Starting phenix.real_space_refine on Sat Aug 8 11:49:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12bz_76301/08_2026/12bz_76301.cif Found real_map, /net/cci-nas-00/data/ceres_data/12bz_76301/08_2026/12bz_76301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/12bz_76301/08_2026/12bz_76301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12bz_76301/08_2026/12bz_76301.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/12bz_76301/08_2026/12bz_76301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12bz_76301/08_2026/12bz_76301.map" } resolution = 3.44 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= 0.009 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 4 9.91 5 P 16 5.49 5 Mg 8 5.21 5 S 180 5.16 5 C 17026 2.51 5 N 4601 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 27027 Number of models: 1 Model: "" Number of chains: 20 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: "J" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 214} 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} Chain: "J" 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: 6.26, per 1000 atoms: 0.23 Number of scatterers: 27027 At special positions: 0 Unit cell: (91.8, 138.24, 277.56, 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 4 19.99 S 180 16.00 P 16 15.00 Mg 8 11.99 O 5192 8.00 N 4601 7.00 C 17026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6334 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 52 sheets defined 49.8% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 93 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.851A 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: 3.590A 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 285 removed outlier: 3.731A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 305 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: 3.972A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.688A 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 251 through 256 Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.628A pdb=" N THR B 260 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.530A 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: 3.940A 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: 3.566A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.775A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.542A pdb=" N THR C 260 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.623A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 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: 3.792A 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 371 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.572A pdb=" N GLU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.606A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.751A 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 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 removed outlier: 3.554A pdb=" N THR D 260 " --> pdb=" O CYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.669A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 348 through 349 No H-bonds generated for 'chain 'D' and resid 348 through 349' Processing helix chain 'D' and resid 350 through 355 removed outlier: 4.083A 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 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.756A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.800A 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: 3.591A 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 296 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: 6.501A pdb=" N THR E 351 " --> pdb=" O SER E 348 " (cutoff:3.500A) removed outlier: 3.950A 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 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 93 removed outlier: 3.596A pdb=" N GLU F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.608A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.791A 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 251 through 256 Processing helix chain 'F' and resid 257 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 296 Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 321 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 347 Processing helix chain 'F' and resid 348 through 349 No H-bonds generated for 'chain 'F' and resid 348 through 349' Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.856A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 93 removed outlier: 3.563A pdb=" N GLU G 93 " --> pdb=" O THR G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.551A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.857A 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 251 through 256 Processing helix chain 'G' and resid 257 through 262 removed outlier: 3.513A pdb=" N THR G 260 " --> pdb=" O CYS G 257 " (cutoff:3.500A) 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 296 removed outlier: 3.754A pdb=" N ARG G 290 " --> pdb=" O ASP G 286 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS G 291 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 347 Processing helix chain 'G' and resid 348 through 349 No H-bonds generated for 'chain 'G' and resid 348 through 349' Processing helix chain 'G' and resid 350 through 355 removed outlier: 3.862A 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 Processing helix chain 'H' and resid 55 through 61 Processing helix chain 'H' and resid 78 through 93 removed outlier: 3.643A pdb=" N GLU H 93 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.835A 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 295 removed outlier: 3.561A pdb=" N ARG H 290 " --> pdb=" O ASP H 286 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 5.577A 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: 3.885A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 369 through 374 removed outlier: 3.597A pdb=" N CYS H 374 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 224 removed outlier: 3.541A 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: 3.860A pdb=" N ILE I 339 " --> pdb=" O ALA I 335 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR I 340 " --> pdb=" O SER I 336 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS I 341 " --> pdb=" O ASP I 337 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET I 342 " --> pdb=" O PHE I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 364 Processing helix chain 'J' and resid 206 through 224 removed outlier: 3.562A pdb=" N ARG J 210 " --> pdb=" O ASN J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 248 Processing helix chain 'J' and resid 261 through 269 Processing helix chain 'J' and resid 295 through 299 Processing helix chain 'J' and resid 324 through 342 removed outlier: 3.833A pdb=" N ILE J 339 " --> pdb=" O ALA J 335 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR J 340 " --> pdb=" O SER J 336 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS J 341 " --> pdb=" O ASP J 337 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET J 342 " --> pdb=" O PHE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 364 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.685A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.554A 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: 6.529A 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: 3.937A 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: 6.542A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.458A 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: 6.559A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.965A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.030A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.676A 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: 4.197A 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: 6.322A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.503A 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: 4.068A 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: 6.710A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.432A 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: 6.535A 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: 4.199A 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: 6.846A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 176 through 178 removed outlier: 6.485A 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: 3.932A 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: 4.350A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 5.259A 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: 6.467A 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: 4.300A pdb=" N THR H 106 " --> pdb=" O CYS H 10 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN H 12 " --> 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: 6.515A 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 Processing sheet with id=AF5, first strand: chain 'I' and resid 285 through 289 removed outlier: 6.756A pdb=" N LEU I 273 " --> pdb=" O VAL I 288 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE I 315 " --> pdb=" O SER I 351 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU I 353 " --> pdb=" O ILE I 315 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL I 317 " --> pdb=" O LEU I 353 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 172 through 175 removed outlier: 6.371A pdb=" N ILE J 197 " --> pdb=" O HIS J 232 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N SER J 234 " --> pdb=" O ILE J 197 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLN J 199 " --> pdb=" O SER J 234 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 285 through 289 removed outlier: 6.778A pdb=" N LEU J 273 " --> pdb=" O VAL J 288 " (cutoff:3.500A) 1391 hydrogen bonds defined for protein. 3456 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: 5.65 Time building geometry restraints manager: 2.93 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: 8847 1.34 - 1.46: 6217 1.46 - 1.58: 12205 1.58 - 1.70: 24 1.70 - 1.82: 314 Bond restraints: 27607 Sorted by residual: bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.47e+00 bond pdb=" C4 ADP G 401 " pdb=" C5 ADP G 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C4 ADP E 401 " pdb=" C5 ADP E 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.37e+00 ... (remaining 27602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 36273 1.36 - 2.72: 884 2.72 - 4.08: 186 4.08 - 5.43: 73 5.43 - 6.79: 25 Bond angle restraints: 37441 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 114.23 117.02 -2.79 8.80e-01 1.29e+00 1.01e+01 angle pdb=" CA ARG D 147 " pdb=" CB ARG D 147 " pdb=" CG ARG D 147 " ideal model delta sigma weight residual 114.10 107.82 6.28 2.00e+00 2.50e-01 9.86e+00 angle pdb=" C CYS E 374 " pdb=" N PHE E 375 " pdb=" CA PHE E 375 " ideal model delta sigma weight residual 121.70 126.70 -5.00 1.80e+00 3.09e-01 7.73e+00 angle pdb=" CA GLY I 167 " pdb=" C GLY I 167 " pdb=" O GLY I 167 " ideal model delta sigma weight residual 122.33 120.37 1.96 8.10e-01 1.52e+00 5.86e+00 angle pdb=" C VAL E 30 " pdb=" N PHE E 31 " pdb=" CA PHE E 31 " ideal model delta sigma weight residual 122.45 117.56 4.89 2.03e+00 2.43e-01 5.79e+00 ... (remaining 37436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 15674 17.88 - 35.76: 693 35.76 - 53.64: 182 53.64 - 71.51: 50 71.51 - 89.39: 22 Dihedral angle restraints: 16621 sinusoidal: 6735 harmonic: 9886 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 29.30 -89.30 1 2.00e+01 2.50e-03 2.37e+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 19.48 -79.48 1 2.00e+01 2.50e-03 1.96e+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 17.51 -77.51 1 2.00e+01 2.50e-03 1.88e+01 ... (remaining 16618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2121 0.027 - 0.054: 1197 0.054 - 0.081: 439 0.081 - 0.108: 269 0.108 - 0.135: 111 Chirality restraints: 4137 Sorted by residual: chirality pdb=" CA ILE A 165 " pdb=" N ILE A 165 " pdb=" C ILE A 165 " pdb=" CB ILE A 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE B 165 " pdb=" N ILE B 165 " pdb=" C ILE B 165 " pdb=" CB ILE B 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE H 165 " pdb=" N ILE H 165 " pdb=" C ILE H 165 " pdb=" CB ILE H 165 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 4134 not shown) Planarity restraints: 4811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 207 " 0.209 9.50e-02 1.11e+02 9.39e-02 5.50e+00 pdb=" NE ARG J 207 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG J 207 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG J 207 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG J 207 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU G 242 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO G 243 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO G 243 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 243 " -0.027 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 4.82e-02 3.72e+00 pdb=" N PRO H 243 " -0.083 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 4808 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 36 2.57 - 3.15: 21197 3.15 - 3.74: 41760 3.74 - 4.32: 59526 4.32 - 4.90: 99303 Nonbonded interactions: 221822 Sorted by model distance: nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.990 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.995 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 1.995 2.170 nonbonded pdb=" O1B ADP H 401 " pdb="MG MG H 402 " model vdw 2.003 2.170 nonbonded pdb=" O1B ADP G 401 " pdb="MG MG G 402 " model vdw 2.013 2.170 ... (remaining 221817 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' } ncs_group { reference = (chain 'I' and (resid 147 through 372 or resid 401 through 402)) selection = chain 'J' } 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.290 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.003 0.038 27607 Z= 0.157 Angle : 0.591 6.792 37441 Z= 0.308 Chirality : 0.045 0.135 4137 Planarity : 0.005 0.094 4811 Dihedral : 12.114 89.392 10287 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.25 % Allowed : 5.33 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.55 (0.15), residues: 3384 helix: 0.31 (0.14), residues: 1307 sheet: 0.28 (0.19), residues: 668 loop : 0.73 (0.18), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 147 TYR 0.009 0.001 TYR D 169 PHE 0.022 0.001 PHE E 375 TRP 0.011 0.002 TRP D 79 HIS 0.003 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (27607) covalent geometry : angle 0.59091 / 0.31 (37441) hydrogen bonds : bond 0.16806 / 11.28 ( 1363) hydrogen bonds : angle 6.90777 / 4.89 ( 3456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 471 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.1709 (tmt) cc_final: 0.1342 (tmt) REVERT: A 123 MET cc_start: 0.9058 (mmt) cc_final: 0.8760 (tpp) REVERT: A 129 VAL cc_start: 0.8765 (m) cc_final: 0.8236 (p) REVERT: A 217 CYS cc_start: 0.7778 (m) cc_final: 0.7415 (m) REVERT: A 269 MET cc_start: 0.8572 (mtp) cc_final: 0.8277 (mtp) REVERT: A 282 ILE cc_start: 0.9267 (mt) cc_final: 0.9029 (mt) REVERT: A 305 MET cc_start: 0.9045 (mmm) cc_final: 0.8763 (mmt) REVERT: A 313 MET cc_start: 0.9330 (mmm) cc_final: 0.9113 (tpt) REVERT: A 352 PHE cc_start: 0.9394 (t80) cc_final: 0.9070 (t80) REVERT: A 355 MET cc_start: 0.8676 (mtt) cc_final: 0.8274 (mtt) REVERT: A 360 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: B 44 MET cc_start: 0.8264 (mtp) cc_final: 0.8029 (pmm) REVERT: B 355 MET cc_start: 0.8923 (mtt) cc_final: 0.8469 (mpp) REVERT: C 41 GLN cc_start: 0.8009 (tp40) cc_final: 0.7808 (tm-30) REVERT: C 53 TYR cc_start: 0.7986 (m-80) cc_final: 0.7332 (m-80) REVERT: C 118 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8675 (tppp) REVERT: C 120 THR cc_start: 0.8798 (m) cc_final: 0.8411 (p) REVERT: C 176 MET cc_start: 0.9032 (mmt) cc_final: 0.8687 (mmm) REVERT: C 211 ASP cc_start: 0.8799 (t70) cc_final: 0.8580 (t0) REVERT: C 361 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8749 (mt-10) REVERT: D 191 LYS cc_start: 0.9143 (tttm) cc_final: 0.8826 (ttmm) REVERT: D 222 ASP cc_start: 0.8656 (t0) cc_final: 0.8198 (p0) REVERT: D 283 MET cc_start: 0.9036 (mmm) cc_final: 0.8828 (mmm) REVERT: E 80 ASP cc_start: 0.8631 (m-30) cc_final: 0.8412 (m-30) REVERT: E 154 ASP cc_start: 0.8135 (t70) cc_final: 0.7739 (t0) REVERT: E 167 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8404 (tm-30) REVERT: F 103 THR cc_start: 0.9326 (m) cc_final: 0.8970 (p) REVERT: F 123 MET cc_start: 0.9104 (mmt) cc_final: 0.8861 (mmm) REVERT: F 154 ASP cc_start: 0.8093 (t70) cc_final: 0.7821 (t0) REVERT: F 176 MET cc_start: 0.8698 (mmt) cc_final: 0.8295 (mpp) REVERT: F 276 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8853 (mt-10) REVERT: F 355 MET cc_start: 0.8797 (mtt) cc_final: 0.8130 (mtm) REVERT: G 123 MET cc_start: 0.8899 (mmt) cc_final: 0.8625 (mmm) REVERT: G 227 MET cc_start: 0.8898 (mmm) cc_final: 0.8055 (tpp) REVERT: G 281 SER cc_start: 0.9020 (t) cc_final: 0.8651 (p) REVERT: G 305 MET cc_start: 0.8945 (mmm) cc_final: 0.8645 (mmm) REVERT: H 82 MET cc_start: 0.8413 (tpt) cc_final: 0.8207 (tpt) REVERT: H 119 MET cc_start: 0.9286 (mtp) cc_final: 0.8617 (mtp) REVERT: H 139 VAL cc_start: 0.9155 (t) cc_final: 0.8926 (p) REVERT: H 176 MET cc_start: 0.7790 (mmt) cc_final: 0.7207 (mmm) REVERT: H 325 MET cc_start: 0.7742 (mmp) cc_final: 0.6418 (mmt) REVERT: I 183 PHE cc_start: 0.8069 (m-80) cc_final: 0.7612 (m-80) REVERT: I 187 ASP cc_start: 0.6391 (m-30) cc_final: 0.5441 (m-30) REVERT: I 189 PHE cc_start: 0.8343 (m-80) cc_final: 0.8071 (m-80) REVERT: I 243 MET cc_start: 0.9229 (mtp) cc_final: 0.9017 (mmm) REVERT: I 274 TYR cc_start: 0.8216 (m-80) cc_final: 0.7527 (m-80) REVERT: I 316 PHE cc_start: 0.7003 (m-80) cc_final: 0.6635 (m-10) REVERT: I 342 MET cc_start: 0.7001 (mpp) cc_final: 0.6623 (mpp) REVERT: I 349 GLN cc_start: 0.8296 (mm110) cc_final: 0.7812 (tp40) REVERT: J 166 LYS cc_start: 0.8712 (pttm) cc_final: 0.8411 (ptmt) REVERT: J 200 TRP cc_start: 0.7853 (t60) cc_final: 0.7536 (t60) REVERT: J 211 LEU cc_start: 0.9422 (mt) cc_final: 0.9116 (pp) REVERT: J 315 ILE cc_start: 0.8054 (mt) cc_final: 0.7642 (tp) REVERT: J 369 TRP cc_start: 0.8232 (t-100) cc_final: 0.6420 (t-100) outliers start: 65 outliers final: 14 residues processed: 524 average time/residue: 0.1793 time to fit residues: 148.6201 Evaluate side-chains 271 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 255 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 165 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 128 ASN A 161 HIS ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN B 128 ASN B 275 HIS C 59 GLN C 92 ASN C 246 GLN D 92 ASN D 161 HIS E 12 ASN E 49 GLN E 101 HIS E 161 HIS E 275 HIS F 40 HIS F 92 ASN F 101 HIS F 246 GLN G 92 ASN G 225 ASN G 275 HIS H 275 HIS ** I 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 215 GLN I 292 ASN J 215 GLN J 309 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.070670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.052958 restraints weight = 105316.639| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.93 r_work: 0.2899 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 27607 Z= 0.307 Angle : 0.762 12.106 37441 Z= 0.385 Chirality : 0.048 0.202 4137 Planarity : 0.005 0.050 4811 Dihedral : 6.758 82.263 3860 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.84 % Allowed : 10.52 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.70 (0.15), residues: 3384 helix: 0.71 (0.15), residues: 1298 sheet: 0.21 (0.20), residues: 630 loop : 0.59 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 28 TYR 0.018 0.002 TYR F 362 PHE 0.018 0.002 PHE D 31 TRP 0.022 0.002 TRP I 180 HIS 0.007 0.002 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.31 (27607) covalent geometry : angle 0.76155 / 0.38 (37441) hydrogen bonds : bond 0.04781 / 3.26 ( 1363) hydrogen bonds : angle 5.59029 / 3.97 ( 3456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 247 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.2133 (OUTLIER) cc_final: 0.1530 (tmt) REVERT: A 123 MET cc_start: 0.9016 (mmt) cc_final: 0.8738 (tpp) REVERT: A 129 VAL cc_start: 0.9092 (m) cc_final: 0.8313 (p) REVERT: A 217 CYS cc_start: 0.7879 (m) cc_final: 0.7495 (m) REVERT: A 269 MET cc_start: 0.8473 (mtp) cc_final: 0.8248 (mtp) REVERT: A 283 MET cc_start: 0.9066 (mmm) cc_final: 0.8683 (mmm) REVERT: A 305 MET cc_start: 0.9099 (mmm) cc_final: 0.8888 (mmt) REVERT: B 47 MET cc_start: 0.4978 (mmt) cc_final: 0.4576 (mmm) REVERT: B 82 MET cc_start: 0.9299 (tpp) cc_final: 0.8647 (tpp) REVERT: B 86 TRP cc_start: 0.9292 (OUTLIER) cc_final: 0.8642 (m-90) REVERT: B 355 MET cc_start: 0.8828 (mtt) cc_final: 0.8464 (mtt) REVERT: C 41 GLN cc_start: 0.8309 (tp40) cc_final: 0.7962 (tm-30) REVERT: C 53 TYR cc_start: 0.8169 (m-80) cc_final: 0.7440 (m-80) REVERT: C 118 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8878 (tppp) REVERT: C 119 MET cc_start: 0.8620 (ptm) cc_final: 0.8366 (ptt) REVERT: C 176 MET cc_start: 0.9032 (mmt) cc_final: 0.8699 (mmm) REVERT: C 313 MET cc_start: 0.9220 (tpp) cc_final: 0.8936 (tpp) REVERT: D 191 LYS cc_start: 0.9227 (tttm) cc_final: 0.8999 (ttpp) REVERT: D 222 ASP cc_start: 0.8737 (t0) cc_final: 0.8137 (p0) REVERT: D 283 MET cc_start: 0.9044 (mmm) cc_final: 0.8811 (mmm) REVERT: E 41 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7534 (tp-100) REVERT: E 80 ASP cc_start: 0.8763 (m-30) cc_final: 0.8352 (p0) REVERT: E 154 ASP cc_start: 0.8577 (t70) cc_final: 0.8196 (t0) REVERT: E 167 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8710 (tm-30) REVERT: F 83 GLU cc_start: 0.9407 (OUTLIER) cc_final: 0.9131 (pp20) REVERT: F 132 MET cc_start: 0.8795 (ptm) cc_final: 0.8512 (ptm) REVERT: F 176 MET cc_start: 0.8832 (mmt) cc_final: 0.8390 (mpp) REVERT: F 205 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8113 (mt-10) REVERT: F 276 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8979 (mt-10) REVERT: F 355 MET cc_start: 0.8573 (mtt) cc_final: 0.7896 (mtp) REVERT: G 83 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8923 (pp20) REVERT: G 125 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8315 (mm-30) REVERT: G 292 ASP cc_start: 0.9022 (m-30) cc_final: 0.8459 (p0) REVERT: G 305 MET cc_start: 0.8963 (mmm) cc_final: 0.8672 (mmm) REVERT: G 374 CYS cc_start: 0.5997 (m) cc_final: 0.5747 (m) REVERT: H 82 MET cc_start: 0.8549 (tpt) cc_final: 0.8296 (tpt) REVERT: H 123 MET cc_start: 0.9172 (mmm) cc_final: 0.8826 (mmm) REVERT: H 276 GLU cc_start: 0.9468 (mt-10) cc_final: 0.9133 (tp30) REVERT: H 325 MET cc_start: 0.7886 (mmp) cc_final: 0.6715 (mmt) REVERT: H 375 PHE cc_start: 0.5199 (OUTLIER) cc_final: 0.4715 (t80) REVERT: I 189 PHE cc_start: 0.8658 (m-80) cc_final: 0.8415 (m-80) REVERT: I 274 TYR cc_start: 0.8169 (m-80) cc_final: 0.7786 (m-80) REVERT: I 342 MET cc_start: 0.7219 (mpp) cc_final: 0.6933 (mpp) REVERT: I 349 GLN cc_start: 0.8498 (mm110) cc_final: 0.8290 (mp10) REVERT: J 200 TRP cc_start: 0.7520 (t60) cc_final: 0.7317 (t60) REVERT: J 211 LEU cc_start: 0.9406 (mt) cc_final: 0.9143 (pp) REVERT: J 243 MET cc_start: 0.9409 (mtm) cc_final: 0.8827 (mmp) REVERT: J 245 GLN cc_start: 0.9264 (tm-30) cc_final: 0.9007 (pp30) REVERT: J 342 MET cc_start: 0.6129 (mmt) cc_final: 0.5766 (mpp) REVERT: J 369 TRP cc_start: 0.8292 (t-100) cc_final: 0.6433 (t-100) outliers start: 82 outliers final: 42 residues processed: 312 average time/residue: 0.1643 time to fit residues: 83.9776 Evaluate side-chains 260 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 201 CYS Chi-restraints excluded: chain J residue 217 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 334 optimal weight: 9.9990 chunk 269 optimal weight: 0.9980 chunk 257 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN C 49 GLN C 59 GLN D 246 GLN H 92 ASN H 128 ASN I 199 GLN ** J 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.071390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.053962 restraints weight = 103168.694| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.93 r_work: 0.2931 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27607 Z= 0.115 Angle : 0.572 9.854 37441 Z= 0.282 Chirality : 0.043 0.174 4137 Planarity : 0.004 0.039 4811 Dihedral : 6.062 74.857 3845 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.80 % Allowed : 11.48 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.15), residues: 3384 helix: 0.96 (0.15), residues: 1340 sheet: 0.53 (0.19), residues: 675 loop : 0.61 (0.18), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 28 TYR 0.010 0.001 TYR E 143 PHE 0.011 0.001 PHE I 362 TRP 0.020 0.002 TRP I 369 HIS 0.006 0.001 HIS D 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (27607) covalent geometry : angle 0.57205 / 0.28 (37441) hydrogen bonds : bond 0.03329 / 2.28 ( 1363) hydrogen bonds : angle 4.97786 / 3.55 ( 3456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 246 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.2069 (OUTLIER) cc_final: 0.1590 (tmt) REVERT: A 123 MET cc_start: 0.9009 (mmt) cc_final: 0.8760 (tpp) REVERT: A 129 VAL cc_start: 0.9011 (m) cc_final: 0.8187 (p) REVERT: A 180 LEU cc_start: 0.9591 (tt) cc_final: 0.9093 (tp) REVERT: A 217 CYS cc_start: 0.7699 (m) cc_final: 0.7279 (m) REVERT: A 269 MET cc_start: 0.8619 (mtp) cc_final: 0.8092 (mtp) REVERT: A 305 MET cc_start: 0.9084 (mmm) cc_final: 0.8819 (mmt) REVERT: A 313 MET cc_start: 0.9483 (mmt) cc_final: 0.9128 (tpp) REVERT: A 355 MET cc_start: 0.8363 (mpp) cc_final: 0.7945 (mtm) REVERT: B 132 MET cc_start: 0.8903 (ppp) cc_final: 0.8230 (ppp) REVERT: B 286 ASP cc_start: 0.8499 (t0) cc_final: 0.8250 (t0) REVERT: B 355 MET cc_start: 0.8872 (mtt) cc_final: 0.8502 (mtt) REVERT: C 41 GLN cc_start: 0.8328 (tp40) cc_final: 0.8005 (tm-30) REVERT: C 118 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8756 (tppp) REVERT: C 119 MET cc_start: 0.8448 (ptm) cc_final: 0.8176 (ptt) REVERT: C 125 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7838 (mp0) REVERT: C 190 MET cc_start: 0.9146 (mtm) cc_final: 0.8872 (mtt) REVERT: C 211 ASP cc_start: 0.8917 (t70) cc_final: 0.8702 (t0) REVERT: D 123 MET cc_start: 0.9173 (tpp) cc_final: 0.8957 (tpp) REVERT: D 191 LYS cc_start: 0.9211 (tttm) cc_final: 0.8969 (ttpp) REVERT: D 222 ASP cc_start: 0.8781 (t0) cc_final: 0.8178 (p0) REVERT: D 226 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7892 (tt0) REVERT: D 283 MET cc_start: 0.8964 (mmm) cc_final: 0.8183 (mpp) REVERT: E 167 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8386 (tm-30) REVERT: F 132 MET cc_start: 0.8724 (ptm) cc_final: 0.8519 (ptm) REVERT: F 176 MET cc_start: 0.8742 (mmt) cc_final: 0.8227 (mpp) REVERT: F 276 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8941 (mt-10) REVERT: F 313 MET cc_start: 0.8964 (tpp) cc_final: 0.8725 (mtp) REVERT: F 355 MET cc_start: 0.8537 (mtt) cc_final: 0.7845 (mtp) REVERT: G 44 MET cc_start: 0.8790 (mmm) cc_final: 0.8437 (mmm) REVERT: G 83 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8871 (pp20) REVERT: G 226 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8132 (tp30) REVERT: G 292 ASP cc_start: 0.9049 (m-30) cc_final: 0.8520 (p0) REVERT: G 305 MET cc_start: 0.8935 (mmm) cc_final: 0.8664 (mmm) REVERT: G 374 CYS cc_start: 0.6109 (m) cc_final: 0.5837 (m) REVERT: H 82 MET cc_start: 0.8506 (tpt) cc_final: 0.8268 (tpt) REVERT: H 246 GLN cc_start: 0.8990 (mt0) cc_final: 0.8531 (mt0) REVERT: H 325 MET cc_start: 0.7932 (mmp) cc_final: 0.6800 (mmt) REVERT: H 375 PHE cc_start: 0.5222 (OUTLIER) cc_final: 0.4719 (t80) REVERT: I 342 MET cc_start: 0.7284 (mpp) cc_final: 0.6974 (mpp) REVERT: I 349 GLN cc_start: 0.8468 (mm110) cc_final: 0.8259 (mp10) REVERT: J 211 LEU cc_start: 0.9429 (mt) cc_final: 0.9129 (pp) REVERT: J 243 MET cc_start: 0.9454 (mtm) cc_final: 0.8737 (tmm) REVERT: J 245 GLN cc_start: 0.9236 (tm-30) cc_final: 0.9004 (pp30) REVERT: J 367 LYS cc_start: 0.8984 (tppp) cc_final: 0.8756 (tppt) REVERT: J 369 TRP cc_start: 0.8267 (t-100) cc_final: 0.6222 (t-100) outliers start: 52 outliers final: 28 residues processed: 289 average time/residue: 0.1719 time to fit residues: 81.6803 Evaluate side-chains 254 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 50 LYS Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 217 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 233 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 328 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 245 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 172 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS C 59 GLN E 128 ASN E 246 GLN I 349 GLN ** J 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 322 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.069631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.052357 restraints weight = 104239.894| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.88 r_work: 0.2892 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27607 Z= 0.180 Angle : 0.612 10.976 37441 Z= 0.299 Chirality : 0.044 0.165 4137 Planarity : 0.004 0.039 4811 Dihedral : 5.971 74.750 3845 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.53 % Allowed : 11.86 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.01 (0.15), residues: 3384 helix: 1.08 (0.15), residues: 1340 sheet: 0.58 (0.20), residues: 670 loop : 0.50 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 28 TYR 0.012 0.001 TYR A 91 PHE 0.019 0.001 PHE H 124 TRP 0.030 0.002 TRP J 200 HIS 0.005 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (27607) covalent geometry : angle 0.61187 / 0.30 (37441) hydrogen bonds : bond 0.03572 / 2.44 ( 1363) hydrogen bonds : angle 4.97257 / 3.55 ( 3456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 213 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.2272 (OUTLIER) cc_final: 0.1913 (tmt) REVERT: A 123 MET cc_start: 0.9157 (mmt) cc_final: 0.8882 (tpp) REVERT: A 129 VAL cc_start: 0.8978 (m) cc_final: 0.8115 (p) REVERT: A 180 LEU cc_start: 0.9614 (tt) cc_final: 0.9312 (tp) REVERT: A 217 CYS cc_start: 0.7966 (m) cc_final: 0.7658 (m) REVERT: A 269 MET cc_start: 0.8559 (mtp) cc_final: 0.8317 (mtp) REVERT: A 283 MET cc_start: 0.9032 (mmm) cc_final: 0.8682 (mmm) REVERT: A 305 MET cc_start: 0.9096 (mmm) cc_final: 0.8772 (mmt) REVERT: A 355 MET cc_start: 0.8396 (mpp) cc_final: 0.7964 (mtm) REVERT: B 107 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7149 (pt0) REVERT: B 286 ASP cc_start: 0.8587 (t0) cc_final: 0.8273 (t0) REVERT: B 305 MET cc_start: 0.8711 (mmt) cc_final: 0.8454 (mmt) REVERT: B 355 MET cc_start: 0.8964 (mtt) cc_final: 0.8598 (mtt) REVERT: C 41 GLN cc_start: 0.8299 (tp40) cc_final: 0.7970 (tm-30) REVERT: C 53 TYR cc_start: 0.7882 (m-80) cc_final: 0.7284 (m-80) REVERT: C 116 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8078 (mtp180) REVERT: C 118 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8798 (tppp) REVERT: C 119 MET cc_start: 0.8443 (ptm) cc_final: 0.8154 (ptt) REVERT: C 190 MET cc_start: 0.9144 (mtm) cc_final: 0.8859 (mtt) REVERT: D 107 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8271 (tm-30) REVERT: D 222 ASP cc_start: 0.8773 (t0) cc_final: 0.8111 (p0) REVERT: D 283 MET cc_start: 0.8967 (mmm) cc_final: 0.8631 (mpp) REVERT: E 41 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7425 (tp-100) REVERT: E 167 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8629 (tm-30) REVERT: F 132 MET cc_start: 0.8792 (ptm) cc_final: 0.8436 (ptm) REVERT: F 176 MET cc_start: 0.8782 (mmt) cc_final: 0.8259 (mpp) REVERT: F 215 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8789 (mptm) REVERT: F 276 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8949 (mt-10) REVERT: F 355 MET cc_start: 0.8500 (mtt) cc_final: 0.7942 (mtp) REVERT: G 44 MET cc_start: 0.8871 (mmm) cc_final: 0.8258 (mmm) REVERT: G 83 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8937 (pp20) REVERT: G 125 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: G 292 ASP cc_start: 0.9076 (m-30) cc_final: 0.8577 (p0) REVERT: G 305 MET cc_start: 0.8877 (mmm) cc_final: 0.8591 (mmm) REVERT: G 374 CYS cc_start: 0.6318 (m) cc_final: 0.6051 (m) REVERT: H 82 MET cc_start: 0.8514 (tpt) cc_final: 0.8269 (tpt) REVERT: H 123 MET cc_start: 0.9409 (mmm) cc_final: 0.9162 (mmm) REVERT: H 205 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: H 299 MET cc_start: 0.8447 (mtp) cc_final: 0.8245 (mtp) REVERT: H 325 MET cc_start: 0.8031 (mmp) cc_final: 0.6980 (mmt) REVERT: H 375 PHE cc_start: 0.5303 (OUTLIER) cc_final: 0.4736 (t80) REVERT: I 274 TYR cc_start: 0.7789 (m-80) cc_final: 0.7548 (m-80) REVERT: I 349 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8212 (mp10) REVERT: J 168 ARG cc_start: 0.7135 (tpt90) cc_final: 0.6563 (tpm170) REVERT: J 200 TRP cc_start: 0.7555 (t60) cc_final: 0.7306 (t60) REVERT: J 211 LEU cc_start: 0.9436 (mt) cc_final: 0.9108 (pp) REVERT: J 243 MET cc_start: 0.9443 (mtm) cc_final: 0.8757 (tmm) REVERT: J 245 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8932 (pp30) REVERT: J 342 MET cc_start: 0.6161 (mmt) cc_final: 0.5857 (mpp) REVERT: J 367 LYS cc_start: 0.9027 (tppp) cc_final: 0.8807 (mtmt) REVERT: J 369 TRP cc_start: 0.8301 (t-100) cc_final: 0.6163 (t60) outliers start: 73 outliers final: 49 residues processed: 275 average time/residue: 0.1671 time to fit residues: 74.5562 Evaluate side-chains 264 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 204 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 351 THR 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 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 297 ASN Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 201 CYS Chi-restraints excluded: chain J residue 217 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 145 optimal weight: 0.0770 chunk 62 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 322 optimal weight: 9.9990 chunk 180 optimal weight: 0.0060 chunk 40 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 overall best weight: 2.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN D 12 ASN I 199 GLN ** J 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.069860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.052728 restraints weight = 104061.037| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.89 r_work: 0.2900 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27607 Z= 0.150 Angle : 0.579 9.183 37441 Z= 0.282 Chirality : 0.044 0.166 4137 Planarity : 0.004 0.039 4811 Dihedral : 5.835 75.013 3845 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.39 % Allowed : 12.56 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.15), residues: 3384 helix: 1.13 (0.15), residues: 1353 sheet: 0.65 (0.20), residues: 659 loop : 0.50 (0.18), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 28 TYR 0.011 0.001 TYR A 91 PHE 0.010 0.001 PHE D 31 TRP 0.016 0.001 TRP J 200 HIS 0.005 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (27607) covalent geometry : angle 0.57901 / 0.28 (37441) hydrogen bonds : bond 0.03238 / 2.21 ( 1363) hydrogen bonds : angle 4.83793 / 3.45 ( 3456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.2779 (OUTLIER) cc_final: 0.2196 (tmm) REVERT: A 123 MET cc_start: 0.9162 (mmt) cc_final: 0.8927 (tpp) REVERT: A 129 VAL cc_start: 0.8989 (m) cc_final: 0.8106 (p) REVERT: A 180 LEU cc_start: 0.9617 (tt) cc_final: 0.9169 (tp) REVERT: A 217 CYS cc_start: 0.7915 (m) cc_final: 0.7610 (m) REVERT: A 269 MET cc_start: 0.8547 (mtp) cc_final: 0.8017 (mtp) REVERT: A 305 MET cc_start: 0.9107 (mmm) cc_final: 0.8782 (mmt) REVERT: A 355 MET cc_start: 0.8435 (mpp) cc_final: 0.7985 (mtm) REVERT: B 286 ASP cc_start: 0.8562 (t0) cc_final: 0.8213 (t0) REVERT: B 355 MET cc_start: 0.8981 (mtt) cc_final: 0.8609 (mtm) REVERT: C 41 GLN cc_start: 0.8300 (tp40) cc_final: 0.7984 (tm-30) REVERT: C 53 TYR cc_start: 0.7766 (m-80) cc_final: 0.7209 (m-80) REVERT: C 116 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7971 (mtp180) REVERT: C 118 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8733 (tppp) REVERT: C 119 MET cc_start: 0.8361 (ptm) cc_final: 0.8038 (ptt) REVERT: C 190 MET cc_start: 0.9142 (mtm) cc_final: 0.8869 (mtt) REVERT: C 338 SER cc_start: 0.9381 (t) cc_final: 0.9110 (p) REVERT: D 123 MET cc_start: 0.9052 (tpp) cc_final: 0.8829 (tpp) REVERT: D 222 ASP cc_start: 0.8790 (t0) cc_final: 0.8186 (p0) REVERT: D 283 MET cc_start: 0.8971 (mmm) cc_final: 0.8630 (mpp) REVERT: E 140 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8369 (mm) REVERT: E 167 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8629 (tm-30) REVERT: F 83 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.9130 (pp20) REVERT: F 176 MET cc_start: 0.8771 (mmt) cc_final: 0.8216 (mpp) REVERT: F 215 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8840 (mptm) REVERT: F 276 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8957 (mt-10) REVERT: F 355 MET cc_start: 0.8419 (mtt) cc_final: 0.7839 (mtp) REVERT: G 83 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8894 (pp20) REVERT: G 292 ASP cc_start: 0.9083 (m-30) cc_final: 0.8632 (p0) REVERT: G 305 MET cc_start: 0.8871 (mmm) cc_final: 0.8577 (mmm) REVERT: G 325 MET cc_start: 0.8493 (mmp) cc_final: 0.7827 (tpp) REVERT: G 374 CYS cc_start: 0.6380 (m) cc_final: 0.6161 (t) REVERT: H 82 MET cc_start: 0.8516 (tpt) cc_final: 0.8283 (tpt) REVERT: H 123 MET cc_start: 0.9421 (mmm) cc_final: 0.9100 (mmm) REVERT: H 132 MET cc_start: 0.8594 (pmm) cc_final: 0.8378 (pmm) REVERT: H 205 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: H 246 GLN cc_start: 0.9041 (mt0) cc_final: 0.8622 (mt0) REVERT: H 325 MET cc_start: 0.8073 (mmp) cc_final: 0.7031 (mmt) REVERT: H 375 PHE cc_start: 0.5186 (OUTLIER) cc_final: 0.4612 (t80) REVERT: I 274 TYR cc_start: 0.7761 (m-80) cc_final: 0.7415 (m-80) REVERT: I 344 TYR cc_start: 0.7984 (m-10) cc_final: 0.7720 (m-80) REVERT: I 349 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8306 (mp10) REVERT: J 168 ARG cc_start: 0.7081 (tpt90) cc_final: 0.6577 (tpm170) REVERT: J 211 LEU cc_start: 0.9412 (mt) cc_final: 0.9065 (pp) REVERT: J 243 MET cc_start: 0.9440 (mtm) cc_final: 0.8815 (tmm) REVERT: J 245 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8970 (pp30) REVERT: J 342 MET cc_start: 0.6061 (mmt) cc_final: 0.5800 (mpp) REVERT: J 367 LYS cc_start: 0.9045 (tppp) cc_final: 0.8825 (mtmt) REVERT: J 369 TRP cc_start: 0.8310 (t-100) cc_final: 0.6094 (t60) outliers start: 69 outliers final: 42 residues processed: 268 average time/residue: 0.1539 time to fit residues: 67.1559 Evaluate side-chains 257 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 206 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 297 ASN Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 217 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 167 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 227 optimal weight: 0.0980 chunk 196 optimal weight: 0.9990 chunk 293 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 301 optimal weight: 9.9990 chunk 265 optimal weight: 0.2980 chunk 18 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** I 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.069121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.052027 restraints weight = 104937.503| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.88 r_work: 0.2860 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 27607 Z= 0.176 Angle : 0.604 10.956 37441 Z= 0.293 Chirality : 0.044 0.156 4137 Planarity : 0.004 0.038 4811 Dihedral : 5.795 75.029 3844 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.84 % Allowed : 12.49 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.96 (0.15), residues: 3384 helix: 1.14 (0.15), residues: 1353 sheet: 0.44 (0.20), residues: 616 loop : 0.42 (0.17), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 372 TYR 0.011 0.001 TYR A 91 PHE 0.010 0.001 PHE D 31 TRP 0.029 0.002 TRP J 200 HIS 0.007 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (27607) covalent geometry : angle 0.60401 / 0.29 (37441) hydrogen bonds : bond 0.03434 / 2.35 ( 1363) hydrogen bonds : angle 4.87283 / 3.49 ( 3456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 207 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.2840 (OUTLIER) cc_final: 0.2221 (tmm) REVERT: A 123 MET cc_start: 0.9182 (mmt) cc_final: 0.8943 (tpp) REVERT: A 129 VAL cc_start: 0.9029 (m) cc_final: 0.8163 (p) REVERT: A 180 LEU cc_start: 0.9624 (tt) cc_final: 0.9201 (tp) REVERT: A 217 CYS cc_start: 0.7973 (m) cc_final: 0.7615 (m) REVERT: A 269 MET cc_start: 0.8560 (mtp) cc_final: 0.8041 (mtp) REVERT: A 283 MET cc_start: 0.8965 (mmm) cc_final: 0.8583 (mmm) REVERT: A 305 MET cc_start: 0.9132 (mmm) cc_final: 0.8801 (mmt) REVERT: A 313 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8937 (tpp) REVERT: A 355 MET cc_start: 0.8481 (mpp) cc_final: 0.8030 (mtm) REVERT: B 86 TRP cc_start: 0.9189 (OUTLIER) cc_final: 0.8666 (m-90) REVERT: B 107 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7114 (pt0) REVERT: B 286 ASP cc_start: 0.8564 (t0) cc_final: 0.8191 (t0) REVERT: B 355 MET cc_start: 0.8966 (mtt) cc_final: 0.8629 (mtt) REVERT: C 41 GLN cc_start: 0.8279 (tp40) cc_final: 0.7964 (tm-30) REVERT: C 44 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7429 (ttp) REVERT: C 53 TYR cc_start: 0.7807 (m-80) cc_final: 0.7177 (m-80) REVERT: C 116 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7952 (mtp180) REVERT: C 118 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8818 (tppp) REVERT: C 119 MET cc_start: 0.8403 (ptm) cc_final: 0.8070 (ptt) REVERT: C 190 MET cc_start: 0.9142 (mtm) cc_final: 0.8854 (mtt) REVERT: C 338 SER cc_start: 0.9398 (t) cc_final: 0.9125 (p) REVERT: D 222 ASP cc_start: 0.8785 (t0) cc_final: 0.8161 (p0) REVERT: D 283 MET cc_start: 0.8929 (mmm) cc_final: 0.8615 (mpp) REVERT: E 41 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7478 (tp-100) REVERT: E 124 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7248 (t80) REVERT: E 140 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8374 (mm) REVERT: E 167 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8641 (tm-30) REVERT: F 83 GLU cc_start: 0.9403 (OUTLIER) cc_final: 0.9138 (pp20) REVERT: F 176 MET cc_start: 0.8770 (mmt) cc_final: 0.8225 (mpp) REVERT: F 215 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8778 (mptm) REVERT: F 276 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8959 (mt-10) REVERT: F 355 MET cc_start: 0.8349 (mtt) cc_final: 0.7624 (mtp) REVERT: F 373 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7781 (ttpp) REVERT: G 83 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8899 (pp20) REVERT: G 125 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: G 292 ASP cc_start: 0.9094 (m-30) cc_final: 0.8651 (p0) REVERT: G 305 MET cc_start: 0.8881 (mmm) cc_final: 0.8584 (mmm) REVERT: G 325 MET cc_start: 0.8528 (mmp) cc_final: 0.7957 (tpp) REVERT: G 374 CYS cc_start: 0.6445 (m) cc_final: 0.6213 (t) REVERT: H 82 MET cc_start: 0.8558 (tpt) cc_final: 0.8330 (tpt) REVERT: H 123 MET cc_start: 0.9385 (mmm) cc_final: 0.9036 (mmm) REVERT: H 132 MET cc_start: 0.8644 (pmm) cc_final: 0.8436 (pmm) REVERT: H 205 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: H 227 MET cc_start: 0.9271 (mmm) cc_final: 0.9012 (mmm) REVERT: H 246 GLN cc_start: 0.9057 (mt0) cc_final: 0.8653 (mt0) REVERT: H 305 MET cc_start: 0.9107 (mmm) cc_final: 0.8859 (mmm) REVERT: H 325 MET cc_start: 0.8126 (mmp) cc_final: 0.7098 (mmt) REVERT: H 375 PHE cc_start: 0.5335 (OUTLIER) cc_final: 0.4707 (t80) REVERT: I 274 TYR cc_start: 0.7845 (m-80) cc_final: 0.7454 (m-80) REVERT: J 168 ARG cc_start: 0.7083 (tpt90) cc_final: 0.6823 (tpt170) REVERT: J 243 MET cc_start: 0.9398 (mtm) cc_final: 0.8783 (tmm) REVERT: J 245 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8945 (pp30) REVERT: J 342 MET cc_start: 0.6177 (mmt) cc_final: 0.5843 (mpp) REVERT: J 369 TRP cc_start: 0.8333 (t-100) cc_final: 0.6084 (t60) outliers start: 82 outliers final: 49 residues processed: 272 average time/residue: 0.1555 time to fit residues: 69.8065 Evaluate side-chains 269 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 203 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 ARG Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 351 THR 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 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 124 PHE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain F residue 373 LYS Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 297 ASN Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 201 CYS Chi-restraints excluded: chain J residue 217 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 67 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 330 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 305 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 HIS ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.069098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.051974 restraints weight = 104290.300| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.85 r_work: 0.2863 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27607 Z= 0.169 Angle : 0.599 10.611 37441 Z= 0.290 Chirality : 0.044 0.149 4137 Planarity : 0.003 0.039 4811 Dihedral : 5.763 74.953 3844 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.66 % Allowed : 13.08 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.93 (0.15), residues: 3384 helix: 1.15 (0.15), residues: 1352 sheet: 0.40 (0.20), residues: 616 loop : 0.38 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 372 TYR 0.010 0.001 TYR A 91 PHE 0.011 0.001 PHE D 31 TRP 0.022 0.001 TRP J 200 HIS 0.008 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (27607) covalent geometry : angle 0.59918 / 0.29 (37441) hydrogen bonds : bond 0.03363 / 2.31 ( 1363) hydrogen bonds : angle 4.84404 / 3.47 ( 3456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 209 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.0307 (ptp) cc_final: 0.0094 (ptp) REVERT: A 47 MET cc_start: 0.2860 (OUTLIER) cc_final: 0.2265 (tmm) REVERT: A 123 MET cc_start: 0.9187 (mmt) cc_final: 0.8948 (tpp) REVERT: A 129 VAL cc_start: 0.9098 (m) cc_final: 0.8289 (p) REVERT: A 180 LEU cc_start: 0.9624 (tt) cc_final: 0.9230 (tp) REVERT: A 217 CYS cc_start: 0.7889 (m) cc_final: 0.7630 (m) REVERT: A 269 MET cc_start: 0.8677 (mtp) cc_final: 0.8140 (mtp) REVERT: A 283 MET cc_start: 0.8980 (mmm) cc_final: 0.8657 (mmm) REVERT: A 305 MET cc_start: 0.9135 (mmm) cc_final: 0.8810 (mmt) REVERT: A 313 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8910 (tpp) REVERT: A 355 MET cc_start: 0.8496 (mpp) cc_final: 0.8083 (mtm) REVERT: B 86 TRP cc_start: 0.9154 (OUTLIER) cc_final: 0.8659 (m-90) REVERT: B 107 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7148 (pt0) REVERT: B 286 ASP cc_start: 0.8620 (t0) cc_final: 0.8241 (t0) REVERT: B 355 MET cc_start: 0.8993 (mtt) cc_final: 0.8625 (mtm) REVERT: C 41 GLN cc_start: 0.8268 (tp40) cc_final: 0.7964 (tm-30) REVERT: C 53 TYR cc_start: 0.7796 (m-80) cc_final: 0.7205 (m-80) REVERT: C 118 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8534 (tppp) REVERT: C 190 MET cc_start: 0.9142 (mtm) cc_final: 0.8855 (mtt) REVERT: C 338 SER cc_start: 0.9412 (t) cc_final: 0.9134 (p) REVERT: D 123 MET cc_start: 0.9117 (tpp) cc_final: 0.8910 (tpp) REVERT: D 222 ASP cc_start: 0.8765 (t0) cc_final: 0.8092 (p0) REVERT: D 283 MET cc_start: 0.8935 (mmm) cc_final: 0.8685 (mmm) REVERT: E 41 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7517 (tp-100) REVERT: E 123 MET cc_start: 0.8809 (tpp) cc_final: 0.8428 (tpt) REVERT: E 140 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8376 (mm) REVERT: E 167 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8635 (tm-30) REVERT: F 56 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7499 (t0) REVERT: F 123 MET cc_start: 0.8948 (mmt) cc_final: 0.8617 (mmm) REVERT: F 176 MET cc_start: 0.8776 (mmt) cc_final: 0.8239 (mpp) REVERT: F 215 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8825 (mptm) REVERT: F 276 GLU cc_start: 0.9277 (mt-10) cc_final: 0.9054 (mt-10) REVERT: F 355 MET cc_start: 0.8316 (mtt) cc_final: 0.7510 (mtp) REVERT: F 362 TYR cc_start: 0.8181 (t80) cc_final: 0.7935 (t80) REVERT: F 373 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7718 (ttpp) REVERT: G 44 MET cc_start: 0.8918 (mmm) cc_final: 0.8201 (mmt) REVERT: G 83 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8902 (pp20) REVERT: G 125 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: G 292 ASP cc_start: 0.9092 (m-30) cc_final: 0.8656 (p0) REVERT: G 305 MET cc_start: 0.8825 (mmm) cc_final: 0.8543 (mmm) REVERT: G 325 MET cc_start: 0.8539 (mmp) cc_final: 0.8010 (tpp) REVERT: H 72 GLU cc_start: 0.8925 (tp30) cc_final: 0.8609 (tm-30) REVERT: H 82 MET cc_start: 0.8541 (tpt) cc_final: 0.8324 (tpt) REVERT: H 123 MET cc_start: 0.9361 (mmm) cc_final: 0.8982 (mmm) REVERT: H 132 MET cc_start: 0.8671 (pmm) cc_final: 0.8441 (pmm) REVERT: H 205 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: H 244 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.8122 (p0) REVERT: H 246 GLN cc_start: 0.9061 (mt0) cc_final: 0.8627 (mt0) REVERT: H 325 MET cc_start: 0.8142 (mmp) cc_final: 0.7118 (mmt) REVERT: H 375 PHE cc_start: 0.5436 (OUTLIER) cc_final: 0.4743 (t80) REVERT: I 243 MET cc_start: 0.9066 (tmm) cc_final: 0.8827 (ttm) REVERT: I 322 GLN cc_start: 0.9151 (mp10) cc_final: 0.8904 (mp-120) REVERT: I 342 MET cc_start: 0.7449 (mpp) cc_final: 0.6915 (mpp) REVERT: J 168 ARG cc_start: 0.7072 (tpt90) cc_final: 0.6369 (tpm170) REVERT: J 243 MET cc_start: 0.9401 (mtm) cc_final: 0.8779 (tmm) REVERT: J 245 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8962 (pp30) REVERT: J 369 TRP cc_start: 0.8368 (t-100) cc_final: 0.6156 (t60) outliers start: 77 outliers final: 51 residues processed: 272 average time/residue: 0.1737 time to fit residues: 78.3013 Evaluate side-chains 263 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 351 THR 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 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain F residue 373 LYS Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain H residue 297 ASN Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 371 ASP Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 217 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 314 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 310 optimal weight: 0.0870 chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 0.0370 chunk 149 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 HIS ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 ASN ** I 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.070399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.053239 restraints weight = 104409.674| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.91 r_work: 0.2903 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27607 Z= 0.099 Angle : 0.572 11.616 37441 Z= 0.272 Chirality : 0.043 0.154 4137 Planarity : 0.003 0.040 4811 Dihedral : 5.553 75.319 3843 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.59 % Allowed : 14.49 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.22 (0.15), residues: 3384 helix: 1.39 (0.15), residues: 1309 sheet: 0.70 (0.20), residues: 657 loop : 0.48 (0.18), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.009 0.001 TYR A 91 PHE 0.010 0.001 PHE I 362 TRP 0.036 0.001 TRP J 200 HIS 0.006 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (27607) covalent geometry : angle 0.57156 / 0.27 (37441) hydrogen bonds : bond 0.02842 / 1.96 ( 1363) hydrogen bonds : angle 4.62846 / 3.31 ( 3456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.2843 (OUTLIER) cc_final: 0.2311 (tmm) REVERT: A 129 VAL cc_start: 0.9033 (m) cc_final: 0.8199 (p) REVERT: A 180 LEU cc_start: 0.9616 (tt) cc_final: 0.9215 (tp) REVERT: A 217 CYS cc_start: 0.8072 (m) cc_final: 0.7668 (m) REVERT: A 269 MET cc_start: 0.8680 (mtp) cc_final: 0.8162 (mtp) REVERT: A 305 MET cc_start: 0.9206 (mmm) cc_final: 0.8924 (mmt) REVERT: A 313 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8874 (tpp) REVERT: A 355 MET cc_start: 0.8567 (mpp) cc_final: 0.8159 (mtm) REVERT: B 72 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: B 286 ASP cc_start: 0.8566 (t0) cc_final: 0.8188 (t0) REVERT: B 355 MET cc_start: 0.8994 (mtt) cc_final: 0.8682 (mtm) REVERT: C 41 GLN cc_start: 0.8266 (tp40) cc_final: 0.7993 (tm-30) REVERT: C 53 TYR cc_start: 0.7649 (m-80) cc_final: 0.7218 (m-80) REVERT: C 118 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8530 (tppp) REVERT: C 119 MET cc_start: 0.8438 (ptm) cc_final: 0.8192 (ptt) REVERT: C 190 MET cc_start: 0.9177 (mtm) cc_final: 0.8883 (mtt) REVERT: C 305 MET cc_start: 0.9233 (tpp) cc_final: 0.8724 (tpp) REVERT: C 314 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8749 (tm-30) REVERT: C 338 SER cc_start: 0.9383 (t) cc_final: 0.9103 (p) REVERT: C 361 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8593 (mt-10) REVERT: D 123 MET cc_start: 0.9083 (tpp) cc_final: 0.8809 (tpp) REVERT: D 222 ASP cc_start: 0.8746 (t0) cc_final: 0.8152 (p0) REVERT: E 140 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8382 (mm) REVERT: E 167 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8656 (tm-30) REVERT: F 56 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7515 (t0) REVERT: F 83 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.9110 (pp20) REVERT: F 215 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8780 (mptm) REVERT: F 276 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8921 (mt-10) REVERT: F 355 MET cc_start: 0.8295 (mtt) cc_final: 0.7703 (mtp) REVERT: F 362 TYR cc_start: 0.8113 (t80) cc_final: 0.7887 (t80) REVERT: G 44 MET cc_start: 0.8996 (mmm) cc_final: 0.8293 (mmt) REVERT: G 81 ASP cc_start: 0.8887 (m-30) cc_final: 0.8561 (m-30) REVERT: G 83 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8898 (pp20) REVERT: G 226 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8087 (tp30) REVERT: G 292 ASP cc_start: 0.9110 (m-30) cc_final: 0.8679 (p0) REVERT: G 305 MET cc_start: 0.8835 (mmm) cc_final: 0.8551 (mmm) REVERT: G 325 MET cc_start: 0.8598 (mmp) cc_final: 0.8128 (tpp) REVERT: H 72 GLU cc_start: 0.8902 (tp30) cc_final: 0.8663 (tm-30) REVERT: H 82 MET cc_start: 0.8533 (tpt) cc_final: 0.8321 (tpt) REVERT: H 123 MET cc_start: 0.9334 (mmm) cc_final: 0.8877 (mmm) REVERT: H 132 MET cc_start: 0.8682 (pmm) cc_final: 0.8452 (pmm) REVERT: H 246 GLN cc_start: 0.9070 (mt0) cc_final: 0.8670 (mt0) REVERT: H 375 PHE cc_start: 0.5523 (OUTLIER) cc_final: 0.4729 (t80) REVERT: I 243 MET cc_start: 0.9019 (tmm) cc_final: 0.8818 (ttm) REVERT: I 342 MET cc_start: 0.7427 (mpp) cc_final: 0.6860 (mpp) REVERT: J 168 ARG cc_start: 0.7040 (tpt90) cc_final: 0.6779 (tpt170) REVERT: J 243 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.8751 (tmm) REVERT: J 245 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8968 (pp30) REVERT: J 369 TRP cc_start: 0.8345 (t-100) cc_final: 0.6056 (t60) outliers start: 46 outliers final: 30 residues processed: 250 average time/residue: 0.1645 time to fit residues: 68.9866 Evaluate side-chains 240 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 201 CYS Chi-restraints excluded: chain J residue 217 SER Chi-restraints excluded: chain J residue 243 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 322 optimal weight: 8.9990 chunk 213 optimal weight: 0.0050 chunk 186 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 24 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 65.7603 > 50:) chunk 226 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 245 GLN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.070779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.053683 restraints weight = 104066.229| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.92 r_work: 0.2915 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27607 Z= 0.095 Angle : 0.576 12.204 37441 Z= 0.272 Chirality : 0.042 0.167 4137 Planarity : 0.003 0.042 4811 Dihedral : 5.455 75.864 3841 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.66 % Allowed : 14.80 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.22 (0.15), residues: 3384 helix: 1.28 (0.15), residues: 1351 sheet: 0.75 (0.20), residues: 659 loop : 0.55 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 372 TYR 0.010 0.001 TYR F 362 PHE 0.009 0.001 PHE I 362 TRP 0.036 0.001 TRP J 200 HIS 0.005 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 (27607) covalent geometry : angle 0.57595 / 0.27 (37441) hydrogen bonds : bond 0.02741 / 1.88 ( 1363) hydrogen bonds : angle 4.55629 / 3.27 ( 3456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.2878 (OUTLIER) cc_final: 0.2394 (tmm) REVERT: A 180 LEU cc_start: 0.9619 (tt) cc_final: 0.9218 (tp) REVERT: A 217 CYS cc_start: 0.8035 (m) cc_final: 0.7586 (m) REVERT: A 269 MET cc_start: 0.8753 (mtp) cc_final: 0.8235 (mtp) REVERT: A 283 MET cc_start: 0.8951 (mmm) cc_final: 0.8502 (mmm) REVERT: A 305 MET cc_start: 0.9191 (mmm) cc_final: 0.8923 (mmt) REVERT: A 313 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8823 (tpp) REVERT: A 355 MET cc_start: 0.8515 (mpp) cc_final: 0.8083 (mtm) REVERT: B 72 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: B 132 MET cc_start: 0.8801 (ppp) cc_final: 0.8249 (tmm) REVERT: B 286 ASP cc_start: 0.8546 (t0) cc_final: 0.8161 (t0) REVERT: B 355 MET cc_start: 0.9002 (mtt) cc_final: 0.8697 (mtm) REVERT: C 41 GLN cc_start: 0.8257 (tp40) cc_final: 0.7971 (tm-30) REVERT: C 53 TYR cc_start: 0.7626 (m-80) cc_final: 0.7303 (m-80) REVERT: C 118 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8504 (tppp) REVERT: C 132 MET cc_start: 0.8408 (tmm) cc_final: 0.7969 (tmm) REVERT: C 190 MET cc_start: 0.9178 (mtm) cc_final: 0.8884 (mtt) REVERT: C 305 MET cc_start: 0.9216 (tpp) cc_final: 0.8741 (tpp) REVERT: C 314 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8727 (tm-30) REVERT: C 338 SER cc_start: 0.9396 (t) cc_final: 0.9120 (p) REVERT: C 360 GLN cc_start: 0.8472 (pm20) cc_final: 0.8214 (pm20) REVERT: D 107 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: D 222 ASP cc_start: 0.8728 (t0) cc_final: 0.8068 (p0) REVERT: E 140 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8396 (mm) REVERT: E 167 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8646 (tm-30) REVERT: E 227 MET cc_start: 0.8540 (tpp) cc_final: 0.8211 (tpt) REVERT: F 56 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7466 (t0) REVERT: F 83 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.9114 (pp20) REVERT: F 176 MET cc_start: 0.8682 (tpp) cc_final: 0.7850 (mpp) REVERT: F 215 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8776 (mptm) REVERT: F 276 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8916 (mt-10) REVERT: F 355 MET cc_start: 0.8305 (mtt) cc_final: 0.7609 (mtp) REVERT: F 362 TYR cc_start: 0.8148 (t80) cc_final: 0.7908 (t80) REVERT: F 373 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7719 (ttpp) REVERT: G 44 MET cc_start: 0.9023 (mmm) cc_final: 0.8560 (mmt) REVERT: G 81 ASP cc_start: 0.8876 (m-30) cc_final: 0.8548 (m-30) REVERT: G 83 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8901 (pp20) REVERT: G 226 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8085 (tp30) REVERT: G 292 ASP cc_start: 0.9101 (m-30) cc_final: 0.8682 (p0) REVERT: G 305 MET cc_start: 0.8843 (mmm) cc_final: 0.8561 (mmm) REVERT: G 325 MET cc_start: 0.8582 (mmp) cc_final: 0.8094 (tpp) REVERT: H 123 MET cc_start: 0.9281 (mmm) cc_final: 0.8829 (mmm) REVERT: H 132 MET cc_start: 0.8702 (pmm) cc_final: 0.8449 (pmm) REVERT: H 246 GLN cc_start: 0.9084 (mt0) cc_final: 0.8690 (mt0) REVERT: H 375 PHE cc_start: 0.5534 (OUTLIER) cc_final: 0.4700 (t80) REVERT: I 342 MET cc_start: 0.7320 (mpp) cc_final: 0.6762 (mpp) REVERT: J 243 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.8740 (tmm) REVERT: J 245 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8987 (pp30) REVERT: J 369 TRP cc_start: 0.8357 (t-100) cc_final: 0.5999 (t60) outliers start: 48 outliers final: 28 residues processed: 246 average time/residue: 0.1673 time to fit residues: 68.8998 Evaluate side-chains 239 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain F residue 373 LYS Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 217 SER Chi-restraints excluded: chain J residue 243 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 330 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 263 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 322 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.069075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.051877 restraints weight = 105326.765| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.87 r_work: 0.2885 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27607 Z= 0.194 Angle : 0.661 13.063 37441 Z= 0.317 Chirality : 0.045 0.247 4137 Planarity : 0.004 0.038 4811 Dihedral : 5.507 75.107 3839 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.56 % Allowed : 15.01 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.03 (0.15), residues: 3384 helix: 1.22 (0.15), residues: 1359 sheet: 0.43 (0.20), residues: 618 loop : 0.46 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.011 0.001 TYR A 91 PHE 0.012 0.001 PHE D 31 TRP 0.034 0.001 TRP J 200 HIS 0.005 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (27607) covalent geometry : angle 0.66126 / 0.32 (37441) hydrogen bonds : bond 0.03385 / 2.33 ( 1363) hydrogen bonds : angle 4.79580 / 3.45 ( 3456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.2732 (OUTLIER) cc_final: 0.2282 (tmm) REVERT: A 123 MET cc_start: 0.9211 (tpp) cc_final: 0.8885 (tpp) REVERT: A 129 VAL cc_start: 0.8909 (m) cc_final: 0.8604 (p) REVERT: A 180 LEU cc_start: 0.9633 (tt) cc_final: 0.9251 (tp) REVERT: A 217 CYS cc_start: 0.8117 (m) cc_final: 0.7684 (m) REVERT: A 269 MET cc_start: 0.8771 (mtp) cc_final: 0.8248 (mtp) REVERT: A 283 MET cc_start: 0.8985 (mmm) cc_final: 0.8713 (mmm) REVERT: A 305 MET cc_start: 0.9223 (mmm) cc_final: 0.8956 (mmt) REVERT: A 313 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.8873 (tpp) REVERT: A 355 MET cc_start: 0.8569 (mpp) cc_final: 0.8123 (mtm) REVERT: B 72 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8329 (tm-30) REVERT: B 355 MET cc_start: 0.9043 (mtt) cc_final: 0.8752 (mtm) REVERT: C 41 GLN cc_start: 0.8299 (tp40) cc_final: 0.8012 (tm-30) REVERT: C 118 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8580 (tppp) REVERT: C 132 MET cc_start: 0.8580 (tmm) cc_final: 0.8358 (tmm) REVERT: C 190 MET cc_start: 0.9134 (mtm) cc_final: 0.8849 (mtt) REVERT: C 314 GLN cc_start: 0.9256 (tm-30) cc_final: 0.8782 (tm-30) REVERT: C 325 MET cc_start: 0.8716 (mmm) cc_final: 0.8116 (mmm) REVERT: C 338 SER cc_start: 0.9424 (t) cc_final: 0.9144 (p) REVERT: D 222 ASP cc_start: 0.8784 (t0) cc_final: 0.8120 (p0) REVERT: D 283 MET cc_start: 0.8903 (mmm) cc_final: 0.8623 (mmm) REVERT: E 140 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8445 (mm) REVERT: E 167 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8641 (tm-30) REVERT: F 56 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7566 (t0) REVERT: F 83 GLU cc_start: 0.9428 (OUTLIER) cc_final: 0.9143 (pp20) REVERT: F 123 MET cc_start: 0.8975 (mmm) cc_final: 0.8581 (mmt) REVERT: F 176 MET cc_start: 0.8802 (tpp) cc_final: 0.8059 (mpp) REVERT: F 215 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8763 (mptm) REVERT: F 276 GLU cc_start: 0.9277 (mt-10) cc_final: 0.9074 (mt-10) REVERT: F 355 MET cc_start: 0.8334 (mtt) cc_final: 0.7648 (mtp) REVERT: F 373 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7780 (ttpp) REVERT: G 44 MET cc_start: 0.8871 (mmm) cc_final: 0.8467 (mmm) REVERT: G 81 ASP cc_start: 0.8928 (m-30) cc_final: 0.8625 (m-30) REVERT: G 83 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8922 (pp20) REVERT: G 292 ASP cc_start: 0.9113 (m-30) cc_final: 0.8702 (p0) REVERT: G 305 MET cc_start: 0.8854 (mmm) cc_final: 0.8566 (mmm) REVERT: G 325 MET cc_start: 0.8595 (mmp) cc_final: 0.8126 (tpp) REVERT: H 123 MET cc_start: 0.9254 (mmm) cc_final: 0.8810 (mmm) REVERT: H 132 MET cc_start: 0.8704 (pmm) cc_final: 0.8466 (pmm) REVERT: H 246 GLN cc_start: 0.9080 (mt0) cc_final: 0.8675 (mt0) REVERT: H 375 PHE cc_start: 0.4901 (OUTLIER) cc_final: 0.4123 (t80) REVERT: I 342 MET cc_start: 0.7439 (mpp) cc_final: 0.6911 (mpp) REVERT: J 168 ARG cc_start: 0.7046 (tpt90) cc_final: 0.6560 (tpm170) REVERT: J 243 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.8766 (tmm) REVERT: J 245 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8977 (pp30) REVERT: J 369 TRP cc_start: 0.8390 (t-100) cc_final: 0.6043 (t60) outliers start: 45 outliers final: 30 residues processed: 232 average time/residue: 0.1616 time to fit residues: 62.7293 Evaluate side-chains 236 residues out of total 2891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 86 TRP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 373 LYS Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 375 PHE Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain J residue 217 SER Chi-restraints excluded: chain J residue 243 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 155 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 338 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 308 optimal weight: 10.0000 chunk 158 optimal weight: 0.3980 chunk 291 optimal weight: 0.0170 chunk 156 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.070542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.053562 restraints weight = 103180.426| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.89 r_work: 0.2932 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27607 Z= 0.101 Angle : 0.608 12.818 37441 Z= 0.288 Chirality : 0.043 0.223 4137 Planarity : 0.003 0.040 4811 Dihedral : 5.376 75.556 3839 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.31 % Allowed : 15.25 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 3384 helix: 1.28 (0.15), residues: 1358 sheet: 0.55 (0.20), residues: 675 loop : 0.61 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 95 TYR 0.023 0.001 TYR F 362 PHE 0.009 0.001 PHE I 362 TRP 0.031 0.001 TRP J 200 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (27607) covalent geometry : angle 0.60808 / 0.29 (37441) hydrogen bonds : bond 0.02782 / 1.91 ( 1363) hydrogen bonds : angle 4.59635 / 3.31 ( 3456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5773.08 seconds wall clock time: 100 minutes 2.66 seconds (6002.66 seconds total)