Starting phenix.real_space_refine on Thu Sep 26 02:45:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/09_2024/8dmy_27549.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/09_2024/8dmy_27549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/09_2024/8dmy_27549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/09_2024/8dmy_27549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/09_2024/8dmy_27549.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmy_27549/09_2024/8dmy_27549.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 80 5.16 5 C 7436 2.51 5 N 1986 2.21 5 O 2282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11796 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2925 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} 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: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2925 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} 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: 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: "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} Time building chain proxies: 7.83, per 1000 atoms: 0.66 Number of scatterers: 11796 At special positions: 0 Unit cell: (78.408, 110.484, 169.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 8 15.00 Mg 4 11.99 O 2282 8.00 N 1986 7.00 C 7436 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: 2.88 Conformation dependent library (CDL) restraints added in 1.5 seconds 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2764 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 48.5% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.859A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.808A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.715A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.106A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.943A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.830A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.768A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.578A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.732A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.695A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.586A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.756A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.527A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.589A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 348 through 355 removed outlier: 6.204A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.182A 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 367 through 372 removed outlier: 3.778A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.859A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.808A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.715A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.106A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.943A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.830A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.769A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.578A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.732A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.695A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.586A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.756A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.527A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.590A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 355 removed outlier: 6.204A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.183A 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 367 through 372 removed outlier: 3.778A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.859A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.807A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.715A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.106A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.943A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.829A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.768A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.579A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.732A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.695A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.586A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.757A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.528A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.591A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 355 removed outlier: 6.204A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.778A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.859A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.808A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.714A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.106A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.943A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.830A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.768A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.578A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.731A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.695A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.587A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.756A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.527A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.590A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 348 through 355 removed outlier: 6.204A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.182A 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 removed outlier: 3.778A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 4.151A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (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 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.553A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 242 removed outlier: 4.592A pdb=" N LEU A 242 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLN A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.151A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (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 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.553A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 242 removed outlier: 4.593A pdb=" N LEU B 242 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLN B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 removed outlier: 4.150A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (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 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.553A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 242 removed outlier: 4.593A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLN C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 31 removed outlier: 4.150A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.553A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 242 removed outlier: 4.593A pdb=" N LEU D 242 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLN D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1188 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: 4.21 Time building geometry restraints manager: 3.22 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: 3660 1.34 - 1.45: 1670 1.45 - 1.57: 6570 1.57 - 1.69: 12 1.69 - 1.81: 140 Bond restraints: 12052 Sorted by residual: bond pdb=" N VAL B 45 " pdb=" CA VAL B 45 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.25e+01 bond pdb=" N VAL C 45 " pdb=" CA VAL C 45 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.22e+01 bond pdb=" N VAL D 45 " pdb=" CA VAL D 45 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.20e+01 bond pdb=" N VAL A 45 " pdb=" CA VAL A 45 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.19e+01 bond pdb=" N ILE C 71 " pdb=" CA ILE C 71 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.12e-02 7.97e+03 1.07e+01 ... (remaining 12047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 15813 1.55 - 3.10: 422 3.10 - 4.65: 95 4.65 - 6.21: 27 6.21 - 7.76: 1 Bond angle restraints: 16358 Sorted by residual: angle pdb=" N VAL A 45 " pdb=" CA VAL A 45 " pdb=" CB VAL A 45 " ideal model delta sigma weight residual 112.36 104.60 7.76 1.85e+00 2.92e-01 1.76e+01 angle pdb=" CA VAL A 45 " pdb=" C VAL A 45 " pdb=" O VAL A 45 " ideal model delta sigma weight residual 121.63 117.98 3.65 9.90e-01 1.02e+00 1.36e+01 angle pdb=" CA VAL D 45 " pdb=" C VAL D 45 " pdb=" O VAL D 45 " ideal model delta sigma weight residual 121.63 117.98 3.65 9.90e-01 1.02e+00 1.36e+01 angle pdb=" CA VAL C 45 " pdb=" C VAL C 45 " pdb=" O VAL C 45 " ideal model delta sigma weight residual 121.63 118.02 3.61 9.90e-01 1.02e+00 1.33e+01 angle pdb=" CA VAL B 45 " pdb=" C VAL B 45 " pdb=" O VAL B 45 " ideal model delta sigma weight residual 121.63 118.06 3.57 9.90e-01 1.02e+00 1.30e+01 ... (remaining 16353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 6943 35.00 - 69.99: 283 69.99 - 104.99: 12 104.99 - 139.98: 4 139.98 - 174.98: 8 Dihedral angle restraints: 7250 sinusoidal: 2932 harmonic: 4318 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 114.98 -174.98 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 114.97 -174.97 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 114.97 -174.96 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 7247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1595 0.075 - 0.150: 202 0.150 - 0.225: 13 0.225 - 0.300: 1 0.300 - 0.375: 3 Chirality restraints: 1814 Sorted by residual: chirality pdb=" CA ILE C 71 " pdb=" N ILE C 71 " pdb=" C ILE C 71 " pdb=" CB ILE C 71 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ILE A 71 " pdb=" N ILE A 71 " pdb=" C ILE A 71 " pdb=" CB ILE A 71 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 1811 not shown) Planarity restraints: 2096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 70 " 0.020 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C PRO D 70 " -0.067 2.00e-02 2.50e+03 pdb=" O PRO D 70 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE D 71 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 111 " -0.033 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO D 112 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 112 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 112 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 111 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO C 112 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " -0.028 5.00e-02 4.00e+02 ... (remaining 2093 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 4368 2.88 - 3.39: 9838 3.39 - 3.89: 17453 3.89 - 4.40: 20097 4.40 - 4.90: 36152 Nonbonded interactions: 87908 Sorted by model distance: nonbonded pdb=" O ALA D 174 " pdb=" OG SER D 281 " model vdw 2.379 3.040 nonbonded pdb=" O ALA A 174 " pdb=" OG SER A 281 " model vdw 2.380 3.040 nonbonded pdb=" O ALA B 174 " pdb=" OG SER B 281 " model vdw 2.380 3.040 nonbonded pdb=" O ALA C 174 " pdb=" OG SER C 281 " model vdw 2.381 3.040 nonbonded pdb=" NH1 ARG B 210 " pdb=" OE2 GLU B 214 " model vdw 2.412 3.120 ... (remaining 87903 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' and (resid 3 through 375 or resid 401 through 402)) selection = (chain 'B' and (resid 3 through 375 or resid 401 through 402)) selection = chain 'C' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.240 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12052 Z= 0.242 Angle : 0.622 7.757 16358 Z= 0.353 Chirality : 0.049 0.375 1814 Planarity : 0.004 0.051 2096 Dihedral : 18.681 174.978 4486 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.63 % Allowed : 21.71 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1474 helix: -1.77 (0.20), residues: 528 sheet: 0.76 (0.30), residues: 268 loop : -0.52 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 356 HIS 0.003 0.001 HIS A 101 PHE 0.004 0.001 PHE B 31 TYR 0.006 0.001 TYR D 306 ARG 0.002 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 202 time to evaluate : 1.382 Fit side-chains REVERT: A 224 GLU cc_start: 0.7798 (mm-30) cc_final: 0.6732 (mp0) REVERT: B 95 ARG cc_start: 0.6816 (mtm110) cc_final: 0.6327 (mtt90) REVERT: B 211 ASP cc_start: 0.8154 (t0) cc_final: 0.7849 (t0) REVERT: B 326 LYS cc_start: 0.8294 (mttp) cc_final: 0.7513 (tttm) REVERT: C 51 ASP cc_start: 0.7386 (p0) cc_final: 0.6942 (t0) REVERT: C 80 ASP cc_start: 0.8122 (m-30) cc_final: 0.7770 (m-30) REVERT: C 95 ARG cc_start: 0.6814 (mtm110) cc_final: 0.6552 (mtm-85) REVERT: C 132 MET cc_start: 0.9013 (ptm) cc_final: 0.8783 (ptm) REVERT: C 211 ASP cc_start: 0.8289 (t0) cc_final: 0.7916 (t0) REVERT: C 326 LYS cc_start: 0.8043 (mttp) cc_final: 0.7675 (mmtt) REVERT: C 372 ARG cc_start: 0.6742 (ttm170) cc_final: 0.6208 (mtm180) REVERT: D 95 ARG cc_start: 0.7151 (mtm110) cc_final: 0.6649 (mtp-110) REVERT: D 358 SER cc_start: 0.8685 (m) cc_final: 0.8414 (t) outliers start: 8 outliers final: 1 residues processed: 206 average time/residue: 0.2416 time to fit residues: 70.1086 Evaluate side-chains 150 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 101 HIS A 121 GLN A 275 HIS A 371 HIS B 12 ASN B 101 HIS B 121 GLN B 275 HIS C 12 ASN C 101 HIS C 121 GLN C 275 HIS C 371 HIS D 12 ASN D 101 HIS D 121 GLN D 275 HIS D 353 GLN D 371 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12052 Z= 0.307 Angle : 0.652 6.053 16358 Z= 0.331 Chirality : 0.050 0.143 1814 Planarity : 0.006 0.054 2096 Dihedral : 13.832 177.541 1680 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.96 % Allowed : 19.81 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1474 helix: -0.88 (0.22), residues: 560 sheet: 0.81 (0.30), residues: 288 loop : -0.88 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 356 HIS 0.005 0.001 HIS A 275 PHE 0.009 0.001 PHE A 255 TYR 0.011 0.001 TYR C 69 ARG 0.004 0.001 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 147 time to evaluate : 1.360 Fit side-chains REVERT: A 305 MET cc_start: 0.8789 (mtp) cc_final: 0.8357 (mtp) REVERT: B 65 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7760 (pp) REVERT: B 82 MET cc_start: 0.8784 (tpt) cc_final: 0.8371 (tpt) REVERT: B 95 ARG cc_start: 0.7062 (mtm110) cc_final: 0.6643 (mtt90) REVERT: B 211 ASP cc_start: 0.7918 (t0) cc_final: 0.7696 (t0) REVERT: B 326 LYS cc_start: 0.8280 (mttp) cc_final: 0.7502 (tttm) REVERT: B 372 ARG cc_start: 0.7465 (mmm-85) cc_final: 0.7132 (mtm180) REVERT: C 51 ASP cc_start: 0.7558 (p0) cc_final: 0.6990 (t0) REVERT: C 80 ASP cc_start: 0.8011 (m-30) cc_final: 0.7710 (m-30) REVERT: C 95 ARG cc_start: 0.7212 (mtm110) cc_final: 0.6979 (mtm-85) REVERT: C 211 ASP cc_start: 0.8103 (t0) cc_final: 0.7693 (t0) REVERT: C 326 LYS cc_start: 0.8202 (mttp) cc_final: 0.7449 (mmtm) REVERT: C 372 ARG cc_start: 0.6616 (ttm170) cc_final: 0.6298 (ttm170) REVERT: D 95 ARG cc_start: 0.7319 (mtm110) cc_final: 0.6984 (mtm110) REVERT: D 358 SER cc_start: 0.8492 (m) cc_final: 0.8239 (t) outliers start: 50 outliers final: 34 residues processed: 181 average time/residue: 0.2285 time to fit residues: 60.0084 Evaluate side-chains 167 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 145 optimal weight: 0.0470 chunk 119 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12052 Z= 0.429 Angle : 0.704 6.855 16358 Z= 0.355 Chirality : 0.053 0.153 1814 Planarity : 0.006 0.055 2096 Dihedral : 12.772 172.795 1678 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.07 % Allowed : 19.73 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1474 helix: -0.69 (0.22), residues: 566 sheet: -0.07 (0.28), residues: 292 loop : -0.95 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 356 HIS 0.006 0.002 HIS D 161 PHE 0.013 0.002 PHE B 90 TYR 0.013 0.002 TYR B 69 ARG 0.005 0.001 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 134 time to evaluate : 1.314 Fit side-chains REVERT: B 65 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7895 (pp) REVERT: B 95 ARG cc_start: 0.7132 (mtm110) cc_final: 0.6825 (mtt90) REVERT: B 123 MET cc_start: 0.8686 (mmt) cc_final: 0.8221 (mmm) REVERT: B 284 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8117 (mttm) REVERT: B 326 LYS cc_start: 0.8325 (mttp) cc_final: 0.7530 (tttm) REVERT: B 328 LYS cc_start: 0.8338 (ptpp) cc_final: 0.7980 (ptmt) REVERT: C 51 ASP cc_start: 0.7783 (p0) cc_final: 0.7115 (t0) REVERT: C 80 ASP cc_start: 0.8212 (m-30) cc_final: 0.7935 (m-30) REVERT: C 93 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: C 95 ARG cc_start: 0.7201 (mtm110) cc_final: 0.6941 (mtm-85) REVERT: C 211 ASP cc_start: 0.8077 (t0) cc_final: 0.7652 (t0) REVERT: D 95 ARG cc_start: 0.7351 (mtm110) cc_final: 0.6981 (mtm180) REVERT: D 334 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6842 (pm20) REVERT: D 358 SER cc_start: 0.8547 (m) cc_final: 0.8292 (t) outliers start: 64 outliers final: 44 residues processed: 186 average time/residue: 0.2287 time to fit residues: 62.0072 Evaluate side-chains 173 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 125 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 143 optimal weight: 0.0370 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12052 Z= 0.337 Angle : 0.643 6.568 16358 Z= 0.320 Chirality : 0.050 0.147 1814 Planarity : 0.005 0.055 2096 Dihedral : 12.274 174.472 1678 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.07 % Allowed : 20.36 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1474 helix: -0.36 (0.23), residues: 556 sheet: -0.18 (0.28), residues: 292 loop : -0.81 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 356 HIS 0.005 0.001 HIS D 161 PHE 0.010 0.001 PHE B 90 TYR 0.009 0.001 TYR C 69 ARG 0.003 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 129 time to evaluate : 1.911 Fit side-chains REVERT: B 65 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7908 (pp) REVERT: B 95 ARG cc_start: 0.7131 (mtm110) cc_final: 0.6801 (mtt90) REVERT: B 326 LYS cc_start: 0.8301 (mttp) cc_final: 0.7531 (tttm) REVERT: B 328 LYS cc_start: 0.8337 (ptpp) cc_final: 0.7980 (ptmt) REVERT: B 372 ARG cc_start: 0.7531 (mmm-85) cc_final: 0.7266 (mtm180) REVERT: C 51 ASP cc_start: 0.7781 (p0) cc_final: 0.7113 (t0) REVERT: C 93 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: C 95 ARG cc_start: 0.7181 (mtm110) cc_final: 0.6970 (mtm-85) REVERT: C 211 ASP cc_start: 0.8060 (t0) cc_final: 0.7684 (t0) REVERT: D 95 ARG cc_start: 0.7305 (mtm110) cc_final: 0.6966 (mtm180) REVERT: D 334 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6849 (pm20) outliers start: 64 outliers final: 45 residues processed: 180 average time/residue: 0.2384 time to fit residues: 61.9289 Evaluate side-chains 173 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 125 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 106 optimal weight: 0.0970 chunk 59 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12052 Z= 0.182 Angle : 0.560 6.880 16358 Z= 0.273 Chirality : 0.046 0.135 1814 Planarity : 0.005 0.056 2096 Dihedral : 11.281 178.613 1678 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.36 % Allowed : 21.00 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1474 helix: 0.10 (0.24), residues: 548 sheet: -0.04 (0.28), residues: 292 loop : -0.63 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 79 HIS 0.004 0.001 HIS D 161 PHE 0.008 0.001 PHE D 31 TYR 0.008 0.001 TYR A 306 ARG 0.003 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 128 time to evaluate : 1.445 Fit side-chains REVERT: A 34 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.7959 (pt) REVERT: A 128 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7489 (t0) REVERT: B 95 ARG cc_start: 0.7143 (mtm110) cc_final: 0.6805 (mtt90) REVERT: B 284 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8002 (mttm) REVERT: B 326 LYS cc_start: 0.8303 (mttp) cc_final: 0.7499 (tttm) REVERT: B 328 LYS cc_start: 0.8347 (ptpp) cc_final: 0.8002 (ptmm) REVERT: C 51 ASP cc_start: 0.7687 (p0) cc_final: 0.7004 (t0) REVERT: C 93 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8270 (mt-10) REVERT: C 95 ARG cc_start: 0.7141 (mtm110) cc_final: 0.6933 (mtm-85) REVERT: C 211 ASP cc_start: 0.8072 (t0) cc_final: 0.7659 (t0) REVERT: D 34 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.7982 (pt) REVERT: D 95 ARG cc_start: 0.7303 (mtm110) cc_final: 0.6961 (mtm180) REVERT: D 334 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6810 (pm20) outliers start: 55 outliers final: 34 residues processed: 171 average time/residue: 0.2324 time to fit residues: 57.2800 Evaluate side-chains 164 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 124 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.1980 chunk 128 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12052 Z= 0.282 Angle : 0.611 7.025 16358 Z= 0.299 Chirality : 0.048 0.143 1814 Planarity : 0.005 0.054 2096 Dihedral : 10.795 178.262 1678 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.36 % Allowed : 20.76 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.22), residues: 1474 helix: 0.10 (0.24), residues: 548 sheet: -0.03 (0.29), residues: 294 loop : -0.75 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 356 HIS 0.005 0.001 HIS D 161 PHE 0.010 0.001 PHE A 223 TYR 0.008 0.001 TYR C 69 ARG 0.002 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 127 time to evaluate : 1.539 Fit side-chains REVERT: A 128 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7548 (t0) REVERT: B 95 ARG cc_start: 0.7125 (mtm110) cc_final: 0.6802 (mtt90) REVERT: B 284 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8019 (mttm) REVERT: B 326 LYS cc_start: 0.8304 (mttp) cc_final: 0.7607 (tttm) REVERT: B 328 LYS cc_start: 0.8314 (ptpp) cc_final: 0.7944 (ptmt) REVERT: C 51 ASP cc_start: 0.7762 (p0) cc_final: 0.7043 (t0) REVERT: C 93 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: C 95 ARG cc_start: 0.7193 (mtm110) cc_final: 0.6985 (mtm-85) REVERT: C 211 ASP cc_start: 0.8101 (t0) cc_final: 0.7736 (t0) REVERT: D 95 ARG cc_start: 0.7337 (mtm110) cc_final: 0.6981 (mtm180) REVERT: D 334 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6840 (pm20) outliers start: 55 outliers final: 46 residues processed: 171 average time/residue: 0.2358 time to fit residues: 58.3564 Evaluate side-chains 178 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 128 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12052 Z= 0.233 Angle : 0.577 6.806 16358 Z= 0.283 Chirality : 0.047 0.139 1814 Planarity : 0.005 0.055 2096 Dihedral : 9.301 178.281 1678 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.91 % Allowed : 20.21 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.22), residues: 1474 helix: 0.20 (0.24), residues: 548 sheet: -0.04 (0.28), residues: 292 loop : -0.67 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 356 HIS 0.004 0.001 HIS D 161 PHE 0.008 0.001 PHE A 223 TYR 0.007 0.001 TYR A 306 ARG 0.002 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 134 time to evaluate : 1.339 Fit side-chains REVERT: A 34 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.7945 (pt) REVERT: A 128 ASN cc_start: 0.7961 (OUTLIER) cc_final: 0.7543 (t0) REVERT: B 95 ARG cc_start: 0.7177 (mtm110) cc_final: 0.6847 (mtt90) REVERT: B 222 ASP cc_start: 0.7586 (t0) cc_final: 0.6885 (t0) REVERT: B 284 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7984 (mttm) REVERT: B 326 LYS cc_start: 0.8280 (mttp) cc_final: 0.7674 (tttm) REVERT: B 328 LYS cc_start: 0.8314 (ptpp) cc_final: 0.7959 (ptmm) REVERT: C 93 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8297 (mt-10) REVERT: C 107 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7300 (tp30) REVERT: C 211 ASP cc_start: 0.8087 (t0) cc_final: 0.7689 (t0) REVERT: D 34 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.7945 (pt) REVERT: D 95 ARG cc_start: 0.7331 (mtm110) cc_final: 0.7118 (mtm110) REVERT: D 334 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6860 (pm20) outliers start: 62 outliers final: 48 residues processed: 183 average time/residue: 0.2317 time to fit residues: 61.3536 Evaluate side-chains 188 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 133 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 93 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.0570 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12052 Z= 0.141 Angle : 0.532 6.277 16358 Z= 0.256 Chirality : 0.044 0.137 1814 Planarity : 0.004 0.056 2096 Dihedral : 7.290 139.905 1678 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.25 % Allowed : 22.42 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1474 helix: 0.50 (0.25), residues: 538 sheet: 0.25 (0.28), residues: 296 loop : -0.57 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 79 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE D 31 TYR 0.008 0.001 TYR A 306 ARG 0.003 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.270 Fit side-chains REVERT: A 93 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: A 128 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7435 (t0) REVERT: B 95 ARG cc_start: 0.7145 (mtm110) cc_final: 0.6834 (mtt90) REVERT: B 222 ASP cc_start: 0.7560 (t0) cc_final: 0.6845 (t0) REVERT: B 284 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7837 (mttm) REVERT: B 326 LYS cc_start: 0.8246 (mttp) cc_final: 0.7655 (tttm) REVERT: C 211 ASP cc_start: 0.7977 (t0) cc_final: 0.7585 (t0) REVERT: D 34 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.7935 (pt) REVERT: D 95 ARG cc_start: 0.7317 (mtm110) cc_final: 0.7104 (mtm110) REVERT: D 125 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7496 (mt-10) REVERT: D 334 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6882 (pm20) outliers start: 41 outliers final: 28 residues processed: 171 average time/residue: 0.2349 time to fit residues: 58.3399 Evaluate side-chains 169 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12052 Z= 0.149 Angle : 0.540 6.094 16358 Z= 0.259 Chirality : 0.045 0.139 1814 Planarity : 0.004 0.056 2096 Dihedral : 6.800 117.646 1678 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.93 % Allowed : 22.35 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1474 helix: 0.57 (0.25), residues: 540 sheet: 0.30 (0.28), residues: 296 loop : -0.49 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 79 HIS 0.003 0.001 HIS D 161 PHE 0.007 0.001 PHE C 31 TYR 0.008 0.001 TYR A 306 ARG 0.005 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 1.456 Fit side-chains REVERT: A 93 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: A 128 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7409 (t0) REVERT: B 95 ARG cc_start: 0.7139 (mtm110) cc_final: 0.6815 (mtt90) REVERT: B 222 ASP cc_start: 0.7592 (t0) cc_final: 0.6940 (t0) REVERT: B 284 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7829 (mttm) REVERT: B 294 TYR cc_start: 0.8763 (m-80) cc_final: 0.8523 (m-80) REVERT: B 326 LYS cc_start: 0.8257 (mttp) cc_final: 0.7670 (tttm) REVERT: B 328 LYS cc_start: 0.8266 (ptpp) cc_final: 0.7912 (ptmt) REVERT: C 211 ASP cc_start: 0.7986 (t0) cc_final: 0.7593 (t0) REVERT: D 34 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.7918 (pt) REVERT: D 95 ARG cc_start: 0.7332 (mtm110) cc_final: 0.7110 (mtm110) REVERT: D 125 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7437 (mt-10) REVERT: D 334 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6902 (pm20) outliers start: 37 outliers final: 30 residues processed: 164 average time/residue: 0.2353 time to fit residues: 56.3706 Evaluate side-chains 172 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12052 Z= 0.340 Angle : 0.648 6.377 16358 Z= 0.318 Chirality : 0.050 0.153 1814 Planarity : 0.005 0.055 2096 Dihedral : 7.095 117.022 1678 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.57 % Allowed : 21.71 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1474 helix: 0.19 (0.24), residues: 548 sheet: 0.16 (0.29), residues: 290 loop : -0.76 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 79 HIS 0.006 0.001 HIS D 161 PHE 0.013 0.001 PHE D 223 TYR 0.010 0.001 TYR C 143 ARG 0.006 0.001 ARG A 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2948 Ramachandran restraints generated. 1474 Oldfield, 0 Emsley, 1474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 133 time to evaluate : 1.463 Fit side-chains REVERT: A 128 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7536 (t0) REVERT: B 95 ARG cc_start: 0.7187 (mtm110) cc_final: 0.6847 (mtt90) REVERT: B 222 ASP cc_start: 0.7555 (t0) cc_final: 0.6848 (t0) REVERT: B 284 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8030 (mttm) REVERT: B 326 LYS cc_start: 0.8274 (mttp) cc_final: 0.7686 (tttm) REVERT: B 328 LYS cc_start: 0.8331 (ptpp) cc_final: 0.7958 (ptmt) REVERT: C 107 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: C 211 ASP cc_start: 0.8100 (t0) cc_final: 0.7707 (t0) REVERT: D 95 ARG cc_start: 0.7418 (mtm110) cc_final: 0.7186 (mtm110) REVERT: D 334 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6949 (pm20) outliers start: 45 outliers final: 35 residues processed: 163 average time/residue: 0.2314 time to fit residues: 54.7265 Evaluate side-chains 172 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.1980 chunk 108 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108359 restraints weight = 14826.005| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.77 r_work: 0.3159 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12052 Z= 0.155 Angle : 0.555 6.238 16358 Z= 0.268 Chirality : 0.045 0.140 1814 Planarity : 0.005 0.055 2096 Dihedral : 6.652 106.582 1678 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.69 % Allowed : 22.50 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1474 helix: 0.50 (0.24), residues: 538 sheet: 0.23 (0.29), residues: 284 loop : -0.59 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.004 0.001 HIS D 161 PHE 0.009 0.001 PHE C 31 TYR 0.008 0.001 TYR A 306 ARG 0.004 0.000 ARG A 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2433.53 seconds wall clock time: 45 minutes 33.89 seconds (2733.89 seconds total)