Starting phenix.real_space_refine on Wed May 21 20:17:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9az6_44013/05_2025/9az6_44013.cif Found real_map, /net/cci-nas-00/data/ceres_data/9az6_44013/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9az6_44013/05_2025/9az6_44013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9az6_44013/05_2025/9az6_44013.map" model { file = "/net/cci-nas-00/data/ceres_data/9az6_44013/05_2025/9az6_44013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9az6_44013/05_2025/9az6_44013.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.40, per 1000 atoms: 0.57 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: 5.82 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.98 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: 8.44 Time building geometry restraints manager: 6.75 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 50.230 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP C 79 HIS 0.005 0.001 HIS B 87 PHE 0.023 0.001 PHE F2341 TYR 0.029 0.001 TYR F2530 ARG 0.013 0.001 ARG F2368 Details of bonding type rmsd hydrogen bonds : bond 0.13357 ( 1369) hydrogen bonds : angle 6.04361 ( 3795) covalent geometry : bond 0.00406 (22187) covalent geometry : angle 0.68029 (29981) *********************** 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 : 2.423 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: 0.8372 (m110) REVERT: F 2465 ARG cc_start: 0.8486 (ptp-110) cc_final: 0.8279 (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: 1.7771 time to fit residues: 579.7405 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 : 2.305 ------------------------------------------------------------------------------- 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 233 optimal weight: 30.0000 chunk 209 optimal weight: 40.0000 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** M2529 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.087828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.059275 restraints weight = 64154.062| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.27 r_work: 0.2604 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22187 Z= 0.182 Angle : 0.632 13.522 29981 Z= 0.309 Chirality : 0.042 0.174 3367 Planarity : 0.004 0.085 3880 Dihedral : 5.959 80.018 3095 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.90 % Allowed : 15.69 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.16), residues: 2762 helix: 1.60 (0.14), residues: 1473 sheet: -0.11 (0.27), residues: 335 loop : 0.83 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP H2389 HIS 0.007 0.001 HIS D 87 PHE 0.025 0.001 PHE M2532 TYR 0.015 0.001 TYR K2530 ARG 0.008 0.001 ARG M2513 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 1369) hydrogen bonds : angle 4.66309 ( 3795) covalent geometry : bond 0.00409 (22187) covalent geometry : angle 0.63230 (29981) *********************** 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 349 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 283 time to evaluate : 2.710 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: 0.7716 (pmt) REVERT: B 72 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7732 (pp20) REVERT: B 355 MET cc_start: 0.9182 (mmp) cc_final: 0.8656 (mtp) REVERT: C 123 MET cc_start: 0.9564 (mmt) cc_final: 0.9343 (mmm) REVERT: E 176 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8810 (mmp) REVERT: E 355 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.8801 (mpp) REVERT: F 2398 ARG cc_start: 0.9381 (mtp-110) cc_final: 0.9132 (ttp80) REVERT: F 2461 ASN cc_start: 0.9011 (m110) cc_final: 0.8513 (m110) REVERT: G 2510 ARG cc_start: 0.9236 (ptm160) cc_final: 0.8952 (ptp-110) REVERT: G 2512 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8460 (mm-30) REVERT: G 2520 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8382 (tmtt) REVERT: G 2524 GLN cc_start: 0.7953 (pp30) cc_final: 0.7153 (pp30) REVERT: G 2536 GLU cc_start: -0.1961 (pt0) cc_final: -0.2366 (tt0) REVERT: H 2399 MET cc_start: 0.9012 (ttm) cc_final: 0.8532 (mtm) REVERT: I 2529 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: J 2405 ASN cc_start: 0.9007 (t0) cc_final: 0.8801 (t0) REVERT: J 2453 MET cc_start: 0.8681 (tpp) cc_final: 0.7683 (tpt) REVERT: J 2456 LEU cc_start: 0.9588 (mm) cc_final: 0.9087 (pp) REVERT: J 2465 ARG cc_start: 0.8903 (ptp-110) cc_final: 0.8703 (ptp-110) REVERT: J 2510 ARG cc_start: 0.8036 (ttm-80) cc_final: 0.7393 (ttm-80) REVERT: K 2514 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8017 (mm-30) REVERT: K 2526 ARG cc_start: 0.8562 (mmm160) cc_final: 0.8344 (mmm-85) REVERT: L 2398 ARG cc_start: 0.9336 (ttm-80) cc_final: 0.9056 (ttp80) REVERT: L 2456 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9449 (tp) REVERT: L 2461 ASN cc_start: 0.9089 (m-40) cc_final: 0.8851 (m-40) REVERT: L 2510 ARG cc_start: 0.8151 (tmm-80) cc_final: 0.7752 (tmm-80) REVERT: M 2510 ARG cc_start: 0.6908 (mmp-170) cc_final: 0.6676 (mmp-170) REVERT: M 2513 ARG cc_start: 0.8809 (ttp-110) cc_final: 0.8394 (ttp80) REVERT: M 2516 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8096 (tm-30) REVERT: M 2529 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7042 (pp30) REVERT: M 2538 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7806 (ppt-90) outliers start: 66 outliers final: 14 residues processed: 308 average time/residue: 1.8015 time to fit residues: 613.3821 Evaluate side-chains 290 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 269 time to evaluate : 2.454 ------------------------------------------------------------------------------- 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 2505 GLN 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 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 Chi-restraints excluded: chain M residue 2538 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 96 optimal weight: 3.9990 chunk 239 optimal weight: 20.0000 chunk 267 optimal weight: 30.0000 chunk 176 optimal weight: 10.0000 chunk 259 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 209 optimal weight: 50.0000 chunk 168 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2406 ASN F2469 ASN ** I2524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2469 ASN K2505 GLN ** K2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2406 ASN L2421 GLN ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.086599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.057768 restraints weight = 64339.796| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.27 r_work: 0.2554 rms_B_bonded: 3.76 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) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 22187 Z= 0.291 Angle : 0.663 12.319 29981 Z= 0.327 Chirality : 0.044 0.149 3367 Planarity : 0.004 0.048 3880 Dihedral : 6.207 95.655 3088 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.08 % Allowed : 15.95 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.16), residues: 2762 helix: 1.55 (0.14), residues: 1503 sheet: -0.03 (0.27), residues: 335 loop : 0.67 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP H2389 HIS 0.007 0.001 HIS D 87 PHE 0.015 0.001 PHE K2532 TYR 0.018 0.001 TYR J2530 ARG 0.009 0.001 ARG I2526 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 1369) hydrogen bonds : angle 4.53775 ( 3795) covalent geometry : bond 0.00664 (22187) covalent geometry : angle 0.66341 (29981) *********************** 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 342 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 272 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9451 (mmm) cc_final: 0.7719 (pmt) REVERT: B 355 MET cc_start: 0.9208 (mmp) cc_final: 0.8722 (mtp) REVERT: C 72 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7837 (pp20) REVERT: C 176 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8739 (mmm) REVERT: D 44 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8605 (mtm) REVERT: E 72 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7909 (pp20) REVERT: E 176 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8782 (mmp) REVERT: E 355 MET cc_start: 0.9348 (mmm) cc_final: 0.9019 (mpp) REVERT: F 2398 ARG cc_start: 0.9413 (mtp-110) cc_final: 0.9201 (ttp80) REVERT: F 2461 ASN cc_start: 0.9087 (m110) cc_final: 0.8352 (m110) REVERT: F 2465 ARG cc_start: 0.8721 (ptp-110) cc_final: 0.8318 (ptp90) REVERT: F 2526 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7935 (mtt180) REVERT: G 2500 GLN cc_start: 0.9249 (mp10) cc_final: 0.9014 (mm-40) REVERT: G 2506 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8892 (mm-30) REVERT: G 2510 ARG cc_start: 0.9232 (ptm160) cc_final: 0.8598 (ptp90) REVERT: G 2512 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8585 (mm-30) REVERT: G 2519 ARG cc_start: 0.9167 (mmt90) cc_final: 0.8895 (mmm160) REVERT: G 2520 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8591 (tmtt) REVERT: G 2522 LEU cc_start: 0.8738 (tm) cc_final: 0.8455 (tm) REVERT: G 2536 GLU cc_start: -0.1809 (pt0) cc_final: -0.2292 (tt0) REVERT: H 2510 ARG cc_start: 0.8179 (ttp-170) cc_final: 0.7937 (ttp80) REVERT: I 2520 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8533 (tptp) REVERT: I 2529 GLN cc_start: 0.8164 (tm130) cc_final: 0.7666 (tm-30) REVERT: J 2368 ARG cc_start: 0.9246 (mmt-90) cc_final: 0.8957 (mmt90) REVERT: J 2398 ARG cc_start: 0.9320 (ttm-80) cc_final: 0.8749 (ttp80) REVERT: J 2405 ASN cc_start: 0.8995 (t0) cc_final: 0.8789 (t0) REVERT: J 2453 MET cc_start: 0.8680 (tpp) cc_final: 0.7710 (tpt) REVERT: J 2456 LEU cc_start: 0.9581 (mm) cc_final: 0.9013 (pp) REVERT: J 2465 ARG cc_start: 0.8964 (ptp-110) cc_final: 0.8729 (ptp-110) REVERT: K 2512 GLU cc_start: 0.9133 (tp30) cc_final: 0.8885 (mm-30) REVERT: K 2516 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8037 (tm-30) REVERT: K 2526 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8317 (mmm-85) REVERT: L 2398 ARG cc_start: 0.9365 (ttm-80) cc_final: 0.9043 (ttp80) REVERT: L 2456 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9500 (tp) REVERT: M 2511 LYS cc_start: 0.8308 (ttmm) cc_final: 0.7481 (ttmm) REVERT: M 2513 ARG cc_start: 0.8802 (ttp-110) cc_final: 0.8423 (ttp-110) REVERT: M 2516 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8160 (tm-30) REVERT: M 2529 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7310 (pp30) REVERT: M 2538 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7929 (ppt-90) outliers start: 70 outliers final: 16 residues processed: 306 average time/residue: 1.7284 time to fit residues: 584.7554 Evaluate side-chains 292 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D 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 2526 ARG 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 2520 LYS Chi-restraints excluded: chain J residue 2447 ASP Chi-restraints excluded: chain J residue 2501 ILE Chi-restraints excluded: chain J residue 2505 GLN Chi-restraints excluded: chain J residue 2531 LYS 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 M residue 2502 ILE Chi-restraints excluded: chain M residue 2529 GLN Chi-restraints excluded: chain M residue 2538 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 264 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 251 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 276 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2388 GLN ** F2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2405 ASN F2406 ASN F2469 ASN ** I2524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3487 r_free = 0.3487 target = 0.088075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.059436 restraints weight = 64363.043| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.27 r_work: 0.2601 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22187 Z= 0.139 Angle : 0.605 13.820 29981 Z= 0.292 Chirality : 0.041 0.145 3367 Planarity : 0.004 0.051 3880 Dihedral : 6.066 89.999 3088 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.03 % Allowed : 16.74 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.16), residues: 2762 helix: 1.68 (0.14), residues: 1503 sheet: 0.09 (0.27), residues: 335 loop : 0.69 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H2389 HIS 0.006 0.001 HIS B 87 PHE 0.019 0.001 PHE M2532 TYR 0.010 0.001 TYR E 362 ARG 0.011 0.001 ARG I2526 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 1369) hydrogen bonds : angle 4.35274 ( 3795) covalent geometry : bond 0.00310 (22187) covalent geometry : angle 0.60482 (29981) *********************** 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 345 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 276 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9467 (mmm) cc_final: 0.7711 (pmt) REVERT: B 72 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7753 (pp20) REVERT: B 355 MET cc_start: 0.9170 (mmp) cc_final: 0.8523 (mtp) REVERT: C 72 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7852 (pp20) REVERT: D 44 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8451 (mtm) REVERT: E 176 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8760 (mmp) REVERT: E 355 MET cc_start: 0.9355 (mmm) cc_final: 0.8884 (mpp) REVERT: F 2398 ARG cc_start: 0.9387 (mtp-110) cc_final: 0.9160 (ttp80) REVERT: F 2461 ASN cc_start: 0.9072 (m110) cc_final: 0.8440 (m110) REVERT: F 2465 ARG cc_start: 0.8722 (ptp-110) cc_final: 0.8378 (ptt90) REVERT: F 2508 MET cc_start: 0.9010 (ttm) cc_final: 0.8798 (mmt) REVERT: F 2510 ARG cc_start: 0.9051 (ttp80) cc_final: 0.8434 (ttp80) REVERT: F 2526 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7883 (mtt180) REVERT: G 2500 GLN cc_start: 0.9274 (mp10) cc_final: 0.9051 (mm-40) REVERT: G 2510 ARG cc_start: 0.9178 (ptm160) cc_final: 0.8848 (ptp90) REVERT: G 2512 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8643 (mm-30) REVERT: G 2536 GLU cc_start: -0.2235 (pt0) cc_final: -0.2555 (tt0) REVERT: H 2399 MET cc_start: 0.8945 (ttm) cc_final: 0.8413 (mtm) REVERT: H 2456 LEU cc_start: 0.9553 (mt) cc_final: 0.8954 (pp) REVERT: I 2520 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8539 (tptp) REVERT: I 2529 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: J 2368 ARG cc_start: 0.9261 (mmt-90) cc_final: 0.8894 (mmt90) REVERT: J 2405 ASN cc_start: 0.8956 (t0) cc_final: 0.8745 (t0) REVERT: J 2453 MET cc_start: 0.8726 (tpp) cc_final: 0.7702 (tpt) REVERT: J 2456 LEU cc_start: 0.9573 (mm) cc_final: 0.9003 (pp) REVERT: J 2461 ASN cc_start: 0.8940 (m110) cc_final: 0.8556 (m110) REVERT: K 2507 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8760 (mm-30) REVERT: K 2510 ARG cc_start: 0.8478 (ptp90) cc_final: 0.7868 (ptp90) REVERT: K 2514 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8026 (mm-30) REVERT: L 2344 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8184 (mp10) REVERT: L 2398 ARG cc_start: 0.9380 (ttm-80) cc_final: 0.9106 (ttp80) REVERT: L 2456 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9501 (tp) REVERT: L 2510 ARG cc_start: 0.8435 (tmm-80) cc_final: 0.8173 (tmm-80) REVERT: M 2500 GLN cc_start: 0.8843 (mp10) cc_final: 0.8550 (pm20) REVERT: M 2508 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8140 (ttm) REVERT: M 2510 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6650 (mmp-170) REVERT: M 2513 ARG cc_start: 0.8841 (ttp-110) cc_final: 0.8312 (ttp-110) REVERT: M 2516 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8101 (tm-30) REVERT: M 2517 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8520 (mm-30) REVERT: M 2529 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7181 (pp30) REVERT: M 2538 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7960 (ppt-90) outliers start: 69 outliers final: 13 residues processed: 304 average time/residue: 1.7346 time to fit residues: 583.6835 Evaluate side-chains 292 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 267 time to evaluate : 2.272 ------------------------------------------------------------------------------- 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 195 GLU Chi-restraints excluded: chain D residue 44 MET 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 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 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 L residue 2344 GLN Chi-restraints excluded: chain L residue 2456 LEU Chi-restraints excluded: chain M residue 2502 ILE Chi-restraints excluded: chain M residue 2508 MET Chi-restraints excluded: chain M residue 2510 ARG Chi-restraints excluded: chain M residue 2529 GLN Chi-restraints excluded: chain M residue 2538 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 204 optimal weight: 30.0000 chunk 274 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 220 optimal weight: 30.0000 chunk 145 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2406 ASN ** G2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2421 GLN ** K2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.085451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.056622 restraints weight = 64975.795| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.31 r_work: 0.2532 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 22187 Z= 0.331 Angle : 0.695 13.015 29981 Z= 0.341 Chirality : 0.045 0.164 3367 Planarity : 0.004 0.048 3880 Dihedral : 6.306 100.108 3088 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.86 % Allowed : 17.75 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.16), residues: 2762 helix: 1.67 (0.14), residues: 1503 sheet: 0.08 (0.27), residues: 335 loop : 0.58 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H2389 HIS 0.004 0.001 HIS D 87 PHE 0.011 0.001 PHE K2532 TYR 0.022 0.001 TYR K2530 ARG 0.013 0.001 ARG I2526 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 1369) hydrogen bonds : angle 4.47605 ( 3795) covalent geometry : bond 0.00753 (22187) covalent geometry : angle 0.69509 (29981) *********************** 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 337 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 272 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9448 (mmm) cc_final: 0.7676 (pmt) REVERT: B 325 MET cc_start: 0.9044 (mmp) cc_final: 0.8836 (mmm) REVERT: B 355 MET cc_start: 0.9228 (mmp) cc_final: 0.8787 (mtp) REVERT: C 72 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7870 (pp20) REVERT: D 44 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8588 (mtm) REVERT: D 47 MET cc_start: 0.8336 (mmt) cc_final: 0.7152 (mmt) REVERT: E 72 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7934 (pp20) REVERT: E 176 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8776 (mmp) REVERT: E 355 MET cc_start: 0.9376 (mmm) cc_final: 0.8992 (mpp) REVERT: F 2398 ARG cc_start: 0.9388 (mtp-110) cc_final: 0.9169 (ttp80) REVERT: F 2461 ASN cc_start: 0.9102 (m110) cc_final: 0.8621 (m110) REVERT: F 2526 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7925 (mtt180) REVERT: G 2500 GLN cc_start: 0.9280 (mp10) cc_final: 0.9042 (mm-40) REVERT: G 2510 ARG cc_start: 0.9238 (ptm160) cc_final: 0.9010 (ptp-110) REVERT: G 2512 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8598 (mm-30) REVERT: G 2513 ARG cc_start: 0.8827 (tmm-80) cc_final: 0.8488 (ttm-80) REVERT: G 2516 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8144 (tm-30) REVERT: G 2517 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7729 (mm-30) REVERT: G 2522 LEU cc_start: 0.8668 (tm) cc_final: 0.8215 (tm) REVERT: G 2524 GLN cc_start: 0.7405 (tm130) cc_final: 0.6714 (tm130) REVERT: G 2526 ARG cc_start: 0.9090 (tpp80) cc_final: 0.8554 (mmm160) REVERT: G 2527 GLN cc_start: 0.9174 (pp30) cc_final: 0.8801 (pp30) REVERT: G 2529 GLN cc_start: 0.8210 (pp30) cc_final: 0.7828 (pm20) REVERT: H 2510 ARG cc_start: 0.8192 (ttp-170) cc_final: 0.7911 (ttp80) REVERT: I 2520 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8486 (tptp) REVERT: I 2529 GLN cc_start: 0.8003 (tm130) cc_final: 0.7377 (tm-30) REVERT: J 2368 ARG cc_start: 0.9265 (mmt-90) cc_final: 0.8862 (mmt90) REVERT: J 2398 ARG cc_start: 0.9318 (ttm-80) cc_final: 0.8782 (ttp80) REVERT: J 2405 ASN cc_start: 0.8955 (t0) cc_final: 0.8736 (t0) REVERT: J 2453 MET cc_start: 0.8735 (tpp) cc_final: 0.7703 (tpt) REVERT: J 2456 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9017 (pp) REVERT: J 2461 ASN cc_start: 0.9015 (m110) cc_final: 0.8606 (m110) REVERT: K 2507 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8732 (mm-30) REVERT: K 2512 GLU cc_start: 0.9093 (tp30) cc_final: 0.8844 (mm-30) REVERT: K 2516 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8010 (tm-30) REVERT: K 2520 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8528 (tptp) REVERT: L 2344 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8199 (mp10) REVERT: L 2398 ARG cc_start: 0.9395 (ttm-80) cc_final: 0.9070 (ttp80) REVERT: L 2456 LEU cc_start: 0.9734 (OUTLIER) cc_final: 0.9516 (tp) REVERT: L 2465 ARG cc_start: 0.9153 (mtm110) cc_final: 0.8849 (ptt-90) REVERT: M 2511 LYS cc_start: 0.8572 (ttmm) cc_final: 0.7606 (tttm) REVERT: M 2513 ARG cc_start: 0.8776 (ttp-110) cc_final: 0.8425 (ttp-110) REVERT: M 2516 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8098 (tm-30) REVERT: M 2529 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7289 (pp30) REVERT: M 2538 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7913 (ppt-90) outliers start: 65 outliers final: 18 residues processed: 304 average time/residue: 1.7553 time to fit residues: 589.7183 Evaluate side-chains 293 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 2.328 ------------------------------------------------------------------------------- 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 44 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 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 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 2509 LEU Chi-restraints excluded: chain L residue 2344 GLN Chi-restraints excluded: chain L residue 2456 LEU Chi-restraints excluded: chain L residue 2490 VAL Chi-restraints excluded: chain M residue 2498 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 218 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 162 optimal weight: 0.0570 chunk 82 optimal weight: 0.9990 chunk 256 optimal weight: 40.0000 chunk 3 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.7704 ------------------------------------------------------------------------------- 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** F2382 ASN F2405 ASN F2406 ASN F2469 ASN J2500 GLN K2528 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.089207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.060471 restraints weight = 63010.358| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.27 r_work: 0.2621 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22187 Z= 0.117 Angle : 0.628 14.101 29981 Z= 0.302 Chirality : 0.041 0.210 3367 Planarity : 0.004 0.053 3880 Dihedral : 6.016 86.896 3088 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.46 % Allowed : 18.15 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.16), residues: 2762 helix: 1.76 (0.14), residues: 1503 sheet: 0.16 (0.27), residues: 335 loop : 0.61 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H2389 HIS 0.004 0.001 HIS D 87 PHE 0.020 0.001 PHE M2532 TYR 0.009 0.001 TYR E 362 ARG 0.013 0.001 ARG L2526 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 1369) hydrogen bonds : angle 4.29710 ( 3795) covalent geometry : bond 0.00252 (22187) covalent geometry : angle 0.62844 (29981) *********************** 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 331 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 275 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9457 (mmm) cc_final: 0.7690 (pmt) REVERT: B 72 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7735 (pp20) REVERT: B 355 MET cc_start: 0.9163 (mmp) cc_final: 0.8539 (mtp) REVERT: C 72 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7860 (pp20) REVERT: D 44 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8376 (mtm) REVERT: E 72 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7875 (pp20) REVERT: E 176 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8722 (mmp) REVERT: E 355 MET cc_start: 0.9362 (mmm) cc_final: 0.8906 (mpp) REVERT: F 2456 LEU cc_start: 0.9607 (mt) cc_final: 0.9273 (pp) REVERT: F 2461 ASN cc_start: 0.9063 (m110) cc_final: 0.8566 (m110) REVERT: G 2500 GLN cc_start: 0.9305 (mp10) cc_final: 0.9063 (mm-40) REVERT: G 2512 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8586 (mm-30) REVERT: G 2526 ARG cc_start: 0.9144 (tpp80) cc_final: 0.8629 (mmm160) REVERT: G 2529 GLN cc_start: 0.8259 (pp30) cc_final: 0.7690 (pp30) REVERT: G 2536 GLU cc_start: -0.2370 (pt0) cc_final: -0.2741 (tt0) REVERT: H 2399 MET cc_start: 0.8996 (ttm) cc_final: 0.8449 (mtm) REVERT: H 2456 LEU cc_start: 0.9562 (mt) cc_final: 0.8985 (pp) REVERT: I 2520 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8482 (tptp) REVERT: I 2529 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: J 2368 ARG cc_start: 0.9268 (mmt-90) cc_final: 0.8842 (mmt90) REVERT: J 2398 ARG cc_start: 0.9318 (ttm-80) cc_final: 0.8862 (ttp80) REVERT: J 2405 ASN cc_start: 0.8930 (t0) cc_final: 0.8721 (t0) REVERT: J 2453 MET cc_start: 0.8796 (tpp) cc_final: 0.7855 (tpt) REVERT: J 2456 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.8999 (pp) REVERT: J 2461 ASN cc_start: 0.8963 (m110) cc_final: 0.8597 (m110) REVERT: K 2509 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8638 (mm) REVERT: K 2512 GLU cc_start: 0.9164 (tp30) cc_final: 0.8870 (mm-30) REVERT: K 2513 ARG cc_start: 0.8737 (mmm160) cc_final: 0.8395 (mtp-110) REVERT: K 2514 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7954 (mm-30) REVERT: K 2528 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7136 (mt0) REVERT: L 2456 LEU cc_start: 0.9729 (OUTLIER) cc_final: 0.9173 (pp) REVERT: L 2465 ARG cc_start: 0.9172 (mtm110) cc_final: 0.8919 (ptp-110) REVERT: M 2500 GLN cc_start: 0.8893 (mp10) cc_final: 0.8636 (pm20) REVERT: M 2510 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6548 (mmp-170) REVERT: M 2513 ARG cc_start: 0.8845 (ttp-110) cc_final: 0.8299 (ttp-110) REVERT: M 2516 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8146 (tm-30) REVERT: M 2517 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8459 (mm-30) REVERT: M 2520 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8702 (mtpp) REVERT: M 2529 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7166 (pp30) REVERT: M 2538 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7967 (ppt-90) outliers start: 56 outliers final: 20 residues processed: 301 average time/residue: 1.7704 time to fit residues: 589.1135 Evaluate side-chains 301 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 268 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain D residue 44 MET 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 F residue 2442 CYS Chi-restraints excluded: chain F residue 2501 ILE 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 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 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 2509 LEU Chi-restraints excluded: chain K residue 2528 GLN Chi-restraints excluded: chain L residue 2344 GLN 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 2510 ARG 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: 2.9990 chunk 160 optimal weight: 0.5980 chunk 155 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 213 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.085328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.057068 restraints weight = 62375.235| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.41 r_work: 0.2583 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22187 Z= 0.167 Angle : 0.647 14.082 29981 Z= 0.312 Chirality : 0.042 0.240 3367 Planarity : 0.004 0.063 3880 Dihedral : 5.943 87.284 3088 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.11 % Allowed : 18.72 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.16), residues: 2762 helix: 1.79 (0.14), residues: 1503 sheet: 0.26 (0.27), residues: 335 loop : 0.57 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H2389 HIS 0.004 0.001 HIS E 87 PHE 0.016 0.001 PHE K2532 TYR 0.022 0.001 TYR K2530 ARG 0.016 0.001 ARG I2526 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 1369) hydrogen bonds : angle 4.27942 ( 3795) covalent geometry : bond 0.00380 (22187) covalent geometry : angle 0.64705 (29981) *********************** 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 318 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9442 (mmm) cc_final: 0.7651 (pmt) REVERT: B 72 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7757 (pp20) REVERT: B 355 MET cc_start: 0.9160 (mmp) cc_final: 0.8482 (mtp) REVERT: C 72 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7849 (pp20) REVERT: E 72 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7881 (pp20) REVERT: E 176 MET cc_start: 0.9029 (mmm) cc_final: 0.8710 (mmp) REVERT: E 355 MET cc_start: 0.9370 (mmm) cc_final: 0.8903 (mpp) REVERT: F 2456 LEU cc_start: 0.9598 (mt) cc_final: 0.9276 (pp) REVERT: F 2461 ASN cc_start: 0.9038 (m110) cc_final: 0.8580 (m110) REVERT: F 2508 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8451 (ttm) REVERT: G 2500 GLN cc_start: 0.9294 (mp10) cc_final: 0.9045 (mm-40) REVERT: G 2510 ARG cc_start: 0.9097 (ptp-110) cc_final: 0.8747 (ptp90) REVERT: G 2512 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8722 (mm-30) REVERT: G 2526 ARG cc_start: 0.9161 (tpp80) cc_final: 0.8652 (mmm160) REVERT: G 2529 GLN cc_start: 0.8240 (pp30) cc_final: 0.7765 (pp30) REVERT: H 2456 LEU cc_start: 0.9539 (mt) cc_final: 0.8994 (pp) REVERT: I 2520 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8465 (tptp) REVERT: I 2529 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: J 2368 ARG cc_start: 0.9260 (mmt-90) cc_final: 0.8859 (mmt90) REVERT: J 2405 ASN cc_start: 0.8921 (t0) cc_final: 0.8720 (t0) REVERT: J 2453 MET cc_start: 0.8759 (tpp) cc_final: 0.7896 (tpt) REVERT: J 2456 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.8973 (pp) REVERT: J 2508 MET cc_start: 0.8886 (ttp) cc_final: 0.8664 (ttp) REVERT: K 2509 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8577 (mm) REVERT: K 2512 GLU cc_start: 0.9162 (tp30) cc_final: 0.8826 (mm-30) REVERT: K 2513 ARG cc_start: 0.8746 (mmm160) cc_final: 0.8419 (mtp-110) REVERT: K 2514 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7964 (mm-30) REVERT: K 2520 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8579 (tptp) REVERT: L 2398 ARG cc_start: 0.9206 (ttm-80) cc_final: 0.8876 (ttm-80) REVERT: L 2456 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9210 (pp) REVERT: L 2465 ARG cc_start: 0.9165 (mtm110) cc_final: 0.8914 (ptp-110) REVERT: M 2500 GLN cc_start: 0.8765 (mp10) cc_final: 0.8499 (pm20) REVERT: M 2511 LYS cc_start: 0.8386 (tttm) cc_final: 0.7604 (tttm) REVERT: M 2513 ARG cc_start: 0.8758 (ttp-110) cc_final: 0.8418 (ttp-110) REVERT: M 2516 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8185 (tm-30) REVERT: M 2517 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8493 (mm-30) REVERT: M 2520 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8673 (mtpp) REVERT: M 2529 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7065 (pp30) REVERT: M 2538 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7813 (ppt-90) outliers start: 48 outliers final: 21 residues processed: 294 average time/residue: 1.7617 time to fit residues: 571.8711 Evaluate side-chains 295 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 264 time to evaluate : 2.489 ------------------------------------------------------------------------------- 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 D residue 338 SER 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 2501 ILE Chi-restraints excluded: chain F residue 2508 MET 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 I residue 2529 GLN 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 2509 LEU Chi-restraints excluded: chain L residue 2456 LEU Chi-restraints excluded: chain L residue 2490 VAL Chi-restraints excluded: chain L residue 2494 MET Chi-restraints excluded: chain M residue 2502 ILE Chi-restraints excluded: chain M residue 2529 GLN Chi-restraints excluded: chain M residue 2538 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 197 optimal weight: 30.0000 chunk 212 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 209 optimal weight: 30.0000 chunk 150 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2469 ASN ** G2524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2529 GLN ** L2406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.089039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.060378 restraints weight = 63406.238| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.24 r_work: 0.2603 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22187 Z= 0.162 Angle : 0.667 14.290 29981 Z= 0.321 Chirality : 0.042 0.238 3367 Planarity : 0.004 0.056 3880 Dihedral : 5.908 86.278 3088 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.28 % Allowed : 18.72 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.16), residues: 2762 helix: 1.73 (0.14), residues: 1508 sheet: 0.34 (0.28), residues: 325 loop : 0.55 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H2389 HIS 0.010 0.001 HIS E 87 PHE 0.025 0.001 PHE M2532 TYR 0.008 0.001 TYR F2530 ARG 0.015 0.001 ARG G2519 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 1369) hydrogen bonds : angle 4.29768 ( 3795) covalent geometry : bond 0.00369 (22187) covalent geometry : angle 0.66699 (29981) *********************** 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: 52 poor density : 271 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9484 (mmm) cc_final: 0.7696 (pmt) REVERT: B 72 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7751 (pp20) REVERT: B 355 MET cc_start: 0.9190 (mmp) cc_final: 0.8577 (mtp) REVERT: C 72 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7831 (pp20) REVERT: E 72 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7872 (pp20) REVERT: E 176 MET cc_start: 0.9063 (mmm) cc_final: 0.8751 (mmp) REVERT: E 355 MET cc_start: 0.9387 (mmm) cc_final: 0.8916 (mpp) REVERT: F 2453 MET cc_start: 0.8934 (tmm) cc_final: 0.8410 (tmm) REVERT: F 2456 LEU cc_start: 0.9625 (mt) cc_final: 0.9285 (pp) REVERT: F 2461 ASN cc_start: 0.9095 (m110) cc_final: 0.8644 (m110) REVERT: G 2500 GLN cc_start: 0.9287 (mp10) cc_final: 0.9024 (mm-40) REVERT: G 2510 ARG cc_start: 0.9129 (ptp-110) cc_final: 0.8742 (ptp90) REVERT: G 2512 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8786 (mm-30) REVERT: G 2526 ARG cc_start: 0.9109 (tpp80) cc_final: 0.8587 (mmm160) REVERT: G 2529 GLN cc_start: 0.8324 (pp30) cc_final: 0.7635 (pp30) REVERT: G 2530 TYR cc_start: 0.8828 (p90) cc_final: 0.8418 (p90) REVERT: G 2531 LYS cc_start: 0.8611 (ptpp) cc_final: 0.7963 (pptt) REVERT: H 2456 LEU cc_start: 0.9573 (mt) cc_final: 0.9019 (pp) REVERT: I 2520 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8512 (tptp) REVERT: I 2526 ARG cc_start: 0.8642 (tpp80) cc_final: 0.8378 (mmm160) REVERT: J 2368 ARG cc_start: 0.9280 (mmt-90) cc_final: 0.8882 (mmt90) REVERT: J 2405 ASN cc_start: 0.8933 (t0) cc_final: 0.8720 (t0) REVERT: J 2453 MET cc_start: 0.8784 (tpp) cc_final: 0.7904 (tpt) REVERT: J 2456 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.8988 (pp) REVERT: K 2512 GLU cc_start: 0.9113 (tp30) cc_final: 0.8834 (mm-30) REVERT: K 2513 ARG cc_start: 0.8663 (mmm160) cc_final: 0.8453 (mtm110) REVERT: K 2514 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8007 (mm-30) REVERT: K 2520 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8532 (tptp) REVERT: L 2398 ARG cc_start: 0.9262 (ttm-80) cc_final: 0.8918 (ttm-80) REVERT: L 2456 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9204 (pp) REVERT: L 2465 ARG cc_start: 0.9165 (mtm110) cc_final: 0.8931 (ptp90) REVERT: M 2500 GLN cc_start: 0.8794 (mp10) cc_final: 0.8495 (pm20) REVERT: M 2513 ARG cc_start: 0.8862 (ttp-110) cc_final: 0.8319 (ttp-110) REVERT: M 2516 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8081 (tm-30) REVERT: M 2517 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8434 (mm-30) REVERT: M 2520 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8680 (mtpp) REVERT: M 2529 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7259 (pp30) REVERT: M 2538 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7833 (ppt-90) outliers start: 52 outliers final: 20 residues processed: 297 average time/residue: 1.7768 time to fit residues: 581.5613 Evaluate side-chains 291 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 2.425 ------------------------------------------------------------------------------- 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 D residue 338 SER 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 2501 ILE 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 2529 GLN Chi-restraints excluded: chain L residue 2456 LEU Chi-restraints excluded: chain L residue 2490 VAL Chi-restraints excluded: chain M residue 2502 ILE Chi-restraints excluded: chain M residue 2529 GLN Chi-restraints excluded: chain M residue 2538 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 4 optimal weight: 0.0030 chunk 45 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 250 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 5 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 251 optimal weight: 8.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- 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** ** G2524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2529 GLN ** L2406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.086588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.058685 restraints weight = 61723.965| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.46 r_work: 0.2621 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22187 Z= 0.126 Angle : 0.669 14.215 29981 Z= 0.324 Chirality : 0.042 0.235 3367 Planarity : 0.004 0.082 3880 Dihedral : 5.790 80.951 3088 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.85 % Allowed : 19.16 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.16), residues: 2762 helix: 1.73 (0.14), residues: 1508 sheet: 0.37 (0.28), residues: 325 loop : 0.55 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H2389 HIS 0.006 0.001 HIS E 87 PHE 0.009 0.001 PHE K2532 TYR 0.018 0.001 TYR J2530 ARG 0.023 0.001 ARG F2465 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 1369) hydrogen bonds : angle 4.29077 ( 3795) covalent geometry : bond 0.00283 (22187) covalent geometry : angle 0.66879 (29981) *********************** 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 315 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 273 time to evaluate : 2.640 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: 0.7692 (pmt) REVERT: B 72 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7748 (pp20) REVERT: B 355 MET cc_start: 0.9124 (mmp) cc_final: 0.8507 (mtp) REVERT: C 72 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7864 (pp20) REVERT: E 72 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7867 (pp20) REVERT: E 176 MET cc_start: 0.9055 (mmm) cc_final: 0.8741 (mmp) REVERT: E 355 MET cc_start: 0.9413 (mmm) cc_final: 0.8433 (mtm) REVERT: F 2453 MET cc_start: 0.8794 (tmm) cc_final: 0.8241 (tmm) REVERT: F 2456 LEU cc_start: 0.9589 (mt) cc_final: 0.9250 (pp) REVERT: F 2461 ASN cc_start: 0.9077 (m110) cc_final: 0.8643 (m110) REVERT: G 2500 GLN cc_start: 0.9305 (mp10) cc_final: 0.9032 (mm-40) REVERT: G 2507 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8742 (mm-30) REVERT: G 2510 ARG cc_start: 0.9048 (ptp-110) cc_final: 0.8835 (ttp80) REVERT: G 2512 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8740 (mm-30) REVERT: G 2519 ARG cc_start: 0.9189 (mmt90) cc_final: 0.8936 (mmm160) REVERT: G 2522 LEU cc_start: 0.8739 (tm) cc_final: 0.8142 (tm) REVERT: G 2526 ARG cc_start: 0.9113 (tpp80) cc_final: 0.8838 (mmm160) REVERT: G 2529 GLN cc_start: 0.8311 (pp30) cc_final: 0.7731 (pp30) REVERT: G 2530 TYR cc_start: 0.8773 (p90) cc_final: 0.8347 (p90) REVERT: G 2531 LYS cc_start: 0.8630 (ptpp) cc_final: 0.7910 (pptt) REVERT: H 2456 LEU cc_start: 0.9524 (mt) cc_final: 0.9003 (pp) REVERT: I 2520 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8456 (tptp) REVERT: I 2526 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8346 (mmm160) REVERT: I 2529 GLN cc_start: 0.7411 (tm-30) cc_final: 0.7002 (tm130) REVERT: J 2368 ARG cc_start: 0.9254 (mmt-90) cc_final: 0.8862 (mmt90) REVERT: J 2453 MET cc_start: 0.8762 (tpp) cc_final: 0.8035 (tpt) REVERT: J 2456 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.8969 (pp) REVERT: J 2513 ARG cc_start: 0.7846 (mpt180) cc_final: 0.7426 (mpt180) REVERT: K 2508 MET cc_start: 0.7995 (ttm) cc_final: 0.7605 (ttm) REVERT: K 2512 GLU cc_start: 0.9130 (tp30) cc_final: 0.8760 (mm-30) REVERT: K 2516 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8378 (tm-30) REVERT: K 2526 ARG cc_start: 0.8657 (tpp80) cc_final: 0.8317 (mmm160) REVERT: L 2398 ARG cc_start: 0.9263 (ttm-80) cc_final: 0.8909 (ttm-80) REVERT: L 2456 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9228 (pp) REVERT: L 2465 ARG cc_start: 0.9151 (mtm110) cc_final: 0.8940 (ptp90) REVERT: L 2508 MET cc_start: 0.7871 (tpp) cc_final: 0.7585 (mmp) REVERT: M 2500 GLN cc_start: 0.8752 (mp10) cc_final: 0.8473 (pm20) REVERT: M 2511 LYS cc_start: 0.8034 (tttm) cc_final: 0.7440 (tttt) REVERT: M 2513 ARG cc_start: 0.8691 (ttp-110) cc_final: 0.8409 (ttp-110) REVERT: M 2516 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8109 (tm-30) REVERT: M 2520 LYS cc_start: 0.8916 (mtpp) cc_final: 0.8568 (mtpp) REVERT: M 2529 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.7241 (pp30) REVERT: M 2538 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7833 (ppt-90) outliers start: 42 outliers final: 20 residues processed: 297 average time/residue: 1.7245 time to fit residues: 566.9979 Evaluate side-chains 297 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 2.562 ------------------------------------------------------------------------------- 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 338 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 72 GLU 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 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 2352 ILE 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 2529 GLN Chi-restraints excluded: chain L residue 2456 LEU Chi-restraints excluded: chain L residue 2490 VAL Chi-restraints excluded: chain M residue 2529 GLN Chi-restraints excluded: chain M residue 2538 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 189 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 187 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2469 ASN ** I2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J2382 ASN K2529 GLN ** M2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3470 r_free = 0.3470 target = 0.085303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.057292 restraints weight = 62662.899| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.47 r_work: 0.2565 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 22187 Z= 0.249 Angle : 0.724 13.855 29981 Z= 0.353 Chirality : 0.045 0.255 3367 Planarity : 0.005 0.095 3880 Dihedral : 5.937 87.602 3088 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.41 % Allowed : 19.55 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.16), residues: 2762 helix: 1.66 (0.14), residues: 1508 sheet: 0.39 (0.28), residues: 325 loop : 0.52 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H2389 HIS 0.003 0.001 HIS B 87 PHE 0.024 0.001 PHE M2532 TYR 0.012 0.001 TYR D 91 ARG 0.019 0.001 ARG K2513 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1369) hydrogen bonds : angle 4.39853 ( 3795) covalent geometry : bond 0.00570 (22187) covalent geometry : angle 0.72422 (29981) ********************** 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 302 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 2.457 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: 0.9468 (mmm) cc_final: 0.7672 (pmt) REVERT: B 72 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7796 (pp20) REVERT: B 355 MET cc_start: 0.9202 (mmp) cc_final: 0.8580 (mtp) REVERT: C 72 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7871 (pp20) REVERT: E 72 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7882 (pp20) REVERT: E 176 MET cc_start: 0.9039 (mmm) cc_final: 0.8721 (mmp) REVERT: E 355 MET cc_start: 0.9388 (mmm) cc_final: 0.8394 (mtm) REVERT: F 2461 ASN cc_start: 0.9036 (m110) cc_final: 0.8701 (m110) REVERT: G 2500 GLN cc_start: 0.9286 (mp10) cc_final: 0.9025 (mm-40) REVERT: G 2507 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8798 (mm-30) REVERT: G 2519 ARG cc_start: 0.9185 (mmt90) cc_final: 0.8929 (mmm160) REVERT: G 2522 LEU cc_start: 0.8784 (tm) cc_final: 0.8117 (tm) REVERT: G 2526 ARG cc_start: 0.9129 (tpp80) cc_final: 0.8882 (mmm160) REVERT: G 2529 GLN cc_start: 0.8346 (pp30) cc_final: 0.7887 (pp30) REVERT: G 2531 LYS cc_start: 0.8640 (ptpp) cc_final: 0.8426 (ptpp) REVERT: H 2456 LEU cc_start: 0.9545 (mt) cc_final: 0.9039 (pp) REVERT: I 2520 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8477 (tptp) REVERT: I 2526 ARG cc_start: 0.8628 (tpp80) cc_final: 0.8376 (mmm160) REVERT: I 2529 GLN cc_start: 0.7593 (tm-30) cc_final: 0.7320 (tm-30) REVERT: J 2368 ARG cc_start: 0.9306 (mmt-90) cc_final: 0.8927 (mmt90) REVERT: J 2453 MET cc_start: 0.8778 (tpp) cc_final: 0.8018 (tpt) REVERT: J 2455 ARG cc_start: 0.9284 (mtm-85) cc_final: 0.8884 (ptp-170) REVERT: J 2456 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.8934 (pp) REVERT: K 2512 GLU cc_start: 0.9141 (tp30) cc_final: 0.8775 (mm-30) REVERT: K 2513 ARG cc_start: 0.8863 (mmm160) cc_final: 0.8450 (mtm110) REVERT: K 2526 ARG cc_start: 0.8666 (tpp80) cc_final: 0.8380 (mmm160) REVERT: K 2529 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6332 (pp30) REVERT: L 2398 ARG cc_start: 0.9274 (ttm-80) cc_final: 0.8944 (ttm-80) REVERT: L 2456 LEU cc_start: 0.9727 (OUTLIER) cc_final: 0.9217 (pp) REVERT: L 2465 ARG cc_start: 0.9165 (mtm110) cc_final: 0.8897 (ptt-90) REVERT: L 2508 MET cc_start: 0.8092 (tpp) cc_final: 0.7874 (mmp) REVERT: M 2513 ARG cc_start: 0.8800 (ttp-110) cc_final: 0.8268 (ttp-110) REVERT: M 2516 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8034 (tm-30) REVERT: M 2520 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8637 (mtpp) REVERT: M 2529 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.7147 (pp30) REVERT: M 2538 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7983 (ppt-90) outliers start: 32 outliers final: 16 residues processed: 289 average time/residue: 1.7713 time to fit residues: 570.6240 Evaluate side-chains 289 residues out of total 2276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 265 time to evaluate : 2.253 ------------------------------------------------------------------------------- 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 338 SER 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 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 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 2529 GLN Chi-restraints excluded: chain L residue 2456 LEU Chi-restraints excluded: chain L residue 2490 VAL Chi-restraints excluded: chain M residue 2529 GLN Chi-restraints excluded: chain M residue 2538 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 155 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 272 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** ** G2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I2529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2529 GLN ** L2406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M2528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.090376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.061023 restraints weight = 62481.748| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.32 r_work: 0.2604 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 22187 Z= 0.162 Angle : 0.716 14.126 29981 Z= 0.348 Chirality : 0.043 0.275 3367 Planarity : 0.004 0.076 3880 Dihedral : 5.903 85.177 3088 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.36 % Allowed : 19.90 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.16), residues: 2762 helix: 1.63 (0.14), residues: 1508 sheet: 0.43 (0.28), residues: 325 loop : 0.53 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H2389 HIS 0.011 0.001 HIS E 87 PHE 0.026 0.001 PHE G2532 TYR 0.016 0.001 TYR J2530 ARG 0.018 0.001 ARG K2513 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 1369) hydrogen bonds : angle 4.38679 ( 3795) covalent geometry : bond 0.00373 (22187) covalent geometry : angle 0.71565 (29981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15540.29 seconds wall clock time: 268 minutes 8.33 seconds (16088.33 seconds total)