Starting phenix.real_space_refine on Sat Aug 8 02:03:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12bw_76298/08_2026/12bw_76298.cif Found real_map, /net/cci-nas-00/data/ceres_data/12bw_76298/08_2026/12bw_76298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/12bw_76298/08_2026/12bw_76298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12bw_76298/08_2026/12bw_76298.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/12bw_76298/08_2026/12bw_76298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12bw_76298/08_2026/12bw_76298.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 16 5.49 5 Mg 8 5.21 5 S 171 5.16 5 C 15367 2.51 5 N 4136 2.21 5 O 4690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24389 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "G" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "H" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "I" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 947 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} 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} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" 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: "H" 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: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.03, per 1000 atoms: 0.21 Number of scatterers: 24389 At special positions: 0 Unit cell: (89.64, 110.16, 279.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 171 16.00 P 16 15.00 Mg 8 11.99 O 4690 8.00 N 4136 7.00 C 15367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 929.4 milliseconds 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5714 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 49 sheets defined 51.7% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 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 removed outlier: 3.550A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.802A 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 193 Processing helix chain 'A' and resid 194 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 285 removed outlier: 3.838A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) 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 296 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.506A pdb=" N MET A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) 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 347 Processing helix chain 'A' and resid 348 through 349 No H-bonds generated for 'chain 'A' and resid 348 through 349' Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.926A 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 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.544A pdb=" N GLU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.648A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.884A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.519A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 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 285 removed outlier: 3.836A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) 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 296 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.562A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 305' 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 347 Processing helix chain 'B' and resid 348 through 349 No H-bonds generated for 'chain 'B' and resid 348 through 349' Processing helix chain 'B' and resid 350 through 355 removed outlier: 4.001A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 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 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.842A 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 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.551A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) 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 296 Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.642A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) 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 349 removed outlier: 3.667A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.788A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.605A pdb=" N GLU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.623A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.877A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.506A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.558A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 257 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 295 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 347 Processing helix chain 'D' and resid 348 through 355 removed outlier: 6.701A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.594A pdb=" N GLU E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.643A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.852A 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 193 Processing helix chain 'E' and resid 194 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 257 Processing helix chain 'E' and resid 258 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 295 Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.524A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (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 347 Processing helix chain 'E' and resid 348 through 355 removed outlier: 6.384A pdb=" N THR E 351 " --> pdb=" O SER E 348 " (cutoff:3.500A) removed outlier: 4.034A 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 367 through 372 removed outlier: 3.760A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 93 removed outlier: 3.535A pdb=" N GLU F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.588A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.909A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.630A pdb=" N SER F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 251 through 256 Processing helix chain 'F' and resid 257 through 262 removed outlier: 3.568A pdb=" N THR F 260 " --> pdb=" O CYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.524A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 removed outlier: 3.561A pdb=" N SER F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 355 removed outlier: 3.939A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 93 Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.875A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.562A pdb=" N SER G 145 " --> pdb=" O SER G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 288 No H-bonds generated for 'chain 'G' and resid 286 through 288' Processing helix chain 'G' and resid 289 through 296 Processing helix chain 'G' and resid 301 through 305 removed outlier: 3.552A pdb=" N THR G 304 " --> pdb=" O GLY G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 347 Processing helix chain 'G' and resid 348 through 349 No H-bonds generated for 'chain 'G' and resid 348 through 349' Processing helix chain 'G' and resid 350 through 355 removed outlier: 3.898A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 369 through 374 removed outlier: 3.606A pdb=" N CYS G 374 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 61 Processing helix chain 'H' and resid 78 through 93 removed outlier: 3.563A pdb=" N GLU H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.896A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 172 through 175 Processing helix chain 'H' and resid 181 through 194 removed outlier: 3.907A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 202 through 217 Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 252 through 260 Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 261 through 262 No H-bonds generated for 'chain 'H' and resid 261 through 262' Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 284 Processing helix chain 'H' and resid 286 through 295 removed outlier: 3.654A pdb=" N ARG H 290 " --> pdb=" O ASP H 286 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 305 Processing helix chain 'H' and resid 308 through 321 Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 347 Processing helix chain 'H' and resid 348 through 355 removed outlier: 6.354A pdb=" N THR H 351 " --> pdb=" O SER H 348 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 369 through 374 removed outlier: 3.519A pdb=" N CYS H 374 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 183 Processing helix chain 'I' and resid 206 through 224 Processing helix chain 'I' and resid 240 through 248 Processing helix chain 'I' and resid 261 through 268 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.570A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.556A 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: 6.542A 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: 4.102A 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: 6.485A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.466A 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: 6.590A 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: 3.851A 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: 4.244A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (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: 6.504A 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: 4.041A 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: 6.627A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (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 176 through 178 removed outlier: 6.509A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.979A pdb=" N GLN F 41 " --> pdb=" O ALA D 170 " (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: 6.817A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (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 176 through 178 removed outlier: 6.408A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 176 through 178 removed outlier: 4.021A pdb=" N GLN G 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 32 removed outlier: 4.149A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ASN F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 176 through 178 removed outlier: 6.531A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 176 through 178 removed outlier: 3.969A pdb=" N GLN H 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'G' and resid 29 through 32 removed outlier: 4.236A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ASN G 12 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.525A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AE7, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.793A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AF2, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.509A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AF4, first strand: chain 'I' and resid 172 through 175 1271 hydrogen bonds defined for protein. 3180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.75 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7860 1.34 - 1.46: 4260 1.46 - 1.58: 12473 1.58 - 1.69: 24 1.69 - 1.81: 300 Bond restraints: 24917 Sorted by residual: bond pdb=" C ASN E 12 " pdb=" N GLY E 13 " ideal model delta sigma weight residual 1.332 1.300 0.032 1.54e-02 4.22e+03 4.21e+00 bond pdb=" C ASN C 12 " pdb=" N GLY C 13 " ideal model delta sigma weight residual 1.328 1.306 0.022 1.34e-02 5.57e+03 2.79e+00 bond pdb=" C ASN B 12 " pdb=" N GLY B 13 " ideal model delta sigma weight residual 1.332 1.307 0.025 1.54e-02 4.22e+03 2.56e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.460 0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.461 0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 24912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 32466 1.56 - 3.12: 1099 3.12 - 4.68: 171 4.68 - 6.24: 70 6.24 - 7.80: 8 Bond angle restraints: 33814 Sorted by residual: angle pdb=" CA GLY I 167 " pdb=" C GLY I 167 " pdb=" N ARG I 168 " ideal model delta sigma weight residual 114.23 117.19 -2.96 8.80e-01 1.29e+00 1.13e+01 angle pdb=" C VAL C 30 " pdb=" N PHE C 31 " pdb=" CA PHE C 31 " ideal model delta sigma weight residual 122.38 117.13 5.25 1.73e+00 3.34e-01 9.21e+00 angle pdb=" C VAL D 30 " pdb=" N PHE D 31 " pdb=" CA PHE D 31 " ideal model delta sigma weight residual 122.38 117.45 4.93 1.73e+00 3.34e-01 8.12e+00 angle pdb=" C ARG C 254 " pdb=" N PHE C 255 " pdb=" CA PHE C 255 " ideal model delta sigma weight residual 122.60 118.36 4.24 1.56e+00 4.11e-01 7.40e+00 angle pdb=" C VAL F 30 " pdb=" N PHE F 31 " pdb=" CA PHE F 31 " ideal model delta sigma weight residual 122.45 116.97 5.48 2.03e+00 2.43e-01 7.28e+00 ... (remaining 33809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.87: 14262 22.87 - 45.74: 589 45.74 - 68.62: 109 68.62 - 91.49: 25 91.49 - 114.36: 5 Dihedral angle restraints: 14990 sinusoidal: 6065 harmonic: 8925 Sorted by residual: dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 54.37 -114.36 1 2.00e+01 2.50e-03 3.39e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 49.77 -109.77 1 2.00e+01 2.50e-03 3.21e+01 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 42.30 -102.30 1 2.00e+01 2.50e-03 2.91e+01 ... (remaining 14987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2623 0.050 - 0.100: 870 0.100 - 0.150: 253 0.150 - 0.200: 2 0.200 - 0.250: 2 Chirality restraints: 3750 Sorted by residual: chirality pdb=" CA VAL I 157 " pdb=" N VAL I 157 " pdb=" C VAL I 157 " pdb=" CB VAL I 157 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB VAL I 152 " pdb=" CA VAL I 152 " pdb=" CG1 VAL I 152 " pdb=" CG2 VAL I 152 " both_signs ideal model delta sigma weight residual False -2.63 -2.83 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2' ADP D 401 " pdb=" C1' ADP D 401 " pdb=" C3' ADP D 401 " pdb=" O2' ADP D 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 3747 not shown) Planarity restraints: 4333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL I 153 " -0.048 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO I 154 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO I 154 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 154 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO B 164 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 163 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO D 164 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " 0.027 5.00e-02 4.00e+02 ... (remaining 4330 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 22 2.55 - 3.14: 18547 3.14 - 3.72: 36623 3.72 - 4.31: 52835 4.31 - 4.90: 89856 Nonbonded interactions: 197883 Sorted by model distance: nonbonded pdb=" O1B ADP G 401 " pdb="MG MG G 402 " model vdw 1.961 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.970 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.977 2.170 nonbonded pdb=" O1B ADP H 401 " pdb="MG MG H 402 " model vdw 1.991 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 1.996 2.170 ... (remaining 197878 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' and resid 5 through 402) selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.220 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.007 0.058 24917 Z= 0.296 Angle : 0.718 7.800 33814 Z= 0.379 Chirality : 0.051 0.250 3750 Planarity : 0.006 0.074 4333 Dihedral : 13.488 114.362 9276 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.95 % Allowed : 7.44 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.15), residues: 3049 helix: 0.13 (0.15), residues: 1210 sheet: 0.15 (0.20), residues: 596 loop : 0.61 (0.19), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 116 TYR 0.015 0.002 TYR D 240 PHE 0.019 0.002 PHE E 375 TRP 0.017 0.002 TRP D 79 HIS 0.013 0.002 HIS I 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.30 (24917) covalent geometry : angle 0.71840 / 0.38 (33814) hydrogen bonds : bond 0.17943 / 12.13 ( 1243) hydrogen bonds : angle 6.68037 / 4.68 ( 3180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 294 time to evaluate : 0.834 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 82 MET cc_start: 0.9287 (tpt) cc_final: 0.8739 (tpt) REVERT: A 86 TRP cc_start: 0.9221 (m-10) cc_final: 0.8567 (m-90) REVERT: A 90 PHE cc_start: 0.9164 (m-10) cc_final: 0.8708 (m-10) REVERT: A 176 MET cc_start: 0.8367 (mmt) cc_final: 0.8009 (mmm) REVERT: A 349 LEU cc_start: 0.8950 (mt) cc_final: 0.8625 (mp) REVERT: B 44 MET cc_start: 0.8926 (mtp) cc_final: 0.8590 (pmt) REVERT: B 82 MET cc_start: 0.8778 (tpt) cc_final: 0.8123 (tpt) REVERT: B 276 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8523 (mt-10) REVERT: B 286 ASP cc_start: 0.8762 (m-30) cc_final: 0.8534 (m-30) REVERT: C 314 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: D 211 ASP cc_start: 0.8675 (t70) cc_final: 0.8376 (t0) REVERT: D 227 MET cc_start: 0.8157 (mmm) cc_final: 0.7670 (mmm) REVERT: D 283 MET cc_start: 0.8646 (mmm) cc_final: 0.8418 (mmt) REVERT: D 286 ASP cc_start: 0.8794 (m-30) cc_final: 0.8585 (m-30) REVERT: D 360 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7822 (tp40) REVERT: D 364 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7830 (mm-30) REVERT: E 83 GLU cc_start: 0.9044 (tt0) cc_final: 0.8820 (mt-10) REVERT: E 122 ILE cc_start: 0.7483 (mt) cc_final: 0.7231 (tt) REVERT: E 211 ASP cc_start: 0.8781 (t70) cc_final: 0.8116 (t0) REVERT: E 360 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8434 (pp30) REVERT: F 100 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8894 (mp0) REVERT: F 123 MET cc_start: 0.8627 (mmt) cc_final: 0.8350 (mmm) REVERT: F 227 MET cc_start: 0.8416 (mmm) cc_final: 0.8176 (mmm) REVERT: F 338 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8909 (p) REVERT: F 360 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8230 (tp40) REVERT: G 57 GLU cc_start: 0.8852 (tp30) cc_final: 0.8620 (pt0) REVERT: G 72 GLU cc_start: 0.8197 (mp0) cc_final: 0.7875 (pp20) REVERT: G 227 MET cc_start: 0.8829 (mmm) cc_final: 0.8245 (mmm) REVERT: H 132 MET cc_start: 0.9196 (ppp) cc_final: 0.8900 (ppp) REVERT: H 176 MET cc_start: 0.7652 (mmt) cc_final: 0.6396 (mpt) REVERT: H 285 CYS cc_start: 0.9049 (m) cc_final: 0.8710 (m) REVERT: H 355 MET cc_start: 0.9058 (mtt) cc_final: 0.8856 (mpp) REVERT: I 150 LYS cc_start: 0.7455 (ptpp) cc_final: 0.6989 (ptmm) REVERT: I 160 GLN cc_start: 0.8485 (tt0) cc_final: 0.8220 (tm-30) REVERT: I 164 GLN cc_start: 0.8157 (tt0) cc_final: 0.7655 (tm-30) REVERT: I 169 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8430 (mmm-85) REVERT: I 185 ASN cc_start: 0.7935 (t0) cc_final: 0.7442 (t0) REVERT: I 187 ASP cc_start: 0.5187 (m-30) cc_final: 0.4589 (m-30) REVERT: I 189 PHE cc_start: 0.7590 (m-80) cc_final: 0.7296 (m-80) REVERT: I 191 LEU cc_start: 0.9175 (tp) cc_final: 0.8937 (tp) REVERT: I 195 ASN cc_start: 0.9178 (m-40) cc_final: 0.8735 (t0) REVERT: I 204 ASN cc_start: 0.8684 (m-40) cc_final: 0.8344 (m-40) REVERT: I 238 THR cc_start: 0.8871 (p) cc_final: 0.8633 (p) outliers start: 77 outliers final: 12 residues processed: 359 average time/residue: 0.6140 time to fit residues: 250.5627 Evaluate side-chains 232 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 360 GLN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 360 GLN Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain H residue 118 LYS Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 169 ARG Chi-restraints excluded: chain I residue 207 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 HIS B 12 ASN B 92 ASN B 246 GLN B 275 HIS C 40 HIS C 92 ASN C 275 HIS D 92 ASN D 246 GLN D 275 HIS D 360 GLN E 246 GLN E 275 HIS E 360 GLN F 92 ASN F 128 ASN F 246 GLN F 275 HIS F 360 GLN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 ASN G 161 HIS G 275 HIS ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 ASN H 275 HIS I 155 ASN ** I 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 215 GLN I 223 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.080912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.061114 restraints weight = 65917.395| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.16 r_work: 0.2911 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24917 Z= 0.119 Angle : 0.583 10.128 33814 Z= 0.291 Chirality : 0.043 0.155 3750 Planarity : 0.004 0.060 4333 Dihedral : 7.046 93.065 3508 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.07 % Allowed : 12.54 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.16), residues: 3049 helix: 0.81 (0.15), residues: 1223 sheet: 0.51 (0.20), residues: 588 loop : 0.79 (0.19), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 210 TYR 0.012 0.001 TYR C 294 PHE 0.010 0.001 PHE E 127 TRP 0.014 0.001 TRP D 79 HIS 0.003 0.001 HIS E 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (24917) covalent geometry : angle 0.58275 / 0.29 (33814) hydrogen bonds : bond 0.03797 / 2.57 ( 1243) hydrogen bonds : angle 4.92255 / 3.41 ( 3180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 236 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.2450 (OUTLIER) cc_final: 0.2094 (pmm) REVERT: A 82 MET cc_start: 0.9324 (tpt) cc_final: 0.8781 (tpp) REVERT: A 86 TRP cc_start: 0.9064 (m-10) cc_final: 0.8640 (m-90) REVERT: A 90 PHE cc_start: 0.9169 (m-10) cc_final: 0.8586 (m-10) REVERT: A 305 MET cc_start: 0.8872 (mmm) cc_final: 0.8493 (mmt) REVERT: A 349 LEU cc_start: 0.8880 (mt) cc_final: 0.8557 (mp) REVERT: B 44 MET cc_start: 0.8613 (mtp) cc_final: 0.8318 (pmt) REVERT: B 82 MET cc_start: 0.8798 (tpt) cc_final: 0.8249 (tpt) REVERT: B 286 ASP cc_start: 0.8570 (m-30) cc_final: 0.8266 (m-30) REVERT: C 107 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: C 176 MET cc_start: 0.8652 (mmm) cc_final: 0.8251 (mmt) REVERT: C 227 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8357 (mmm) REVERT: C 286 ASP cc_start: 0.8267 (t0) cc_final: 0.7636 (m-30) REVERT: D 211 ASP cc_start: 0.8654 (t70) cc_final: 0.8374 (t0) REVERT: D 227 MET cc_start: 0.8064 (mmm) cc_final: 0.7606 (mmm) REVERT: D 286 ASP cc_start: 0.8705 (m-30) cc_final: 0.8472 (m-30) REVERT: D 325 MET cc_start: 0.8466 (mmp) cc_final: 0.8034 (mmp) REVERT: E 211 ASP cc_start: 0.8681 (t70) cc_final: 0.8085 (t0) REVERT: E 314 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: F 100 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8777 (mp0) REVERT: F 211 ASP cc_start: 0.8414 (t70) cc_final: 0.8117 (t0) REVERT: F 227 MET cc_start: 0.8328 (mmm) cc_final: 0.8121 (mmm) REVERT: F 314 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: G 44 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8313 (mtm) REVERT: G 355 MET cc_start: 0.9479 (OUTLIER) cc_final: 0.9142 (mtm) REVERT: H 132 MET cc_start: 0.8865 (ppp) cc_final: 0.8311 (ppp) REVERT: H 176 MET cc_start: 0.7567 (mmt) cc_final: 0.6350 (mpt) REVERT: H 276 GLU cc_start: 0.9489 (mt-10) cc_final: 0.8852 (tp30) REVERT: H 285 CYS cc_start: 0.8993 (m) cc_final: 0.8696 (m) REVERT: H 355 MET cc_start: 0.9044 (mtt) cc_final: 0.8784 (mpm) REVERT: I 150 LYS cc_start: 0.7582 (ptpp) cc_final: 0.7109 (ptmm) REVERT: I 153 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8126 (p) REVERT: I 164 GLN cc_start: 0.8097 (tt0) cc_final: 0.7598 (tm-30) REVERT: I 166 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7162 (tttt) REVERT: I 175 GLU cc_start: 0.8148 (tp30) cc_final: 0.7467 (tp30) REVERT: I 179 SER cc_start: 0.9249 (t) cc_final: 0.8959 (p) REVERT: I 187 ASP cc_start: 0.5060 (m-30) cc_final: 0.4434 (m-30) REVERT: I 195 ASN cc_start: 0.9201 (m-40) cc_final: 0.8742 (t0) REVERT: I 204 ASN cc_start: 0.8588 (m-40) cc_final: 0.8300 (m-40) REVERT: I 218 LYS cc_start: 0.8960 (mmtp) cc_final: 0.8553 (mmtp) REVERT: I 221 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7402 (tmm160) REVERT: I 222 ASP cc_start: 0.8357 (m-30) cc_final: 0.7700 (m-30) REVERT: I 224 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8161 (tt0) REVERT: I 244 LEU cc_start: 0.9387 (mt) cc_final: 0.9138 (mm) REVERT: I 253 LEU cc_start: 0.8582 (mm) cc_final: 0.8380 (tm) outliers start: 54 outliers final: 15 residues processed: 265 average time/residue: 0.6290 time to fit residues: 190.0471 Evaluate side-chains 231 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain F residue 313 MET Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 355 MET Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 166 LYS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 250 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 103 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 185 optimal weight: 10.0000 chunk 47 optimal weight: 0.1980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 12 ASN I 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.078860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.059414 restraints weight = 66010.282| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.07 r_work: 0.2878 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24917 Z= 0.123 Angle : 0.562 8.498 33814 Z= 0.276 Chirality : 0.043 0.145 3750 Planarity : 0.004 0.051 4333 Dihedral : 6.319 88.601 3472 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.69 % Allowed : 13.23 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.16), residues: 3049 helix: 1.16 (0.15), residues: 1216 sheet: 0.57 (0.20), residues: 587 loop : 0.88 (0.19), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 161 TYR 0.010 0.001 TYR C 294 PHE 0.009 0.001 PHE E 31 TRP 0.013 0.001 TRP C 79 HIS 0.003 0.001 HIS E 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (24917) covalent geometry : angle 0.56187 / 0.28 (33814) hydrogen bonds : bond 0.03532 / 2.39 ( 1243) hydrogen bonds : angle 4.65251 / 3.22 ( 3180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.2652 (pmm) cc_final: 0.2309 (pmm) REVERT: A 82 MET cc_start: 0.9320 (tpt) cc_final: 0.8735 (tpp) REVERT: A 86 TRP cc_start: 0.9095 (m-10) cc_final: 0.8609 (m-90) REVERT: A 90 PHE cc_start: 0.9149 (m-10) cc_final: 0.8733 (m-10) REVERT: A 123 MET cc_start: 0.8932 (tpp) cc_final: 0.8647 (tpp) REVERT: A 349 LEU cc_start: 0.8814 (mt) cc_final: 0.8478 (mp) REVERT: B 44 MET cc_start: 0.8652 (mtp) cc_final: 0.8295 (pmt) REVERT: B 82 MET cc_start: 0.8858 (tpt) cc_final: 0.8424 (tpt) REVERT: B 132 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8454 (ttt) REVERT: C 176 MET cc_start: 0.8650 (mmm) cc_final: 0.8271 (mmt) REVERT: C 227 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8545 (mmm) REVERT: C 286 ASP cc_start: 0.8274 (t0) cc_final: 0.7644 (m-30) REVERT: C 314 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8560 (tt0) REVERT: D 211 ASP cc_start: 0.8672 (t70) cc_final: 0.8396 (t0) REVERT: D 227 MET cc_start: 0.8066 (mmm) cc_final: 0.7589 (mmm) REVERT: E 176 MET cc_start: 0.8783 (tpp) cc_final: 0.8447 (mtt) REVERT: E 211 ASP cc_start: 0.8718 (t70) cc_final: 0.8127 (t0) REVERT: E 314 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: F 100 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8788 (mp0) REVERT: F 211 ASP cc_start: 0.8486 (t70) cc_final: 0.8197 (t0) REVERT: F 314 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: G 72 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8213 (pp20) REVERT: G 372 ARG cc_start: 0.9040 (mtm-85) cc_final: 0.8749 (mpp80) REVERT: H 132 MET cc_start: 0.8863 (ppp) cc_final: 0.8213 (ppp) REVERT: H 176 MET cc_start: 0.7701 (mmt) cc_final: 0.6405 (mpt) REVERT: H 276 GLU cc_start: 0.9460 (mt-10) cc_final: 0.8883 (tp30) REVERT: H 285 CYS cc_start: 0.9070 (m) cc_final: 0.8802 (m) REVERT: H 355 MET cc_start: 0.9061 (mtt) cc_final: 0.8800 (mpm) REVERT: I 150 LYS cc_start: 0.7675 (ptpp) cc_final: 0.7132 (ptmm) REVERT: I 153 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8182 (p) REVERT: I 164 GLN cc_start: 0.8232 (tt0) cc_final: 0.7773 (tm-30) REVERT: I 166 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.6844 (tttt) REVERT: I 179 SER cc_start: 0.9197 (t) cc_final: 0.8879 (p) REVERT: I 187 ASP cc_start: 0.5305 (m-30) cc_final: 0.4547 (m-30) REVERT: I 195 ASN cc_start: 0.9139 (m-40) cc_final: 0.8622 (t0) REVERT: I 204 ASN cc_start: 0.8507 (m110) cc_final: 0.8222 (m-40) REVERT: I 218 LYS cc_start: 0.8967 (mmtp) cc_final: 0.8631 (mmtp) REVERT: I 222 ASP cc_start: 0.8450 (m-30) cc_final: 0.8113 (m-30) outliers start: 44 outliers final: 15 residues processed: 232 average time/residue: 0.5534 time to fit residues: 148.0289 Evaluate side-chains 217 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 166 LYS Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 203 SER Chi-restraints excluded: chain I residue 217 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 277 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 242 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 214 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 246 GLN D 12 ASN D 162 ASN E 12 ASN G 12 ASN I 204 ASN ** I 232 HIS ** 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 = 0.3372 r_free = 0.3372 target = 0.075754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.056419 restraints weight = 67432.568| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.07 r_work: 0.2793 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 24917 Z= 0.313 Angle : 0.691 10.392 33814 Z= 0.347 Chirality : 0.049 0.151 3750 Planarity : 0.005 0.050 4333 Dihedral : 6.840 101.297 3472 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.15 % Allowed : 14.11 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3049 helix: 0.57 (0.15), residues: 1306 sheet: 0.37 (0.20), residues: 587 loop : 0.46 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 95 TYR 0.015 0.001 TYR F 240 PHE 0.015 0.002 PHE F 31 TRP 0.014 0.002 TRP C 79 HIS 0.007 0.001 HIS E 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.31 (24917) covalent geometry : angle 0.69067 / 0.35 (33814) hydrogen bonds : bond 0.05134 / 3.44 ( 1243) hydrogen bonds : angle 4.94549 / 3.42 ( 3180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 198 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.2718 (pmm) cc_final: 0.2358 (pmm) REVERT: A 82 MET cc_start: 0.9372 (tpt) cc_final: 0.8482 (tpt) REVERT: A 86 TRP cc_start: 0.9090 (m-10) cc_final: 0.8642 (m-90) REVERT: A 349 LEU cc_start: 0.8824 (mt) cc_final: 0.8478 (mp) REVERT: B 44 MET cc_start: 0.8524 (mtp) cc_final: 0.8133 (pmt) REVERT: B 82 MET cc_start: 0.8794 (tpt) cc_final: 0.8459 (tpp) REVERT: C 176 MET cc_start: 0.8688 (mmm) cc_final: 0.8334 (mmt) REVERT: C 227 MET cc_start: 0.9039 (mmp) cc_final: 0.8609 (mmm) REVERT: C 286 ASP cc_start: 0.8458 (t0) cc_final: 0.7748 (m-30) REVERT: D 176 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8426 (mmp) REVERT: D 211 ASP cc_start: 0.8768 (t70) cc_final: 0.8470 (t0) REVERT: D 227 MET cc_start: 0.8239 (mmm) cc_final: 0.7828 (mmm) REVERT: E 176 MET cc_start: 0.8918 (tpp) cc_final: 0.8561 (mtt) REVERT: E 211 ASP cc_start: 0.8782 (t70) cc_final: 0.8185 (t0) REVERT: E 314 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: F 100 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8730 (mp0) REVERT: F 314 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: G 57 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7794 (pm20) REVERT: G 72 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8219 (pp20) REVERT: G 355 MET cc_start: 0.9465 (OUTLIER) cc_final: 0.9199 (mtm) REVERT: H 132 MET cc_start: 0.8977 (ppp) cc_final: 0.8301 (ppp) REVERT: H 176 MET cc_start: 0.7811 (mmt) cc_final: 0.7299 (mpt) REVERT: H 276 GLU cc_start: 0.9441 (mt-10) cc_final: 0.8776 (tp30) REVERT: H 285 CYS cc_start: 0.9218 (m) cc_final: 0.8932 (m) REVERT: H 305 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8394 (mmm) REVERT: I 150 LYS cc_start: 0.7772 (ptpp) cc_final: 0.7210 (ptmm) REVERT: I 153 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.7904 (m) REVERT: I 164 GLN cc_start: 0.8333 (tt0) cc_final: 0.7590 (tm-30) REVERT: I 187 ASP cc_start: 0.5590 (m-30) cc_final: 0.5388 (m-30) REVERT: I 195 ASN cc_start: 0.9074 (m-40) cc_final: 0.8555 (t0) REVERT: I 218 LYS cc_start: 0.8977 (mmtp) cc_final: 0.8542 (mmtp) REVERT: I 221 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7418 (tmm160) REVERT: I 222 ASP cc_start: 0.8449 (m-30) cc_final: 0.7770 (m-30) REVERT: I 245 GLN cc_start: 0.9513 (tm-30) cc_final: 0.9246 (pp30) outliers start: 56 outliers final: 20 residues processed: 237 average time/residue: 0.5839 time to fit residues: 158.7572 Evaluate side-chains 219 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 355 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 250 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 157 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 293 optimal weight: 9.9990 chunk 242 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 255 optimal weight: 5.9990 chunk 269 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 162 ASN E 12 ASN I 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.077628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.058204 restraints weight = 65135.802| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.13 r_work: 0.2829 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24917 Z= 0.106 Angle : 0.570 8.895 33814 Z= 0.276 Chirality : 0.043 0.165 3750 Planarity : 0.004 0.053 4333 Dihedral : 6.334 90.252 3472 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.46 % Allowed : 15.30 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.16), residues: 3049 helix: 0.86 (0.15), residues: 1307 sheet: 0.56 (0.21), residues: 581 loop : 0.60 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 172 TYR 0.015 0.001 TYR H 294 PHE 0.023 0.001 PHE H 223 TRP 0.015 0.001 TRP C 79 HIS 0.005 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (24917) covalent geometry : angle 0.57003 / 0.28 (33814) hydrogen bonds : bond 0.03200 / 2.18 ( 1243) hydrogen bonds : angle 4.57457 / 3.18 ( 3180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.3192 (pmm) cc_final: 0.2750 (pmm) REVERT: A 82 MET cc_start: 0.9338 (tpt) cc_final: 0.8618 (tpp) REVERT: A 86 TRP cc_start: 0.9074 (m-10) cc_final: 0.8714 (m-90) REVERT: A 90 PHE cc_start: 0.9156 (m-10) cc_final: 0.8864 (m-10) REVERT: A 123 MET cc_start: 0.8917 (tpp) cc_final: 0.8586 (tpp) REVERT: A 305 MET cc_start: 0.8921 (mmm) cc_final: 0.8651 (mmt) REVERT: A 349 LEU cc_start: 0.8893 (mt) cc_final: 0.8537 (mp) REVERT: B 44 MET cc_start: 0.8593 (mtp) cc_final: 0.8180 (pmt) REVERT: B 82 MET cc_start: 0.8817 (tpt) cc_final: 0.8364 (tpt) REVERT: C 176 MET cc_start: 0.8568 (mmm) cc_final: 0.8177 (mmt) REVERT: C 227 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8498 (mmm) REVERT: C 286 ASP cc_start: 0.8374 (t0) cc_final: 0.7652 (m-30) REVERT: C 314 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8617 (tt0) REVERT: D 211 ASP cc_start: 0.8731 (t70) cc_final: 0.8443 (t0) REVERT: D 227 MET cc_start: 0.8083 (mmm) cc_final: 0.7620 (mmm) REVERT: E 176 MET cc_start: 0.8823 (tpp) cc_final: 0.8513 (mtt) REVERT: E 211 ASP cc_start: 0.8721 (t70) cc_final: 0.8146 (t0) REVERT: E 314 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: F 100 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8801 (mp0) REVERT: F 211 ASP cc_start: 0.8465 (t70) cc_final: 0.8142 (t0) REVERT: F 314 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: G 44 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8417 (mtm) REVERT: G 72 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8197 (pp20) REVERT: G 355 MET cc_start: 0.9419 (OUTLIER) cc_final: 0.9021 (mtm) REVERT: G 372 ARG cc_start: 0.9027 (mtm-85) cc_final: 0.8717 (mpp80) REVERT: H 132 MET cc_start: 0.8903 (ppp) cc_final: 0.8221 (ppp) REVERT: H 176 MET cc_start: 0.7714 (mmt) cc_final: 0.7286 (mpt) REVERT: H 276 GLU cc_start: 0.9427 (mt-10) cc_final: 0.8674 (tp30) REVERT: H 285 CYS cc_start: 0.9136 (m) cc_final: 0.8854 (m) REVERT: H 305 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8318 (mmm) REVERT: H 355 MET cc_start: 0.9162 (mpp) cc_final: 0.8910 (mpm) REVERT: I 150 LYS cc_start: 0.7870 (ptpp) cc_final: 0.7280 (ptmm) REVERT: I 164 GLN cc_start: 0.8293 (tt0) cc_final: 0.7678 (tm-30) REVERT: I 166 LYS cc_start: 0.7663 (ptmm) cc_final: 0.6830 (tttt) REVERT: I 179 SER cc_start: 0.9100 (t) cc_final: 0.8810 (p) REVERT: I 187 ASP cc_start: 0.5360 (m-30) cc_final: 0.4728 (m-30) REVERT: I 195 ASN cc_start: 0.9113 (m-40) cc_final: 0.8598 (t0) REVERT: I 224 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8330 (tt0) outliers start: 38 outliers final: 13 residues processed: 229 average time/residue: 0.5447 time to fit residues: 143.8342 Evaluate side-chains 216 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 355 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain I residue 217 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 141 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 204 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN E 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.077327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.057906 restraints weight = 65370.160| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.13 r_work: 0.2823 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24917 Z= 0.129 Angle : 0.573 9.054 33814 Z= 0.277 Chirality : 0.043 0.154 3750 Planarity : 0.004 0.055 4333 Dihedral : 6.150 87.307 3472 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.46 % Allowed : 15.57 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.16), residues: 3049 helix: 0.98 (0.15), residues: 1307 sheet: 0.57 (0.21), residues: 581 loop : 0.65 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 172 TYR 0.012 0.001 TYR H 294 PHE 0.010 0.001 PHE E 31 TRP 0.016 0.001 TRP I 180 HIS 0.004 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (24917) covalent geometry : angle 0.57348 / 0.28 (33814) hydrogen bonds : bond 0.03321 / 2.26 ( 1243) hydrogen bonds : angle 4.51695 / 3.14 ( 3180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.3115 (pmm) cc_final: 0.2625 (pmm) REVERT: A 82 MET cc_start: 0.9351 (tpt) cc_final: 0.8563 (tpp) REVERT: A 86 TRP cc_start: 0.9086 (m-10) cc_final: 0.8701 (m-90) REVERT: A 90 PHE cc_start: 0.9122 (m-10) cc_final: 0.8862 (m-10) REVERT: A 123 MET cc_start: 0.8975 (tpp) cc_final: 0.8678 (tpp) REVERT: A 305 MET cc_start: 0.8969 (mmm) cc_final: 0.8699 (mmt) REVERT: A 349 LEU cc_start: 0.8907 (mt) cc_final: 0.8556 (mp) REVERT: B 44 MET cc_start: 0.8571 (mtp) cc_final: 0.7952 (pmt) REVERT: B 80 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8449 (p0) REVERT: B 82 MET cc_start: 0.8828 (tpt) cc_final: 0.8386 (tpt) REVERT: C 176 MET cc_start: 0.8625 (mmm) cc_final: 0.8230 (mmt) REVERT: C 211 ASP cc_start: 0.8728 (t70) cc_final: 0.8137 (t0) REVERT: C 227 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8496 (mmm) REVERT: C 314 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: D 211 ASP cc_start: 0.8722 (t70) cc_final: 0.8430 (t0) REVERT: D 227 MET cc_start: 0.8077 (mmm) cc_final: 0.7599 (mmm) REVERT: E 176 MET cc_start: 0.8847 (tpp) cc_final: 0.8512 (mtt) REVERT: E 211 ASP cc_start: 0.8726 (t70) cc_final: 0.8129 (t0) REVERT: E 314 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: F 44 MET cc_start: 0.8919 (mtm) cc_final: 0.8525 (mtm) REVERT: F 100 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8771 (mp0) REVERT: F 314 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: G 44 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8326 (mtm) REVERT: G 72 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8226 (pp20) REVERT: G 372 ARG cc_start: 0.9030 (mtm-85) cc_final: 0.8725 (mpp80) REVERT: H 132 MET cc_start: 0.8943 (ppp) cc_final: 0.8252 (ppp) REVERT: H 176 MET cc_start: 0.7719 (mmt) cc_final: 0.7305 (mpt) REVERT: H 276 GLU cc_start: 0.9430 (mt-10) cc_final: 0.9170 (mm-30) REVERT: H 285 CYS cc_start: 0.9105 (m) cc_final: 0.8818 (m) REVERT: H 305 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8383 (mmm) REVERT: I 150 LYS cc_start: 0.7875 (ptpp) cc_final: 0.7266 (ptmm) REVERT: I 153 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7515 (m) REVERT: I 164 GLN cc_start: 0.8308 (tt0) cc_final: 0.7721 (tm-30) REVERT: I 166 LYS cc_start: 0.7805 (ptmm) cc_final: 0.6851 (tttt) REVERT: I 168 ARG cc_start: 0.8570 (tmt-80) cc_final: 0.8355 (tpp-160) REVERT: I 169 ARG cc_start: 0.7290 (mmm160) cc_final: 0.7043 (tpm170) REVERT: I 171 VAL cc_start: 0.8265 (t) cc_final: 0.8064 (t) REVERT: I 179 SER cc_start: 0.9040 (t) cc_final: 0.8761 (p) REVERT: I 187 ASP cc_start: 0.5190 (m-30) cc_final: 0.4518 (m-30) REVERT: I 195 ASN cc_start: 0.9157 (m-40) cc_final: 0.8644 (t0) REVERT: I 224 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8402 (tt0) REVERT: I 245 GLN cc_start: 0.9499 (tm-30) cc_final: 0.9249 (pp30) outliers start: 38 outliers final: 19 residues processed: 225 average time/residue: 0.5995 time to fit residues: 155.3071 Evaluate side-chains 223 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 250 LYS Chi-restraints excluded: chain I residue 257 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 134 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 102 optimal weight: 0.0270 chunk 129 optimal weight: 3.9990 chunk 306 optimal weight: 0.0970 chunk 95 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 12 ASN D 161 HIS I 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.077923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.058652 restraints weight = 65250.757| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.13 r_work: 0.2840 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24917 Z= 0.107 Angle : 0.567 12.082 33814 Z= 0.269 Chirality : 0.043 0.348 3750 Planarity : 0.004 0.061 4333 Dihedral : 5.943 80.539 3472 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.65 % Allowed : 15.57 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.16), residues: 3049 helix: 1.20 (0.15), residues: 1265 sheet: 0.60 (0.21), residues: 581 loop : 0.70 (0.19), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 172 TYR 0.012 0.001 TYR H 294 PHE 0.010 0.001 PHE H 223 TRP 0.013 0.001 TRP C 79 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (24917) covalent geometry : angle 0.56702 / 0.27 (33814) hydrogen bonds : bond 0.03022 / 2.06 ( 1243) hydrogen bonds : angle 4.43131 / 3.08 ( 3180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.3188 (pmm) cc_final: 0.2329 (pmm) REVERT: A 82 MET cc_start: 0.9310 (tpt) cc_final: 0.8575 (tpp) REVERT: A 86 TRP cc_start: 0.9091 (m-10) cc_final: 0.8729 (m-90) REVERT: A 90 PHE cc_start: 0.9109 (m-10) cc_final: 0.8734 (m-10) REVERT: A 123 MET cc_start: 0.8974 (tpp) cc_final: 0.8728 (tpp) REVERT: A 305 MET cc_start: 0.9000 (mmm) cc_final: 0.8703 (mmt) REVERT: A 349 LEU cc_start: 0.8902 (mt) cc_final: 0.8541 (mp) REVERT: B 44 MET cc_start: 0.8804 (mtp) cc_final: 0.8359 (pmt) REVERT: B 80 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8395 (p0) REVERT: B 82 MET cc_start: 0.8791 (tpt) cc_final: 0.8405 (tpt) REVERT: C 176 MET cc_start: 0.8552 (mmm) cc_final: 0.8174 (mmt) REVERT: C 211 ASP cc_start: 0.8744 (t70) cc_final: 0.8156 (t0) REVERT: C 227 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8533 (mmm) REVERT: C 286 ASP cc_start: 0.8332 (t0) cc_final: 0.7598 (m-30) REVERT: C 314 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8621 (tt0) REVERT: D 211 ASP cc_start: 0.8706 (t70) cc_final: 0.8427 (t0) REVERT: D 227 MET cc_start: 0.8054 (mmm) cc_final: 0.7578 (mmm) REVERT: E 176 MET cc_start: 0.8838 (tpp) cc_final: 0.8501 (mtt) REVERT: E 211 ASP cc_start: 0.8726 (t70) cc_final: 0.8131 (t0) REVERT: E 314 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: F 100 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8782 (mp0) REVERT: F 211 ASP cc_start: 0.8460 (t70) cc_final: 0.8166 (t0) REVERT: F 314 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: G 44 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8342 (mtm) REVERT: G 57 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7767 (pm20) REVERT: G 72 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8239 (pp20) REVERT: G 372 ARG cc_start: 0.9025 (mtm-85) cc_final: 0.8715 (mpp80) REVERT: H 132 MET cc_start: 0.8953 (ppp) cc_final: 0.8260 (ppp) REVERT: H 176 MET cc_start: 0.7651 (mmt) cc_final: 0.7279 (mpt) REVERT: H 276 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9156 (mm-30) REVERT: H 285 CYS cc_start: 0.9085 (m) cc_final: 0.8806 (m) REVERT: H 305 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8385 (mmm) REVERT: I 150 LYS cc_start: 0.7876 (ptpp) cc_final: 0.7266 (ptmm) REVERT: I 160 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: I 164 GLN cc_start: 0.8393 (tt0) cc_final: 0.7947 (tm-30) REVERT: I 166 LYS cc_start: 0.7849 (ptmm) cc_final: 0.6985 (tttt) REVERT: I 171 VAL cc_start: 0.8229 (t) cc_final: 0.7991 (t) REVERT: I 179 SER cc_start: 0.9018 (t) cc_final: 0.8608 (p) REVERT: I 187 ASP cc_start: 0.5168 (m-30) cc_final: 0.4474 (m-30) REVERT: I 195 ASN cc_start: 0.9158 (m-40) cc_final: 0.8675 (t0) REVERT: I 221 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7362 (tmm160) REVERT: I 222 ASP cc_start: 0.8611 (m-30) cc_final: 0.7926 (m-30) REVERT: I 224 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8500 (tt0) REVERT: I 243 MET cc_start: 0.9188 (ttm) cc_final: 0.8616 (tmm) REVERT: I 245 GLN cc_start: 0.9453 (tm-30) cc_final: 0.9249 (pp30) outliers start: 43 outliers final: 21 residues processed: 235 average time/residue: 0.6151 time to fit residues: 165.4844 Evaluate side-chains 229 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain I residue 160 GLN Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 257 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 190 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 254 optimal weight: 0.0170 chunk 299 optimal weight: 4.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN G 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.077920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.058562 restraints weight = 65586.872| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.15 r_work: 0.2839 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24917 Z= 0.114 Angle : 0.578 11.512 33814 Z= 0.274 Chirality : 0.043 0.249 3750 Planarity : 0.004 0.053 4333 Dihedral : 5.844 78.015 3472 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.61 % Allowed : 15.64 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.16), residues: 3049 helix: 1.07 (0.15), residues: 1307 sheet: 0.61 (0.21), residues: 581 loop : 0.72 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 172 TYR 0.011 0.001 TYR H 294 PHE 0.015 0.001 PHE I 189 TRP 0.012 0.001 TRP C 79 HIS 0.004 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (24917) covalent geometry : angle 0.57786 / 0.27 (33814) hydrogen bonds : bond 0.03060 / 2.09 ( 1243) hydrogen bonds : angle 4.40426 / 3.06 ( 3180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9305 (tpt) cc_final: 0.8543 (tpp) REVERT: A 86 TRP cc_start: 0.9101 (m-10) cc_final: 0.8774 (m-90) REVERT: A 90 PHE cc_start: 0.9136 (m-10) cc_final: 0.8727 (m-10) REVERT: A 305 MET cc_start: 0.9009 (mmm) cc_final: 0.8702 (mmt) REVERT: A 349 LEU cc_start: 0.8926 (mt) cc_final: 0.8561 (mp) REVERT: B 44 MET cc_start: 0.8624 (mtp) cc_final: 0.8162 (pmt) REVERT: B 80 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8395 (p0) REVERT: C 47 MET cc_start: 0.7742 (mmm) cc_final: 0.7473 (mmm) REVERT: C 211 ASP cc_start: 0.8750 (t70) cc_final: 0.8169 (t0) REVERT: C 227 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8542 (mmm) REVERT: C 314 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8644 (tt0) REVERT: D 211 ASP cc_start: 0.8740 (t70) cc_final: 0.8461 (t0) REVERT: D 227 MET cc_start: 0.8082 (mmm) cc_final: 0.7606 (mmm) REVERT: E 176 MET cc_start: 0.8864 (tpp) cc_final: 0.8530 (mtt) REVERT: E 211 ASP cc_start: 0.8745 (t70) cc_final: 0.8151 (t0) REVERT: E 314 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8481 (tt0) REVERT: F 100 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8763 (mp0) REVERT: F 211 ASP cc_start: 0.8465 (t70) cc_final: 0.8179 (t0) REVERT: F 314 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: G 44 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8312 (mtm) REVERT: G 57 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: G 72 GLU cc_start: 0.8810 (mp0) cc_final: 0.8272 (pp20) REVERT: G 372 ARG cc_start: 0.9021 (mtm-85) cc_final: 0.8718 (mpp80) REVERT: H 132 MET cc_start: 0.8947 (ppp) cc_final: 0.8268 (ppp) REVERT: H 176 MET cc_start: 0.7702 (mmt) cc_final: 0.7083 (mpp) REVERT: H 276 GLU cc_start: 0.9412 (mt-10) cc_final: 0.9149 (mm-30) REVERT: H 285 CYS cc_start: 0.9065 (m) cc_final: 0.8786 (m) REVERT: H 305 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8386 (mmm) REVERT: I 150 LYS cc_start: 0.7936 (ptpp) cc_final: 0.7334 (ptmm) REVERT: I 164 GLN cc_start: 0.8432 (tt0) cc_final: 0.7967 (tm-30) REVERT: I 166 LYS cc_start: 0.7648 (ptmm) cc_final: 0.6776 (tttt) REVERT: I 171 VAL cc_start: 0.8277 (t) cc_final: 0.8068 (t) REVERT: I 179 SER cc_start: 0.8978 (t) cc_final: 0.8642 (p) REVERT: I 187 ASP cc_start: 0.5183 (m-30) cc_final: 0.4564 (m-30) REVERT: I 195 ASN cc_start: 0.9122 (m-40) cc_final: 0.8673 (t0) REVERT: I 218 LYS cc_start: 0.8951 (mmtp) cc_final: 0.8551 (mmtp) REVERT: I 221 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7370 (tmm160) REVERT: I 222 ASP cc_start: 0.8617 (m-30) cc_final: 0.7944 (m-30) REVERT: I 224 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8515 (tt0) REVERT: I 235 GLU cc_start: 0.8814 (pm20) cc_final: 0.8305 (tp30) REVERT: I 243 MET cc_start: 0.9161 (ttm) cc_final: 0.8633 (tmm) REVERT: I 263 GLU cc_start: 0.5502 (OUTLIER) cc_final: 0.4326 (pm20) outliers start: 42 outliers final: 22 residues processed: 229 average time/residue: 0.5693 time to fit residues: 149.7399 Evaluate side-chains 225 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 263 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 143 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 231 optimal weight: 6.9990 chunk 102 optimal weight: 0.3980 chunk 249 optimal weight: 6.9990 chunk 287 optimal weight: 0.0770 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 204 ASN ** I 245 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 = 0.3405 r_free = 0.3405 target = 0.078046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.058733 restraints weight = 65768.427| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.16 r_work: 0.2844 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24917 Z= 0.110 Angle : 0.584 12.221 33814 Z= 0.277 Chirality : 0.043 0.219 3750 Planarity : 0.004 0.057 4333 Dihedral : 5.763 74.764 3472 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.69 % Allowed : 15.80 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.16), residues: 3049 helix: 1.10 (0.15), residues: 1307 sheet: 0.63 (0.21), residues: 581 loop : 0.74 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 172 TYR 0.010 0.001 TYR H 294 PHE 0.018 0.001 PHE I 189 TRP 0.015 0.001 TRP H 356 HIS 0.004 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (24917) covalent geometry : angle 0.58414 / 0.28 (33814) hydrogen bonds : bond 0.03031 / 2.09 ( 1243) hydrogen bonds : angle 4.37040 / 3.03 ( 3180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.3372 (pmm) cc_final: 0.3134 (pmt) REVERT: A 47 MET cc_start: 0.3323 (OUTLIER) cc_final: 0.2675 (ptp) REVERT: A 82 MET cc_start: 0.9290 (tpt) cc_final: 0.8540 (tpp) REVERT: A 86 TRP cc_start: 0.9101 (m-10) cc_final: 0.8772 (m-90) REVERT: A 90 PHE cc_start: 0.9226 (m-10) cc_final: 0.8760 (m-10) REVERT: A 124 PHE cc_start: 0.6590 (OUTLIER) cc_final: 0.6290 (m-10) REVERT: A 305 MET cc_start: 0.9024 (mmm) cc_final: 0.8737 (mmt) REVERT: A 349 LEU cc_start: 0.8947 (mt) cc_final: 0.8577 (mp) REVERT: B 44 MET cc_start: 0.8539 (mtp) cc_final: 0.8168 (pmt) REVERT: B 80 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8447 (p0) REVERT: C 227 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8548 (mmm) REVERT: C 314 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8659 (tt0) REVERT: C 355 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8052 (mtm) REVERT: D 211 ASP cc_start: 0.8752 (t70) cc_final: 0.8479 (t0) REVERT: D 227 MET cc_start: 0.8071 (mmm) cc_final: 0.7598 (mmm) REVERT: E 176 MET cc_start: 0.8869 (tpp) cc_final: 0.8538 (mtt) REVERT: E 211 ASP cc_start: 0.8746 (t70) cc_final: 0.8162 (t0) REVERT: E 314 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: F 100 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8773 (mp0) REVERT: F 211 ASP cc_start: 0.8474 (t70) cc_final: 0.8192 (t0) REVERT: F 314 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: G 44 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8276 (mtm) REVERT: G 57 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: G 72 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8281 (pp20) REVERT: G 372 ARG cc_start: 0.9013 (mtm-85) cc_final: 0.8705 (mpp80) REVERT: H 132 MET cc_start: 0.8967 (ppp) cc_final: 0.8308 (ppp) REVERT: H 176 MET cc_start: 0.7734 (mmt) cc_final: 0.7111 (mpp) REVERT: H 276 GLU cc_start: 0.9424 (mt-10) cc_final: 0.9162 (mm-30) REVERT: H 285 CYS cc_start: 0.9004 (m) cc_final: 0.8721 (m) REVERT: H 305 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8361 (mmm) REVERT: I 150 LYS cc_start: 0.7897 (ptpp) cc_final: 0.7287 (ptmm) REVERT: I 164 GLN cc_start: 0.8450 (tt0) cc_final: 0.8086 (tm-30) REVERT: I 166 LYS cc_start: 0.7812 (ptmm) cc_final: 0.6920 (tttt) REVERT: I 171 VAL cc_start: 0.8240 (t) cc_final: 0.8012 (t) REVERT: I 179 SER cc_start: 0.8972 (t) cc_final: 0.8742 (p) REVERT: I 187 ASP cc_start: 0.5077 (m-30) cc_final: 0.4464 (m-30) REVERT: I 195 ASN cc_start: 0.9146 (m-40) cc_final: 0.8700 (t0) REVERT: I 218 LYS cc_start: 0.8960 (mmtp) cc_final: 0.8550 (mmtp) REVERT: I 221 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7339 (tmm160) REVERT: I 222 ASP cc_start: 0.8618 (m-30) cc_final: 0.7932 (m-30) REVERT: I 224 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8497 (tt0) REVERT: I 243 MET cc_start: 0.9140 (ttm) cc_final: 0.8653 (tmm) REVERT: I 263 GLU cc_start: 0.5457 (OUTLIER) cc_final: 0.4277 (pm20) outliers start: 44 outliers final: 23 residues processed: 234 average time/residue: 0.6149 time to fit residues: 164.7623 Evaluate side-chains 232 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 230 ARG Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 263 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 13 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 278 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.076314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.056823 restraints weight = 65877.935| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.14 r_work: 0.2798 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24917 Z= 0.199 Angle : 0.651 12.396 33814 Z= 0.312 Chirality : 0.046 0.358 3750 Planarity : 0.004 0.095 4333 Dihedral : 6.055 81.654 3472 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.46 % Allowed : 16.03 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.15), residues: 3049 helix: 1.13 (0.15), residues: 1271 sheet: 0.56 (0.21), residues: 581 loop : 0.58 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 172 TYR 0.018 0.001 TYR H 294 PHE 0.022 0.001 PHE I 189 TRP 0.013 0.002 TRP C 86 HIS 0.006 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (24917) covalent geometry : angle 0.65077 / 0.31 (33814) hydrogen bonds : bond 0.03943 / 2.67 ( 1243) hydrogen bonds : angle 4.56365 / 3.16 ( 3180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6098 Ramachandran restraints generated. 3049 Oldfield, 0 Emsley, 3049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.3204 (pmm) cc_final: 0.2952 (pmt) REVERT: A 47 MET cc_start: 0.2840 (OUTLIER) cc_final: 0.2146 (ptp) REVERT: A 82 MET cc_start: 0.9323 (tpt) cc_final: 0.8497 (tpt) REVERT: A 86 TRP cc_start: 0.9112 (m-10) cc_final: 0.8854 (m-90) REVERT: A 90 PHE cc_start: 0.9235 (m-10) cc_final: 0.8791 (m-10) REVERT: A 124 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.6348 (m-10) REVERT: A 349 LEU cc_start: 0.8956 (mt) cc_final: 0.8584 (mp) REVERT: C 132 MET cc_start: 0.7922 (ttm) cc_final: 0.7325 (mtp) REVERT: C 227 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8619 (mmm) REVERT: C 314 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8691 (tt0) REVERT: C 361 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7736 (mt-10) REVERT: D 211 ASP cc_start: 0.8801 (t70) cc_final: 0.8516 (t0) REVERT: D 227 MET cc_start: 0.8178 (mmm) cc_final: 0.7696 (mmm) REVERT: E 176 MET cc_start: 0.8913 (tpp) cc_final: 0.8562 (mtt) REVERT: E 211 ASP cc_start: 0.8781 (t70) cc_final: 0.8172 (t0) REVERT: E 314 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: F 100 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8760 (mp0) REVERT: F 314 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8030 (tm-30) REVERT: G 57 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7984 (pm20) REVERT: G 72 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8235 (pp20) REVERT: G 372 ARG cc_start: 0.9016 (mtm-85) cc_final: 0.8721 (mpp80) REVERT: H 132 MET cc_start: 0.9009 (ppp) cc_final: 0.8321 (ppp) REVERT: H 176 MET cc_start: 0.7810 (mmt) cc_final: 0.7432 (mpt) REVERT: H 276 GLU cc_start: 0.9422 (mt-10) cc_final: 0.9161 (mm-30) REVERT: H 285 CYS cc_start: 0.9040 (m) cc_final: 0.8763 (m) REVERT: H 305 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8390 (mmm) REVERT: I 150 LYS cc_start: 0.7850 (ptpp) cc_final: 0.7246 (ptmm) REVERT: I 160 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: I 164 GLN cc_start: 0.8442 (tt0) cc_final: 0.7767 (tm-30) REVERT: I 166 LYS cc_start: 0.7746 (ptmm) cc_final: 0.6777 (tttt) REVERT: I 171 VAL cc_start: 0.8287 (t) cc_final: 0.8042 (t) REVERT: I 187 ASP cc_start: 0.5539 (m-30) cc_final: 0.5046 (m-30) REVERT: I 189 PHE cc_start: 0.7675 (m-10) cc_final: 0.7218 (m-80) REVERT: I 195 ASN cc_start: 0.9146 (m-40) cc_final: 0.8696 (t0) REVERT: I 218 LYS cc_start: 0.9003 (mmtp) cc_final: 0.8565 (mmtp) REVERT: I 221 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7386 (tmm160) REVERT: I 222 ASP cc_start: 0.8625 (m-30) cc_final: 0.8075 (m-30) REVERT: I 224 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8477 (tt0) REVERT: I 243 MET cc_start: 0.9143 (ttm) cc_final: 0.8696 (tmm) REVERT: I 263 GLU cc_start: 0.5697 (OUTLIER) cc_final: 0.4383 (pm20) outliers start: 38 outliers final: 22 residues processed: 219 average time/residue: 0.6260 time to fit residues: 156.6300 Evaluate side-chains 221 residues out of total 2608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain I residue 160 GLN Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 263 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 7.9990 chunk 173 optimal weight: 0.8980 chunk 246 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 251 optimal weight: 8.9990 chunk 299 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 305 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.076227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056804 restraints weight = 66198.391| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.14 r_work: 0.2797 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.214 24917 Z= 0.233 Angle : 0.788 59.200 33814 Z= 0.410 Chirality : 0.048 0.847 3750 Planarity : 0.004 0.093 4333 Dihedral : 6.058 81.628 3472 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.57 % Allowed : 16.07 % Favored : 82.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.15), residues: 3049 helix: 1.08 (0.15), residues: 1278 sheet: 0.56 (0.21), residues: 581 loop : 0.60 (0.19), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 172 TYR 0.017 0.001 TYR H 294 PHE 0.019 0.001 PHE I 189 TRP 0.012 0.002 TRP C 86 HIS 0.005 0.001 HIS E 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (24917) covalent geometry : angle 0.78770 / 0.41 (33814) hydrogen bonds : bond 0.03978 / 2.69 ( 1243) hydrogen bonds : angle 4.56426 / 3.16 ( 3180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5998.19 seconds wall clock time: 103 minutes 14.28 seconds (6194.28 seconds total)