Starting phenix.real_space_refine on Sat Aug 8 05:26:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12by_76300/08_2026/12by_76300.cif Found real_map, /net/cci-nas-00/data/ceres_data/12by_76300/08_2026/12by_76300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/12by_76300/08_2026/12by_76300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12by_76300/08_2026/12by_76300.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/12by_76300/08_2026/12by_76300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12by_76300/08_2026/12by_76300.map" } resolution = 2.76 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 2 9.91 5 P 16 5.49 5 Mg 8 5.21 5 S 174 5.16 5 C 15918 2.51 5 N 4281 2.21 5 O 4857 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: 25256 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: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1813 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 220} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.21, per 1000 atoms: 0.21 Number of scatterers: 25256 At special positions: 0 Unit cell: (89.64, 118.8, 278.64, 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 2 19.99 S 174 16.00 P 16 15.00 Mg 8 11.99 O 4857 8.00 N 4281 7.00 C 15918 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: 1.56 Conformation dependent library (CDL) restraints added in 797.2 milliseconds 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5918 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 50 sheets defined 50.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 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: 3.622A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.814A 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 251 through 256 Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.558A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 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: 3.905A 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 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.697A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.773A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 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: 3.876A 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: 3.777A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 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: 4.003A 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 removed outlier: 3.531A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.880A 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: 3.539A 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 285 removed outlier: 3.783A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 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 347 Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.807A 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 removed outlier: 3.618A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.582A pdb=" N GLU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.769A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.543A 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 removed outlier: 3.505A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) 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 348 Processing helix chain 'D' and resid 349 through 355 removed outlier: 3.557A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.940A 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: 3.717A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.883A 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 251 through 256 Processing helix chain 'E' and resid 257 through 262 removed outlier: 3.508A pdb=" N THR E 260 " --> pdb=" O CYS E 257 " (cutoff:3.500A) 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 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: 6.454A 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 369 through 374 removed outlier: 3.519A pdb=" N CYS E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 93 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.654A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.899A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 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 197 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 262 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 295 Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.608A 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: 3.764A pdb=" N SER F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.894A 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 removed outlier: 3.578A pdb=" N CYS F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) 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 removed outlier: 3.509A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.882A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 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 295 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 348 removed outlier: 3.646A pdb=" N SER G 348 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 355 removed outlier: 3.824A 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: 3.509A 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 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.950A 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 193 Processing helix chain 'H' and resid 194 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 257 Processing helix chain 'H' and resid 258 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 296 removed outlier: 3.628A pdb=" N ARG H 290 " --> pdb=" O ASP H 286 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 5.613A 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 349 No H-bonds generated for 'chain 'H' and resid 348 through 349' Processing helix chain 'H' and resid 350 through 355 removed outlier: 3.895A 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 Processing helix chain 'I' and resid 206 through 223 removed outlier: 3.514A pdb=" N ARG I 210 " --> pdb=" O ASN I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 248 Processing helix chain 'I' and resid 261 through 269 Processing helix chain 'I' and resid 295 through 299 Processing helix chain 'I' and resid 324 through 342 removed outlier: 3.894A pdb=" N ILE I 339 " --> pdb=" O ALA I 335 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR I 340 " --> pdb=" O SER I 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS I 341 " --> pdb=" O ASP I 337 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET I 342 " --> pdb=" O PHE I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 366 removed outlier: 3.699A pdb=" N PHE I 365 " --> pdb=" O PHE I 362 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.551A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.529A 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: 6.568A 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: 4.010A 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: 6.370A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.407A 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: 6.534A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.115A 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: 3.989A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 357 " --> pdb=" O MET C 132 " (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: 6.577A 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: 4.082A 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: 6.437A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR D 103 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 3.553A 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: 6.518A 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: 4.051A 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: 6.778A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.553A 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: 6.545A 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: 4.041A 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: 4.151A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE F 357 " --> pdb=" O MET F 132 " (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: 6.493A 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: 3.906A 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: 4.267A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 5.424A 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: 6.559A 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: 6.833A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.880A 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: 6.597A 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 removed outlier: 6.423A pdb=" N ILE I 197 " --> pdb=" O HIS I 232 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N SER I 234 " --> pdb=" O ILE I 197 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN I 199 " --> pdb=" O SER I 234 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 285 through 289 removed outlier: 6.761A pdb=" N LEU I 273 " --> pdb=" O VAL I 288 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE I 315 " --> pdb=" O SER I 351 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU I 353 " --> pdb=" O ILE I 315 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL I 317 " --> pdb=" O LEU I 353 " (cutoff:3.500A) 1289 hydrogen bonds defined for protein. 3237 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: 5.48 Time building geometry restraints manager: 2.19 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: 8160 1.34 - 1.46: 4229 1.46 - 1.57: 13084 1.57 - 1.69: 24 1.69 - 1.81: 305 Bond restraints: 25802 Sorted by residual: bond pdb=" C ASN E 12 " pdb=" N GLY E 13 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.54e-02 4.22e+03 4.01e+00 bond pdb=" C ASN G 12 " pdb=" N GLY G 13 " ideal model delta sigma weight residual 1.332 1.305 0.026 1.54e-02 4.22e+03 2.89e+00 bond pdb=" C ASN C 12 " pdb=" N GLY C 13 " ideal model delta sigma weight residual 1.332 1.308 0.024 1.54e-02 4.22e+03 2.41e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.78e+00 ... (remaining 25797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 33551 1.39 - 2.78: 1122 2.78 - 4.17: 227 4.17 - 5.56: 76 5.56 - 6.95: 30 Bond angle restraints: 35006 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 114.23 117.32 -3.09 8.80e-01 1.29e+00 1.23e+01 angle pdb=" C VAL I 152 " pdb=" N VAL I 153 " pdb=" CA VAL I 153 " ideal model delta sigma weight residual 123.33 120.57 2.76 8.70e-01 1.32e+00 1.01e+01 angle pdb=" C VAL D 30 " pdb=" N PHE D 31 " pdb=" CA PHE D 31 " ideal model delta sigma weight residual 122.38 117.15 5.23 1.73e+00 3.34e-01 9.14e+00 angle pdb=" C CYS E 374 " pdb=" N PHE E 375 " pdb=" CA PHE E 375 " ideal model delta sigma weight residual 121.70 126.86 -5.16 1.80e+00 3.09e-01 8.22e+00 angle pdb=" CA GLY I 167 " pdb=" C GLY I 167 " pdb=" O GLY I 167 " ideal model delta sigma weight residual 122.33 120.15 2.18 8.10e-01 1.52e+00 7.27e+00 ... (remaining 35001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.24: 14645 20.24 - 40.48: 679 40.48 - 60.71: 161 60.71 - 80.95: 26 80.95 - 101.19: 14 Dihedral angle restraints: 15525 sinusoidal: 6283 harmonic: 9242 Sorted by residual: 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 41.19 -101.19 1 2.00e+01 2.50e-03 2.87e+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 40.96 -100.96 1 2.00e+01 2.50e-03 2.86e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 38.78 -98.78 1 2.00e+01 2.50e-03 2.77e+01 ... (remaining 15522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1866 0.029 - 0.058: 1205 0.058 - 0.087: 448 0.087 - 0.116: 281 0.116 - 0.145: 77 Chirality restraints: 3877 Sorted by residual: chirality pdb=" CB ILE F 287 " pdb=" CA ILE F 287 " pdb=" CG1 ILE F 287 " pdb=" CG2 ILE F 287 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA VAL E 35 " pdb=" N VAL E 35 " pdb=" C VAL E 35 " pdb=" CB VAL E 35 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE I 197 " pdb=" N ILE I 197 " pdb=" C ILE I 197 " pdb=" CB ILE I 197 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 3874 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL I 153 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO I 154 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO I 154 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 154 " -0.032 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 5.20e-02 4.32e+00 pdb=" N PRO B 164 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 242 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO H 243 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 243 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 243 " 0.027 5.00e-02 4.00e+02 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 27 2.57 - 3.15: 19813 3.15 - 3.73: 38166 3.73 - 4.32: 55473 4.32 - 4.90: 93205 Nonbonded interactions: 206684 Sorted by model distance: nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.987 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.991 2.170 nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 2.008 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 2.012 2.170 nonbonded pdb=" O1B ADP H 401 " pdb="MG MG H 402 " model vdw 2.016 2.170 ... (remaining 206679 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.150 Find NCS groups from input model: 0.570 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:9.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 : 0.005 0.055 25802 Z= 0.239 Angle : 0.672 6.947 35006 Z= 0.354 Chirality : 0.048 0.145 3877 Planarity : 0.006 0.057 4488 Dihedral : 12.978 101.189 9607 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.55 % Allowed : 6.48 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.37 (0.15), residues: 3160 helix: 0.22 (0.15), residues: 1244 sheet: 0.10 (0.19), residues: 631 loop : 0.63 (0.18), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 268 TYR 0.012 0.001 TYR D 240 PHE 0.022 0.002 PHE E 375 TRP 0.017 0.002 TRP D 79 HIS 0.006 0.001 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (25802) covalent geometry : angle 0.67202 / 0.35 (35006) hydrogen bonds : bond 0.17112 / 11.70 ( 1261) hydrogen bonds : angle 6.60769 / 4.64 ( 3237) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 251 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8973 (mtp) cc_final: 0.8593 (pmt) REVERT: A 120 THR cc_start: 0.8310 (m) cc_final: 0.8054 (p) REVERT: A 305 MET cc_start: 0.9061 (mmm) cc_final: 0.8846 (mmt) REVERT: A 349 LEU cc_start: 0.9136 (mt) cc_final: 0.8746 (mt) REVERT: B 44 MET cc_start: 0.8797 (mtp) cc_final: 0.8588 (pmt) REVERT: B 82 MET cc_start: 0.8936 (tpt) cc_final: 0.7541 (tpt) REVERT: B 86 TRP cc_start: 0.9004 (m-10) cc_final: 0.8203 (m-90) REVERT: B 328 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7614 (mptt) REVERT: B 355 MET cc_start: 0.8509 (mtt) cc_final: 0.8104 (mtm) REVERT: C 269 MET cc_start: 0.9038 (mtp) cc_final: 0.8829 (mtp) REVERT: C 338 SER cc_start: 0.9201 (OUTLIER) cc_final: 0.8941 (p) REVERT: D 227 MET cc_start: 0.8570 (mmm) cc_final: 0.8226 (mmm) REVERT: D 314 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8637 (tm-30) REVERT: E 227 MET cc_start: 0.8421 (mmm) cc_final: 0.8091 (mmm) REVERT: E 229 THR cc_start: 0.9156 (m) cc_final: 0.8923 (p) REVERT: E 276 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8402 (mt-10) REVERT: F 132 MET cc_start: 0.8110 (ppp) cc_final: 0.7759 (ppp) REVERT: G 82 MET cc_start: 0.9006 (tpt) cc_final: 0.8632 (tpp) REVERT: G 297 ASN cc_start: 0.9186 (m110) cc_final: 0.8975 (m-40) REVERT: G 355 MET cc_start: 0.9182 (mtt) cc_final: 0.8855 (mtp) REVERT: G 372 ARG cc_start: 0.8896 (mtm-85) cc_final: 0.8447 (mpp80) REVERT: H 176 MET cc_start: 0.7811 (mmt) cc_final: 0.7151 (mpt) REVERT: H 227 MET cc_start: 0.9267 (mmm) cc_final: 0.8947 (mmm) REVERT: H 305 MET cc_start: 0.9045 (mmm) cc_final: 0.8733 (tpp) REVERT: H 355 MET cc_start: 0.9311 (mtt) cc_final: 0.9006 (mpm) REVERT: H 356 TRP cc_start: 0.8368 (m100) cc_final: 0.7719 (m100) REVERT: I 195 ASN cc_start: 0.8931 (m-40) cc_final: 0.7913 (t0) REVERT: I 245 GLN cc_start: 0.9362 (tm-30) cc_final: 0.9120 (tm-30) REVERT: I 322 GLN cc_start: 0.8797 (mp10) cc_final: 0.8369 (mp10) outliers start: 69 outliers final: 12 residues processed: 309 average time/residue: 0.6923 time to fit residues: 242.8122 Evaluate side-chains 198 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 253 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN A 275 HIS B 92 ASN B 246 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 275 HIS D 92 ASN D 246 GLN D 275 HIS E 246 GLN E 275 HIS F 92 ASN F 128 ASN F 275 HIS F 314 GLN G 92 ASN G 275 HIS H 92 ASN H 275 HIS I 155 ASN I 215 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.081140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.061877 restraints weight = 70892.103| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.95 r_work: 0.3025 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25802 Z= 0.159 Angle : 0.598 8.498 35006 Z= 0.299 Chirality : 0.044 0.134 3877 Planarity : 0.004 0.043 4488 Dihedral : 6.932 91.542 3611 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.41 % Allowed : 11.59 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 3160 helix: 0.87 (0.15), residues: 1245 sheet: 0.27 (0.20), residues: 632 loop : 0.79 (0.19), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 95 TYR 0.009 0.001 TYR G 294 PHE 0.012 0.001 PHE D 31 TRP 0.014 0.001 TRP D 79 HIS 0.007 0.001 HIS A 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (25802) covalent geometry : angle 0.59783 / 0.30 (35006) hydrogen bonds : bond 0.04105 / 2.81 ( 1261) hydrogen bonds : angle 5.04988 / 3.55 ( 3237) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9338 (tpt) cc_final: 0.8576 (tpp) REVERT: A 86 TRP cc_start: 0.9290 (m-10) cc_final: 0.8775 (m-90) REVERT: A 123 MET cc_start: 0.9059 (tpp) cc_final: 0.8595 (tpp) REVERT: A 305 MET cc_start: 0.9020 (mmm) cc_final: 0.8730 (mmt) REVERT: A 355 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7715 (mmm) REVERT: B 44 MET cc_start: 0.8804 (mtp) cc_final: 0.8565 (pmt) REVERT: B 82 MET cc_start: 0.9006 (tpt) cc_final: 0.8285 (tpp) REVERT: B 86 TRP cc_start: 0.8930 (m-10) cc_final: 0.8188 (m-90) REVERT: B 123 MET cc_start: 0.9015 (tpp) cc_final: 0.8780 (tpp) REVERT: B 286 ASP cc_start: 0.8584 (m-30) cc_final: 0.8375 (m-30) REVERT: B 305 MET cc_start: 0.8853 (mmm) cc_final: 0.8595 (mmt) REVERT: B 328 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7792 (mptt) REVERT: D 104 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8174 (tt) REVERT: D 227 MET cc_start: 0.8595 (mmm) cc_final: 0.8135 (mmm) REVERT: D 314 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8680 (tm-30) REVERT: E 227 MET cc_start: 0.8291 (mmm) cc_final: 0.8012 (mmm) REVERT: E 229 THR cc_start: 0.9120 (m) cc_final: 0.8899 (p) REVERT: E 276 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8489 (mt-10) REVERT: F 132 MET cc_start: 0.8305 (ppp) cc_final: 0.7985 (ppp) REVERT: G 355 MET cc_start: 0.9222 (mtt) cc_final: 0.8919 (mtp) REVERT: G 372 ARG cc_start: 0.8916 (mtm-85) cc_final: 0.8451 (mpp80) REVERT: H 47 MET cc_start: 0.7472 (tpp) cc_final: 0.7251 (tpp) REVERT: H 176 MET cc_start: 0.7778 (mmt) cc_final: 0.6900 (mpt) REVERT: H 227 MET cc_start: 0.9157 (mmm) cc_final: 0.8822 (mmm) REVERT: H 305 MET cc_start: 0.9030 (mmm) cc_final: 0.8786 (tpp) REVERT: H 355 MET cc_start: 0.9246 (mtt) cc_final: 0.8982 (mpm) REVERT: H 356 TRP cc_start: 0.8030 (m100) cc_final: 0.7180 (m100) REVERT: I 195 ASN cc_start: 0.8939 (m-40) cc_final: 0.7930 (t0) REVERT: I 322 GLN cc_start: 0.8733 (mp10) cc_final: 0.8288 (mp10) REVERT: I 349 GLN cc_start: 0.7061 (mp10) cc_final: 0.6443 (mp10) outliers start: 38 outliers final: 9 residues processed: 220 average time/residue: 0.6497 time to fit residues: 164.4539 Evaluate side-chains 179 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 371 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 155 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 304 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 195 optimal weight: 0.0570 chunk 208 optimal weight: 4.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS G 128 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.078292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058830 restraints weight = 71755.433| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.94 r_work: 0.2955 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25802 Z= 0.222 Angle : 0.620 8.779 35006 Z= 0.311 Chirality : 0.045 0.173 3877 Planarity : 0.004 0.043 4488 Dihedral : 6.750 95.820 3599 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.85 % Allowed : 12.07 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 0.84 (0.15), residues: 3160 helix: 0.85 (0.15), residues: 1280 sheet: 0.35 (0.20), residues: 615 loop : 0.60 (0.19), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 290 TYR 0.011 0.001 TYR D 69 PHE 0.024 0.002 PHE H 124 TRP 0.015 0.002 TRP D 79 HIS 0.005 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (25802) covalent geometry : angle 0.62010 / 0.31 (35006) hydrogen bonds : bond 0.04368 / 2.99 ( 1261) hydrogen bonds : angle 4.92170 / 3.48 ( 3237) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8211 (tpp) cc_final: 0.7960 (tpp) REVERT: A 82 MET cc_start: 0.9343 (tpt) cc_final: 0.8547 (tpp) REVERT: A 86 TRP cc_start: 0.9263 (m-10) cc_final: 0.8645 (m-90) REVERT: A 123 MET cc_start: 0.9102 (tpp) cc_final: 0.8451 (tpp) REVERT: A 227 MET cc_start: 0.8705 (tpt) cc_final: 0.8362 (tmm) REVERT: A 260 THR cc_start: 0.9635 (OUTLIER) cc_final: 0.9423 (p) REVERT: A 305 MET cc_start: 0.8975 (mmm) cc_final: 0.8726 (mmt) REVERT: B 44 MET cc_start: 0.8858 (mtp) cc_final: 0.8436 (pmt) REVERT: B 47 MET cc_start: 0.8912 (mmm) cc_final: 0.8702 (mmt) REVERT: B 286 ASP cc_start: 0.8700 (m-30) cc_final: 0.8438 (m-30) REVERT: B 313 MET cc_start: 0.9044 (tpp) cc_final: 0.8645 (tpt) REVERT: B 328 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7563 (mptt) REVERT: B 355 MET cc_start: 0.8457 (mmm) cc_final: 0.7994 (mtm) REVERT: C 3 ASP cc_start: 0.3038 (OUTLIER) cc_final: 0.2712 (p0) REVERT: C 44 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8481 (mtt) REVERT: C 176 MET cc_start: 0.9131 (mmm) cc_final: 0.8826 (mpt) REVERT: D 104 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8169 (tt) REVERT: D 227 MET cc_start: 0.8609 (mmm) cc_final: 0.8208 (mmm) REVERT: E 227 MET cc_start: 0.8353 (mmm) cc_final: 0.8074 (mmm) REVERT: E 229 THR cc_start: 0.9107 (m) cc_final: 0.8879 (p) REVERT: E 276 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8448 (mt-10) REVERT: E 372 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8350 (mtm-85) REVERT: F 132 MET cc_start: 0.8285 (ppp) cc_final: 0.7898 (ppp) REVERT: F 373 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8535 (tptm) REVERT: G 176 MET cc_start: 0.8494 (tpp) cc_final: 0.8258 (mmm) REVERT: G 355 MET cc_start: 0.9184 (mtt) cc_final: 0.8863 (mtp) REVERT: G 372 ARG cc_start: 0.9023 (mtm-85) cc_final: 0.8635 (mpp80) REVERT: H 123 MET cc_start: 0.9128 (mmm) cc_final: 0.8593 (mmm) REVERT: H 124 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.8325 (m-80) REVERT: H 176 MET cc_start: 0.7693 (mmt) cc_final: 0.6866 (mpt) REVERT: H 227 MET cc_start: 0.9109 (mmm) cc_final: 0.8778 (mmm) REVERT: H 305 MET cc_start: 0.9013 (mmm) cc_final: 0.8744 (tpp) REVERT: H 355 MET cc_start: 0.9337 (mtt) cc_final: 0.9060 (mpm) REVERT: I 195 ASN cc_start: 0.8919 (m-40) cc_final: 0.7897 (t0) outliers start: 50 outliers final: 16 residues processed: 205 average time/residue: 0.6142 time to fit residues: 145.2548 Evaluate side-chains 182 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 373 LYS Chi-restraints excluded: chain H residue 124 PHE Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 313 MET Chi-restraints excluded: chain I residue 371 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 161 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 299 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 0.0370 chunk 160 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 HIS B 275 HIS C 12 ASN E 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.078219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.058877 restraints weight = 71114.607| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.91 r_work: 0.2962 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25802 Z= 0.189 Angle : 0.594 9.486 35006 Z= 0.294 Chirality : 0.045 0.147 3877 Planarity : 0.004 0.042 4488 Dihedral : 6.564 92.938 3595 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.78 % Allowed : 12.88 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 1.08 (0.15), residues: 3160 helix: 1.34 (0.16), residues: 1196 sheet: 0.32 (0.20), residues: 608 loop : 0.53 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 372 TYR 0.011 0.001 TYR D 69 PHE 0.013 0.001 PHE D 31 TRP 0.015 0.002 TRP D 79 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (25802) covalent geometry : angle 0.59356 / 0.29 (35006) hydrogen bonds : bond 0.03904 / 2.68 ( 1261) hydrogen bonds : angle 4.77396 / 3.38 ( 3237) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9308 (tpt) cc_final: 0.8484 (tpp) REVERT: A 86 TRP cc_start: 0.9226 (m-10) cc_final: 0.8598 (m-90) REVERT: A 123 MET cc_start: 0.9003 (tpp) cc_final: 0.8560 (tpp) REVERT: A 305 MET cc_start: 0.8970 (mmm) cc_final: 0.8704 (mmt) REVERT: B 44 MET cc_start: 0.8802 (mtp) cc_final: 0.8363 (pmt) REVERT: B 286 ASP cc_start: 0.8686 (m-30) cc_final: 0.8422 (m-30) REVERT: B 305 MET cc_start: 0.8869 (mmm) cc_final: 0.8626 (mmt) REVERT: C 64 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9186 (pp) REVERT: C 227 MET cc_start: 0.8416 (mmm) cc_final: 0.8024 (mmp) REVERT: C 355 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8553 (mtm) REVERT: D 104 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8148 (tt) REVERT: D 132 MET cc_start: 0.8339 (ttt) cc_final: 0.7939 (ttm) REVERT: D 227 MET cc_start: 0.8589 (mmm) cc_final: 0.8105 (mmm) REVERT: D 314 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8605 (tm-30) REVERT: E 227 MET cc_start: 0.8311 (mmm) cc_final: 0.8002 (mmm) REVERT: E 229 THR cc_start: 0.9097 (m) cc_final: 0.8870 (p) REVERT: E 276 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8465 (mt-10) REVERT: E 286 ASP cc_start: 0.8473 (t0) cc_final: 0.8181 (t0) REVERT: E 372 ARG cc_start: 0.8738 (mtm-85) cc_final: 0.8342 (mtm-85) REVERT: F 132 MET cc_start: 0.8297 (ppp) cc_final: 0.7911 (ppp) REVERT: F 373 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8512 (tptm) REVERT: G 372 ARG cc_start: 0.9021 (mtm-85) cc_final: 0.8452 (mpp80) REVERT: H 176 MET cc_start: 0.7715 (mmt) cc_final: 0.6847 (mpt) REVERT: H 227 MET cc_start: 0.9132 (mmm) cc_final: 0.8827 (mmm) REVERT: H 276 GLU cc_start: 0.9510 (mt-10) cc_final: 0.9168 (mm-30) REVERT: H 305 MET cc_start: 0.9016 (mmm) cc_final: 0.8709 (tpp) REVERT: H 355 MET cc_start: 0.9309 (mtt) cc_final: 0.9040 (mpm) REVERT: I 195 ASN cc_start: 0.8900 (m-40) cc_final: 0.7907 (t0) outliers start: 48 outliers final: 23 residues processed: 198 average time/residue: 0.6611 time to fit residues: 151.0937 Evaluate side-chains 188 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 328 LYS Chi-restraints excluded: chain F residue 373 LYS Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 313 MET Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 371 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 262 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 162 ASN H 128 ASN H 173 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059220 restraints weight = 70891.794| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.91 r_work: 0.2968 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25802 Z= 0.161 Angle : 0.583 9.849 35006 Z= 0.285 Chirality : 0.044 0.176 3877 Planarity : 0.004 0.040 4488 Dihedral : 6.377 90.786 3591 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.89 % Allowed : 13.18 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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 (0.15), residues: 3160 helix: 1.47 (0.16), residues: 1196 sheet: 0.35 (0.20), residues: 610 loop : 0.55 (0.18), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 372 TYR 0.011 0.001 TYR D 69 PHE 0.011 0.001 PHE D 31 TRP 0.015 0.001 TRP D 79 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (25802) covalent geometry : angle 0.58339 / 0.28 (35006) hydrogen bonds : bond 0.03621 / 2.48 ( 1261) hydrogen bonds : angle 4.65869 / 3.30 ( 3237) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9257 (tpt) cc_final: 0.8421 (tpp) REVERT: A 86 TRP cc_start: 0.9202 (m-10) cc_final: 0.8580 (m-90) REVERT: A 123 MET cc_start: 0.8966 (tpp) cc_final: 0.8579 (tpp) REVERT: A 305 MET cc_start: 0.8961 (mmm) cc_final: 0.8672 (mmt) REVERT: B 44 MET cc_start: 0.8784 (mtp) cc_final: 0.8334 (pmt) REVERT: B 286 ASP cc_start: 0.8660 (m-30) cc_final: 0.8390 (m-30) REVERT: B 305 MET cc_start: 0.8827 (mmm) cc_final: 0.8590 (mmt) REVERT: B 328 LYS cc_start: 0.8236 (mmmt) cc_final: 0.7870 (mttp) REVERT: B 355 MET cc_start: 0.8410 (mmm) cc_final: 0.7955 (mtm) REVERT: C 3 ASP cc_start: 0.2817 (OUTLIER) cc_final: 0.2562 (p0) REVERT: C 64 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9161 (pp) REVERT: C 227 MET cc_start: 0.8381 (mmm) cc_final: 0.8012 (mmp) REVERT: C 355 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8662 (mtm) REVERT: D 86 TRP cc_start: 0.8442 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: D 104 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8128 (tt) REVERT: D 132 MET cc_start: 0.8330 (ttt) cc_final: 0.7926 (ttm) REVERT: D 227 MET cc_start: 0.8600 (mmm) cc_final: 0.8150 (mmm) REVERT: D 314 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8621 (tm-30) REVERT: D 373 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8009 (tppp) REVERT: E 227 MET cc_start: 0.8294 (mmm) cc_final: 0.7954 (mmm) REVERT: E 229 THR cc_start: 0.9086 (m) cc_final: 0.8859 (p) REVERT: E 276 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8464 (mt-10) REVERT: E 286 ASP cc_start: 0.8507 (t0) cc_final: 0.7826 (m-30) REVERT: E 372 ARG cc_start: 0.8765 (mtm-85) cc_final: 0.8378 (mtm-85) REVERT: F 132 MET cc_start: 0.8300 (ppp) cc_final: 0.7913 (ppp) REVERT: F 373 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8515 (tptm) REVERT: G 176 MET cc_start: 0.8485 (tpp) cc_final: 0.8245 (mmm) REVERT: G 372 ARG cc_start: 0.9028 (mtm-85) cc_final: 0.8462 (mpp80) REVERT: H 176 MET cc_start: 0.7621 (mmt) cc_final: 0.6894 (mpt) REVERT: H 227 MET cc_start: 0.9158 (mmm) cc_final: 0.8854 (mmm) REVERT: H 276 GLU cc_start: 0.9514 (mt-10) cc_final: 0.9171 (mm-30) REVERT: H 305 MET cc_start: 0.9011 (mmm) cc_final: 0.8704 (tpp) REVERT: H 355 MET cc_start: 0.9321 (mtt) cc_final: 0.9003 (mpm) REVERT: I 195 ASN cc_start: 0.8895 (m-40) cc_final: 0.7913 (t0) outliers start: 51 outliers final: 24 residues processed: 210 average time/residue: 0.6559 time to fit residues: 158.6168 Evaluate side-chains 191 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 159 VAL 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 5 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 360 GLN Chi-restraints excluded: chain F residue 373 LYS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 313 MET Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 371 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 112 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 253 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 302 optimal weight: 0.1980 chunk 144 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 268 optimal weight: 0.0570 overall best weight: 2.2504 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.077858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058721 restraints weight = 71064.439| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.95 r_work: 0.2951 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25802 Z= 0.181 Angle : 0.592 10.415 35006 Z= 0.291 Chirality : 0.044 0.168 3877 Planarity : 0.004 0.040 4488 Dihedral : 6.361 91.493 3591 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.85 % Allowed : 13.59 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 1.17 (0.15), residues: 3160 helix: 1.48 (0.16), residues: 1196 sheet: 0.33 (0.20), residues: 610 loop : 0.52 (0.18), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 147 TYR 0.012 0.001 TYR D 69 PHE 0.015 0.001 PHE H 127 TRP 0.014 0.001 TRP D 79 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (25802) covalent geometry : angle 0.59235 / 0.29 (35006) hydrogen bonds : bond 0.03754 / 2.57 ( 1261) hydrogen bonds : angle 4.67319 / 3.31 ( 3237) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9325 (tpt) cc_final: 0.8493 (tpp) REVERT: A 86 TRP cc_start: 0.9203 (m-10) cc_final: 0.8567 (m-90) REVERT: A 123 MET cc_start: 0.8995 (tpp) cc_final: 0.8594 (tpp) REVERT: A 305 MET cc_start: 0.9061 (mmm) cc_final: 0.8751 (mmt) REVERT: B 44 MET cc_start: 0.8804 (mtp) cc_final: 0.7955 (pmt) REVERT: B 47 MET cc_start: 0.9139 (mmm) cc_final: 0.8606 (mpt) REVERT: B 286 ASP cc_start: 0.8666 (m-30) cc_final: 0.8412 (m-30) REVERT: B 305 MET cc_start: 0.8846 (mmm) cc_final: 0.8601 (mmt) REVERT: B 313 MET cc_start: 0.8898 (tpp) cc_final: 0.8594 (tpt) REVERT: B 328 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7948 (mttp) REVERT: C 64 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9164 (pp) REVERT: C 355 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8549 (mtm) REVERT: D 86 TRP cc_start: 0.8491 (OUTLIER) cc_final: 0.8124 (m-10) REVERT: D 104 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8093 (tt) REVERT: D 227 MET cc_start: 0.8572 (mmm) cc_final: 0.8111 (mmm) REVERT: D 314 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8656 (tm-30) REVERT: D 373 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8020 (tppp) REVERT: E 227 MET cc_start: 0.8322 (mmm) cc_final: 0.7981 (mmm) REVERT: E 229 THR cc_start: 0.9094 (m) cc_final: 0.8865 (p) REVERT: E 276 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8479 (mt-10) REVERT: E 286 ASP cc_start: 0.8544 (t0) cc_final: 0.7792 (m-30) REVERT: E 372 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8259 (mtm-85) REVERT: F 44 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8028 (mtm) REVERT: F 132 MET cc_start: 0.8284 (ppp) cc_final: 0.7901 (ppp) REVERT: F 373 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8505 (tptm) REVERT: G 372 ARG cc_start: 0.9021 (mtm-85) cc_final: 0.8474 (mpp80) REVERT: H 123 MET cc_start: 0.9340 (tpt) cc_final: 0.8964 (mmm) REVERT: H 176 MET cc_start: 0.7661 (mmt) cc_final: 0.6860 (mpt) REVERT: H 227 MET cc_start: 0.9163 (mmm) cc_final: 0.8864 (mmm) REVERT: H 305 MET cc_start: 0.9038 (mmm) cc_final: 0.8741 (tpp) REVERT: H 355 MET cc_start: 0.9310 (mtt) cc_final: 0.8989 (mpm) REVERT: I 195 ASN cc_start: 0.8871 (m-40) cc_final: 0.7861 (t0) outliers start: 50 outliers final: 25 residues processed: 201 average time/residue: 0.6749 time to fit residues: 157.0275 Evaluate side-chains 191 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 159 VAL 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 5 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 360 GLN Chi-restraints excluded: chain F residue 373 LYS Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 313 MET Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 371 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 255 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 300 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058168 restraints weight = 70823.677| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.94 r_work: 0.2939 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 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 = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25802 Z= 0.204 Angle : 0.609 11.433 35006 Z= 0.299 Chirality : 0.045 0.177 3877 Planarity : 0.004 0.040 4488 Dihedral : 6.415 92.711 3591 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.07 % Allowed : 13.74 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 1.11 (0.15), residues: 3160 helix: 1.45 (0.16), residues: 1197 sheet: 0.30 (0.20), residues: 608 loop : 0.46 (0.18), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 147 TYR 0.013 0.001 TYR D 69 PHE 0.012 0.001 PHE D 31 TRP 0.015 0.002 TRP D 79 HIS 0.005 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (25802) covalent geometry : angle 0.60878 / 0.30 (35006) hydrogen bonds : bond 0.03939 / 2.70 ( 1261) hydrogen bonds : angle 4.71005 / 3.34 ( 3237) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9321 (tpt) cc_final: 0.8434 (tpp) REVERT: A 86 TRP cc_start: 0.9197 (m-10) cc_final: 0.8588 (m-90) REVERT: A 123 MET cc_start: 0.9038 (tpp) cc_final: 0.8672 (tpp) REVERT: A 305 MET cc_start: 0.9068 (mmm) cc_final: 0.8773 (mmt) REVERT: A 314 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8605 (tm-30) REVERT: A 355 MET cc_start: 0.8788 (mtp) cc_final: 0.7832 (tpt) REVERT: B 44 MET cc_start: 0.8819 (mtp) cc_final: 0.8364 (pmt) REVERT: B 286 ASP cc_start: 0.8665 (m-30) cc_final: 0.8418 (m-30) REVERT: B 305 MET cc_start: 0.8859 (mmm) cc_final: 0.8610 (mmt) REVERT: B 313 MET cc_start: 0.8973 (tpp) cc_final: 0.8592 (tpt) REVERT: B 328 LYS cc_start: 0.8277 (mmmt) cc_final: 0.8004 (mttp) REVERT: C 355 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8540 (mtm) REVERT: D 86 TRP cc_start: 0.8480 (OUTLIER) cc_final: 0.8108 (m-10) REVERT: D 104 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8104 (tt) REVERT: D 122 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7419 (mp) REVERT: D 227 MET cc_start: 0.8586 (mmm) cc_final: 0.8193 (mmm) REVERT: D 314 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8669 (tm-30) REVERT: D 373 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8034 (tppp) REVERT: E 176 MET cc_start: 0.8904 (mmt) cc_final: 0.8680 (mmt) REVERT: E 227 MET cc_start: 0.8297 (mmm) cc_final: 0.7996 (mmm) REVERT: E 229 THR cc_start: 0.9096 (m) cc_final: 0.8867 (p) REVERT: E 276 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8474 (mt-10) REVERT: E 286 ASP cc_start: 0.8581 (t0) cc_final: 0.7851 (m-30) REVERT: E 372 ARG cc_start: 0.8707 (mtm-85) cc_final: 0.8270 (mtm-85) REVERT: F 44 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8118 (mtm) REVERT: F 132 MET cc_start: 0.8280 (ppp) cc_final: 0.7959 (ppp) REVERT: F 373 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8503 (tptm) REVERT: H 176 MET cc_start: 0.7664 (mmt) cc_final: 0.6875 (mpt) REVERT: H 227 MET cc_start: 0.9141 (mmm) cc_final: 0.8835 (mmm) REVERT: H 305 MET cc_start: 0.9044 (mmm) cc_final: 0.8741 (tpp) REVERT: H 355 MET cc_start: 0.9296 (mtt) cc_final: 0.9018 (mpm) REVERT: I 195 ASN cc_start: 0.8885 (m-40) cc_final: 0.7887 (t0) REVERT: I 342 MET cc_start: 0.8379 (mpt) cc_final: 0.8154 (mpp) outliers start: 56 outliers final: 28 residues processed: 203 average time/residue: 0.6555 time to fit residues: 154.2371 Evaluate side-chains 195 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 159 VAL 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 5 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 360 GLN Chi-restraints excluded: chain F residue 373 LYS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 313 MET Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 371 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 281 optimal weight: 9.9990 chunk 123 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 250 optimal weight: 0.9990 chunk 271 optimal weight: 10.0000 chunk 289 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.077332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.058207 restraints weight = 70932.090| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.94 r_work: 0.2943 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 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 = 0.2949 r_free = 0.2949 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: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25802 Z= 0.197 Angle : 0.612 11.896 35006 Z= 0.298 Chirality : 0.045 0.189 3877 Planarity : 0.004 0.040 4488 Dihedral : 6.396 92.154 3591 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.00 % Allowed : 14.07 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 1.13 (0.15), residues: 3160 helix: 1.52 (0.16), residues: 1190 sheet: 0.18 (0.20), residues: 617 loop : 0.50 (0.18), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 147 TYR 0.013 0.001 TYR D 69 PHE 0.012 0.001 PHE H 255 TRP 0.015 0.002 TRP D 79 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (25802) covalent geometry : angle 0.61221 / 0.30 (35006) hydrogen bonds : bond 0.03856 / 2.64 ( 1261) hydrogen bonds : angle 4.69887 / 3.33 ( 3237) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 161 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7213 (tmm) cc_final: 0.6995 (tmm) REVERT: A 82 MET cc_start: 0.9315 (tpt) cc_final: 0.8397 (tpp) REVERT: A 86 TRP cc_start: 0.9184 (m-10) cc_final: 0.8609 (m-90) REVERT: A 123 MET cc_start: 0.9031 (tpp) cc_final: 0.8684 (tpp) REVERT: A 305 MET cc_start: 0.9076 (mmm) cc_final: 0.8745 (mmt) REVERT: B 44 MET cc_start: 0.8848 (mtp) cc_final: 0.8366 (pmt) REVERT: B 286 ASP cc_start: 0.8675 (m-30) cc_final: 0.8429 (m-30) REVERT: B 305 MET cc_start: 0.8856 (mmm) cc_final: 0.8606 (mmt) REVERT: B 313 MET cc_start: 0.8931 (tpp) cc_final: 0.8589 (tpt) REVERT: B 355 MET cc_start: 0.8301 (mmm) cc_final: 0.7751 (mtm) REVERT: C 227 MET cc_start: 0.8414 (mmm) cc_final: 0.8058 (mmp) REVERT: C 355 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8586 (mtm) REVERT: D 86 TRP cc_start: 0.8448 (OUTLIER) cc_final: 0.8024 (m-10) REVERT: D 104 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8112 (tt) REVERT: D 227 MET cc_start: 0.8582 (mmm) cc_final: 0.8186 (mmm) REVERT: D 314 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8678 (tm-30) REVERT: D 373 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8018 (tppp) REVERT: E 176 MET cc_start: 0.8901 (mmt) cc_final: 0.8658 (mmt) REVERT: E 227 MET cc_start: 0.8297 (mmm) cc_final: 0.7997 (mmm) REVERT: E 229 THR cc_start: 0.9099 (m) cc_final: 0.8870 (p) REVERT: E 276 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8469 (mt-10) REVERT: E 286 ASP cc_start: 0.8536 (t0) cc_final: 0.7781 (m-30) REVERT: E 372 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8261 (mtm-85) REVERT: F 44 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8291 (mtm) REVERT: F 132 MET cc_start: 0.8275 (ppp) cc_final: 0.7956 (ppp) REVERT: F 373 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8511 (tptm) REVERT: H 176 MET cc_start: 0.7677 (mmt) cc_final: 0.6883 (mpt) REVERT: H 227 MET cc_start: 0.9154 (mmm) cc_final: 0.8848 (mmm) REVERT: H 283 MET cc_start: 0.8965 (mmm) cc_final: 0.8754 (mmm) REVERT: H 305 MET cc_start: 0.9042 (mmm) cc_final: 0.8746 (tpp) REVERT: H 355 MET cc_start: 0.9324 (mtt) cc_final: 0.9037 (mpm) REVERT: I 195 ASN cc_start: 0.8897 (m-40) cc_final: 0.7872 (t0) REVERT: I 283 MET cc_start: 0.7572 (mmm) cc_final: 0.6017 (tmm) REVERT: I 342 MET cc_start: 0.8350 (mpt) cc_final: 0.8112 (mpp) outliers start: 54 outliers final: 32 residues processed: 204 average time/residue: 0.5789 time to fit residues: 136.7370 Evaluate side-chains 196 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 159 VAL 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 5 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 360 GLN Chi-restraints excluded: chain F residue 373 LYS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 313 MET Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 371 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 75 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 237 optimal weight: 7.9990 chunk 310 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.078026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058970 restraints weight = 70900.815| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.95 r_work: 0.2960 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 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 = 0.2966 r_free = 0.2966 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: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25802 Z= 0.146 Angle : 0.587 12.227 35006 Z= 0.283 Chirality : 0.044 0.168 3877 Planarity : 0.004 0.039 4488 Dihedral : 6.227 88.492 3591 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.67 % Allowed : 14.66 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 1.12 (0.15), residues: 3160 helix: 1.45 (0.16), residues: 1232 sheet: 0.19 (0.21), residues: 606 loop : 0.52 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 147 TYR 0.011 0.001 TYR D 69 PHE 0.010 0.001 PHE H 255 TRP 0.015 0.001 TRP D 79 HIS 0.004 0.001 HIS F 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (25802) covalent geometry : angle 0.58731 / 0.28 (35006) hydrogen bonds : bond 0.03449 / 2.37 ( 1261) hydrogen bonds : angle 4.59439 / 3.25 ( 3237) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9305 (tpt) cc_final: 0.8408 (tpp) REVERT: A 86 TRP cc_start: 0.9171 (m-10) cc_final: 0.8561 (m-90) REVERT: A 123 MET cc_start: 0.9016 (tpp) cc_final: 0.8695 (tpp) REVERT: A 305 MET cc_start: 0.9050 (mmm) cc_final: 0.8712 (mmt) REVERT: A 314 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: A 355 MET cc_start: 0.8833 (mtp) cc_final: 0.7744 (tpt) REVERT: B 44 MET cc_start: 0.8881 (mtp) cc_final: 0.8075 (pmt) REVERT: B 47 MET cc_start: 0.9186 (mmm) cc_final: 0.8651 (mpt) REVERT: B 286 ASP cc_start: 0.8597 (m-30) cc_final: 0.8360 (m-30) REVERT: B 305 MET cc_start: 0.8825 (mmm) cc_final: 0.8584 (mmt) REVERT: B 313 MET cc_start: 0.8906 (tpp) cc_final: 0.8559 (tpt) REVERT: B 355 MET cc_start: 0.8251 (mmm) cc_final: 0.7785 (mmm) REVERT: C 44 MET cc_start: 0.8734 (mtp) cc_final: 0.7919 (mtt) REVERT: C 227 MET cc_start: 0.8407 (mmm) cc_final: 0.8050 (mmp) REVERT: D 86 TRP cc_start: 0.8450 (OUTLIER) cc_final: 0.8081 (m-10) REVERT: D 104 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8118 (tt) REVERT: D 227 MET cc_start: 0.8577 (mmm) cc_final: 0.8122 (mmm) REVERT: D 314 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8655 (tm-30) REVERT: D 373 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8009 (tppp) REVERT: E 176 MET cc_start: 0.8875 (mmt) cc_final: 0.8612 (mmt) REVERT: E 227 MET cc_start: 0.8281 (mmm) cc_final: 0.7955 (mmm) REVERT: E 229 THR cc_start: 0.9089 (m) cc_final: 0.8855 (p) REVERT: E 276 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8453 (mt-10) REVERT: E 286 ASP cc_start: 0.8514 (t0) cc_final: 0.7753 (m-30) REVERT: E 372 ARG cc_start: 0.8721 (mtm-85) cc_final: 0.8272 (mtm-85) REVERT: F 44 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8291 (mtm) REVERT: F 132 MET cc_start: 0.8280 (ppp) cc_final: 0.7903 (ppp) REVERT: F 373 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8501 (tptm) REVERT: G 44 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8641 (mtm) REVERT: H 123 MET cc_start: 0.9158 (tpp) cc_final: 0.8892 (mmm) REVERT: H 176 MET cc_start: 0.7650 (mmt) cc_final: 0.6871 (mpt) REVERT: H 227 MET cc_start: 0.9158 (mmm) cc_final: 0.8854 (mmm) REVERT: H 305 MET cc_start: 0.9048 (mmm) cc_final: 0.8767 (tpp) REVERT: H 355 MET cc_start: 0.9333 (mtt) cc_final: 0.9043 (mpm) REVERT: I 283 MET cc_start: 0.7484 (mmm) cc_final: 0.6123 (tmm) REVERT: I 342 MET cc_start: 0.8331 (mpt) cc_final: 0.8101 (mpp) outliers start: 45 outliers final: 27 residues processed: 197 average time/residue: 0.6554 time to fit residues: 149.3523 Evaluate side-chains 192 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 159 VAL 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 86 TRP Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 360 GLN Chi-restraints excluded: chain F residue 373 LYS Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 313 MET Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 371 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 64 optimal weight: 3.9990 chunk 224 optimal weight: 0.3980 chunk 40 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 266 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 246 optimal weight: 6.9990 chunk 14 optimal weight: 0.0970 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 12 ASN I 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.079290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060303 restraints weight = 70643.479| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.95 r_work: 0.2989 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25802 Z= 0.101 Angle : 0.562 12.673 35006 Z= 0.267 Chirality : 0.043 0.196 3877 Planarity : 0.003 0.038 4488 Dihedral : 5.890 78.746 3591 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.11 % Allowed : 15.18 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 1.32 (0.15), residues: 3160 helix: 1.61 (0.16), residues: 1232 sheet: 0.26 (0.21), residues: 606 loop : 0.65 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 147 TYR 0.009 0.001 TYR D 69 PHE 0.010 0.001 PHE F 31 TRP 0.015 0.001 TRP D 79 HIS 0.004 0.001 HIS F 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (25802) covalent geometry : angle 0.56201 / 0.27 (35006) hydrogen bonds : bond 0.02914 / 2.01 ( 1261) hydrogen bonds : angle 4.45358 / 3.15 ( 3237) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6320 Ramachandran restraints generated. 3160 Oldfield, 0 Emsley, 3160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9286 (tpt) cc_final: 0.8364 (tpp) REVERT: A 86 TRP cc_start: 0.9153 (m-10) cc_final: 0.8514 (m-90) REVERT: A 123 MET cc_start: 0.8984 (tpp) cc_final: 0.8669 (tpp) REVERT: A 305 MET cc_start: 0.8997 (mmm) cc_final: 0.8669 (mmt) REVERT: A 314 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8478 (tm-30) REVERT: A 355 MET cc_start: 0.8821 (mtp) cc_final: 0.7732 (tpt) REVERT: B 44 MET cc_start: 0.8888 (mtp) cc_final: 0.8080 (pmt) REVERT: B 47 MET cc_start: 0.9171 (mmm) cc_final: 0.8650 (mpt) REVERT: B 286 ASP cc_start: 0.8553 (m-30) cc_final: 0.8330 (m-30) REVERT: B 305 MET cc_start: 0.8823 (mmm) cc_final: 0.8571 (mmt) REVERT: B 313 MET cc_start: 0.8855 (tpp) cc_final: 0.8500 (tpt) REVERT: B 355 MET cc_start: 0.8322 (mmm) cc_final: 0.7878 (mmm) REVERT: C 44 MET cc_start: 0.8468 (mtp) cc_final: 0.8040 (mtt) REVERT: D 86 TRP cc_start: 0.8381 (OUTLIER) cc_final: 0.8047 (m-10) REVERT: D 227 MET cc_start: 0.8542 (mmm) cc_final: 0.8105 (mmm) REVERT: D 314 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8686 (tm-30) REVERT: E 227 MET cc_start: 0.8288 (mmm) cc_final: 0.7981 (mmm) REVERT: E 229 THR cc_start: 0.9076 (m) cc_final: 0.8845 (p) REVERT: E 276 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8440 (mt-10) REVERT: E 286 ASP cc_start: 0.8476 (t0) cc_final: 0.7715 (m-30) REVERT: E 372 ARG cc_start: 0.8714 (mtm-85) cc_final: 0.8249 (mtm-85) REVERT: F 44 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7885 (mtm) REVERT: F 132 MET cc_start: 0.8264 (ppp) cc_final: 0.7883 (ppp) REVERT: G 44 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8598 (mtm) REVERT: H 176 MET cc_start: 0.7645 (mmt) cc_final: 0.6860 (mpt) REVERT: H 227 MET cc_start: 0.9171 (mmm) cc_final: 0.8883 (mmm) REVERT: H 283 MET cc_start: 0.8877 (mmm) cc_final: 0.8641 (mmm) REVERT: H 305 MET cc_start: 0.9043 (mmm) cc_final: 0.8749 (tpp) REVERT: H 355 MET cc_start: 0.9332 (mtt) cc_final: 0.9027 (mpm) REVERT: I 195 ASN cc_start: 0.8868 (m-40) cc_final: 0.7902 (t0) REVERT: I 283 MET cc_start: 0.7435 (mmm) cc_final: 0.6248 (tmm) REVERT: I 342 MET cc_start: 0.8245 (mpt) cc_final: 0.8009 (mpp) outliers start: 30 outliers final: 19 residues processed: 191 average time/residue: 0.6427 time to fit residues: 141.8404 Evaluate side-chains 186 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 159 VAL 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 86 TRP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 157 VAL Chi-restraints excluded: chain I residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 307 optimal weight: 10.0000 chunk 195 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 242 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 297 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 60 optimal weight: 0.0670 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.078964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059913 restraints weight = 70779.888| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.96 r_work: 0.2983 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25802 Z= 0.118 Angle : 0.571 12.929 35006 Z= 0.272 Chirality : 0.043 0.199 3877 Planarity : 0.003 0.039 4488 Dihedral : 5.817 78.143 3590 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.04 % Allowed : 15.36 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: 1.33 (0.15), residues: 3160 helix: 1.63 (0.15), residues: 1232 sheet: 0.26 (0.21), residues: 606 loop : 0.65 (0.18), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 147 TYR 0.009 0.001 TYR D 69 PHE 0.010 0.001 PHE F 31 TRP 0.014 0.001 TRP D 79 HIS 0.004 0.001 HIS F 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (25802) covalent geometry : angle 0.57103 / 0.27 (35006) hydrogen bonds : bond 0.03077 / 2.12 ( 1261) hydrogen bonds : angle 4.44074 / 3.14 ( 3237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6917.32 seconds wall clock time: 118 minutes 54.72 seconds (7134.72 seconds total)