8502 time to fit residues: 268.5981 Evaluate side-chains 290 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain F residue 2442 CYS Chi-restraints excluded: chain F residue 2525 ILE Chi-restraints excluded: chain F residue 2526 ARG Chi-restraints excluded: chain F residue 2530 TYR Chi-restraints excluded: chain H residue 2425 ILE Chi-restraints excluded: chain H residue 2431 VAL Chi-restraints excluded: chain H residue 2490 VAL Chi-restraints excluded: chain I residue 2520 LYS Chi-restraints excluded: chain J residue 2442 CYS Chi-restraints excluded: chain J residue 2456 LEU Chi-restraints excluded: chain J residue 2490 VAL Chi-restraints excluded: chain J residue 2501 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 212 optimal weight: 0.0370 chunk 36 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2405 ASN F2469 ASN ** G2524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2529 GLN L2406 ASN L2416 GLN ** M2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.091186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.061616 restraints weight = 62577.309| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.33 r_work: 0.2598 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22187 Z= 0.138 Angle : 0.702 17.085 29981 Z= 0.338 Chirality : 0.043 0.263 3367 Planarity : 0.004 0.067 3880 Dihedral : 5.784 86.595 3083 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.32 % Allowed : 19.82 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.16), residues: 2762 helix: 1.72 (0.14), residues: 1504 sheet: 0.33 (0.27), residues: 335 loop : 0.52 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I2519 TYR 0.019 0.001 TYR K2530 PHE 0.029 0.001 PHE G2532 TRP 0.092 0.003 TRP H2389 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00313 (22187) covalent geometry : angle 0.70201 (29981) hydrogen bonds : bond 0.03651 ( 1369) hydrogen bonds : angle 4.36238 ( 3795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9454 (mmm) cc_final: 0.7707 (pmt) REVERT: B 47 MET cc_start: -0.0350 (OUTLIER) cc_final: -0.0748 (ptt) REVERT: B 72 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7789 (pp20) REVERT: B 355 MET cc_start: 0.9197 (mmp) cc_final: 0.8608 (mtp) REVERT: C 72 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7861 (pp20) REVERT: E 72 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7884 (pp20) REVERT: E 176 MET cc_start: 0.9060 (mmm) cc_final: 0.8745 (mmp) REVERT: E 355 MET cc_start: 0.9393 (mmm) cc_final: 0.8925 (mpp) REVERT: F 2453 MET cc_start: 0.8922 (tmm) cc_final: 0.8369 (tmm) REVERT: F 2456 LEU cc_start: 0.9626 (mt) cc_final: 0.9265 (pp) REVERT: F 2461 ASN cc_start: 0.9058 (m110) cc_final: 0.8630 (m110) REVERT: G 2500 GLN cc_start: 0.9273 (mp10) cc_final: 0.9024 (mm-40) REVERT: G 2512 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8670 (mm-30) REVERT: G 2519 ARG cc_start: 0.9143 (mmt90) cc_final: 0.8901 (mmm160) REVERT: G 2526 ARG cc_start: 0.9125 (tpp80) cc_final: 0.8764 (mmm160) REVERT: G 2529 GLN cc_start: 0.8219 (pp30) cc_final: 0.7444 (pp30) REVERT: G 2538 ARG cc_start: 0.7886 (ptm-80) cc_final: 0.7423 (tpm170) REVERT: H 2399 MET cc_start: 0.8783 (ttm) cc_final: 0.8185 (mtm) REVERT: H 2456 LEU cc_start: 0.9562 (mt) cc_final: 0.9033 (pp) REVERT: I 2520 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8497 (tptp) REVERT: I 2526 ARG cc_start: 0.8615 (tpp80) cc_final: 0.8377 (mmm160) REVERT: I 2529 GLN cc_start: 0.7683 (tm-30) cc_final: 0.7152 (tm130) REVERT: J 2368 ARG cc_start: 0.9311 (mmt-90) cc_final: 0.8919 (mmt90) REVERT: J 2453 MET cc_start: 0.8788 (tpp) cc_final: 0.7925 (tpt) REVERT: J 2456 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.8997 (pp) REVERT: J 2461 ASN cc_start: 0.8833 (m110) cc_final: 0.8590 (m110) REVERT: K 2506 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8679 (mm-30) REVERT: K 2507 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8802 (mm-30) REVERT: K 2508 MET cc_start: 0.7934 (ttm) cc_final: 0.7357 (ttm) REVERT: K 2510 ARG cc_start: 0.8571 (ptp90) cc_final: 0.7916 (ptp90) REVERT: K 2512 GLU cc_start: 0.9114 (tp30) cc_final: 0.8780 (mm-30) REVERT: K 2513 ARG cc_start: 0.8680 (mmm160) cc_final: 0.8472 (mtm110) REVERT: K 2514 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8119 (mm-30) REVERT: K 2519 ARG cc_start: 0.8858 (ttm110) cc_final: 0.8485 (ttm110) REVERT: K 2526 ARG cc_start: 0.8726 (tpp80) cc_final: 0.8373 (mmm160) REVERT: K 2531 LYS cc_start: 0.8992 (ptpp) cc_final: 0.8717 (ptpp) REVERT: L 2398 ARG cc_start: 0.9262 (ttm-80) cc_final: 0.8936 (ttm-80) REVERT: L 2456 LEU cc_start: 0.9802 (tp) cc_final: 0.9387 (pp) REVERT: M 2500 GLN cc_start: 0.8785 (mp10) cc_final: 0.8485 (pm20) REVERT: M 2513 ARG cc_start: 0.8567 (tmm-80) cc_final: 0.8296 (ttp80) REVERT: M 2520 LYS cc_start: 0.8932 (mtpp) cc_final: 0.8700 (mtpp) outliers start: 30 outliers final: 13 residues processed: 286 average time/residue: 0.8230 time to fit residues: 258.7597 Evaluate side-chains 281 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 263 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 2442 CYS Chi-restraints excluded: chain F residue 2526 ARG Chi-restraints excluded: chain F residue 2530 TYR Chi-restraints excluded: chain H residue 2425 ILE Chi-restraints excluded: chain H residue 2431 VAL Chi-restraints excluded: chain H residue 2490 VAL Chi-restraints excluded: chain I residue 2520 LYS Chi-restraints excluded: chain J residue 2442 CYS Chi-restraints excluded: chain J residue 2456 LEU Chi-restraints excluded: chain J residue 2501 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 191 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 258 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2529 GLN L2406 ASN ** M2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.083155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.055285 restraints weight = 63196.581| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.35 r_work: 0.2558 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22187 Z= 0.233 Angle : 0.726 13.986 29981 Z= 0.352 Chirality : 0.044 0.284 3367 Planarity : 0.004 0.072 3880 Dihedral : 5.848 90.006 3083 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.23 % Allowed : 19.95 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.16), residues: 2762 helix: 1.67 (0.14), residues: 1504 sheet: 0.35 (0.27), residues: 335 loop : 0.51 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I2519 TYR 0.019 0.001 TYR L2530 PHE 0.026 0.001 PHE G2532 TRP 0.077 0.003 TRP H2389 HIS 0.009 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00534 (22187) covalent geometry : angle 0.72640 (29981) hydrogen bonds : bond 0.03851 ( 1369) hydrogen bonds : angle 4.41918 ( 3795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7983.20 seconds wall clock time: 136 minutes 30.34 seconds (8190.34 seconds total)