Starting phenix.real_space_refine on Wed Jul 30 02:34:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmy_27549/07_2025/8dmy_27549.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmy_27549/07_2025/8dmy_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/cci-nas-00/data/ceres_data/8dmy_27549/07_2025/8dmy_27549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmy_27549/07_2025/8dmy_27549.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmy_27549/07_2025/8dmy_27549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmy_27549/07_2025/8dmy_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-5711/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: 8.10, per 1000 atoms: 0.69 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: 2.74 Conformation dependent library (CDL) restraints added in 1.6 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: 1.60 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: 4.31 Time building geometry restraints manager: 3.31 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: 0.03 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.430 Find NCS groups from input model: 0.640 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: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- 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 Details of bonding type rmsd hydrogen bonds : bond 0.34375 ( 476) hydrogen bonds : angle 7.92257 ( 1188) covalent geometry : bond 0.00359 (12052) covalent geometry : angle 0.62157 (16358) *********************** 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 to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 1.434 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: 0.2666 time to fit residues: 77.3681 Evaluate side-chains 150 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107539 restraints weight = 14990.909| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.80 r_work: 0.3130 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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= 0.189 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 Details of bonding type rmsd hydrogen bonds : bond 0.06258 ( 476) hydrogen bonds : angle 5.11703 ( 1188) covalent geometry : bond 0.00465 (12052) covalent geometry : angle 0.65239 (16358) *********************** 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 to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 1.382 Fit side-chains REVERT: A 305 MET cc_start: 0.9080 (mtp) cc_final: 0.8675 (mtp) REVERT: B 65 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8386 (pp) REVERT: B 82 MET cc_start: 0.9037 (tpt) cc_final: 0.8617 (tpt) REVERT: B 95 ARG cc_start: 0.7519 (mtm110) cc_final: 0.7115 (mtt90) REVERT: B 326 LYS cc_start: 0.8254 (mttp) cc_final: 0.7371 (tttm) REVERT: B 372 ARG cc_start: 0.7353 (mmm-85) cc_final: 0.7049 (mtm180) REVERT: C 51 ASP cc_start: 0.7671 (p0) cc_final: 0.7228 (t0) REVERT: C 80 ASP cc_start: 0.8370 (m-30) cc_final: 0.8168 (m-30) REVERT: C 211 ASP cc_start: 0.8670 (t0) cc_final: 0.8321 (t0) REVERT: C 326 LYS cc_start: 0.8354 (mttp) cc_final: 0.7786 (mmtm) REVERT: C 372 ARG cc_start: 0.6977 (ttm170) cc_final: 0.6685 (ttm170) REVERT: D 95 ARG cc_start: 0.7534 (mtm110) cc_final: 0.7275 (mtm110) outliers start: 50 outliers final: 34 residues processed: 181 average time/residue: 0.2185 time to fit residues: 57.7971 Evaluate side-chains 165 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 46 optimal weight: 8.9990 chunk 132 optimal weight: 0.0060 chunk 143 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 106 optimal weight: 0.0040 overall best weight: 0.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS B 12 ASN C 371 HIS D 121 GLN D 371 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112794 restraints weight = 15177.060| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.77 r_work: 0.3215 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12052 Z= 0.093 Angle : 0.533 6.140 16358 Z= 0.260 Chirality : 0.044 0.134 1814 Planarity : 0.004 0.053 2096 Dihedral : 12.778 179.412 1678 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.90 % Allowed : 22.50 % Favored : 75.59 % 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: -0.17 (0.22), residues: 1474 helix: 0.16 (0.24), residues: 536 sheet: 0.70 (0.29), residues: 296 loop : -0.64 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 356 HIS 0.002 0.001 HIS D 161 PHE 0.007 0.001 PHE B 375 TYR 0.006 0.001 TYR A 306 ARG 0.003 0.000 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 476) hydrogen bonds : angle 4.57809 ( 1188) covalent geometry : bond 0.00198 (12052) covalent geometry : angle 0.53257 (16358) *********************** 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 169 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 1.279 Fit side-chains REVERT: B 95 ARG cc_start: 0.7551 (mtm110) cc_final: 0.7091 (mtt90) REVERT: B 326 LYS cc_start: 0.8276 (mttp) cc_final: 0.7414 (tttm) REVERT: C 51 ASP cc_start: 0.7523 (p0) cc_final: 0.7151 (t0) REVERT: C 93 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: C 211 ASP cc_start: 0.8592 (t0) cc_final: 0.8252 (t0) REVERT: C 326 LYS cc_start: 0.8341 (mttp) cc_final: 0.7801 (mmtm) REVERT: C 372 ARG cc_start: 0.6896 (ttm170) cc_final: 0.6498 (ttm170) REVERT: D 34 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.7815 (pt) REVERT: D 95 ARG cc_start: 0.7535 (mtm110) cc_final: 0.7308 (mtm110) outliers start: 24 outliers final: 14 residues processed: 161 average time/residue: 0.2324 time to fit residues: 54.3979 Evaluate side-chains 149 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 93 GLU 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 160 THR Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 215 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 0 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 134 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.113737 restraints weight = 15012.143| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.80 r_work: 0.3228 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12052 Z= 0.090 Angle : 0.518 7.382 16358 Z= 0.248 Chirality : 0.044 0.135 1814 Planarity : 0.004 0.050 2096 Dihedral : 10.857 169.194 1678 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.46 % Allowed : 22.19 % Favored : 75.36 % 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: 0.11 (0.22), residues: 1474 helix: 0.56 (0.25), residues: 536 sheet: 0.61 (0.29), residues: 296 loop : -0.50 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 79 HIS 0.002 0.001 HIS D 161 PHE 0.007 0.001 PHE B 375 TYR 0.007 0.001 TYR B 69 ARG 0.003 0.000 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.03108 ( 476) hydrogen bonds : angle 4.29239 ( 1188) covalent geometry : bond 0.00198 (12052) covalent geometry : angle 0.51791 (16358) *********************** 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 181 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 1.372 Fit side-chains REVERT: A 34 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8056 (pt) REVERT: B 65 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8492 (pp) REVERT: B 95 ARG cc_start: 0.7504 (mtm110) cc_final: 0.7047 (mtt90) REVERT: B 176 MET cc_start: 0.8594 (mmt) cc_final: 0.8386 (mmm) REVERT: B 326 LYS cc_start: 0.8257 (mttp) cc_final: 0.7364 (tttm) REVERT: B 372 ARG cc_start: 0.7436 (mmm-85) cc_final: 0.6952 (mtp180) REVERT: C 51 ASP cc_start: 0.7595 (p0) cc_final: 0.7184 (t0) REVERT: C 211 ASP cc_start: 0.8552 (t0) cc_final: 0.8214 (t0) REVERT: C 326 LYS cc_start: 0.8342 (mttp) cc_final: 0.7785 (mmtm) REVERT: D 12 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7703 (m110) REVERT: D 34 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.7822 (pt) REVERT: D 95 ARG cc_start: 0.7509 (mtm110) cc_final: 0.7284 (mtm110) REVERT: D 334 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6909 (pm20) outliers start: 31 outliers final: 17 residues processed: 173 average time/residue: 0.2393 time to fit residues: 59.8520 Evaluate side-chains 160 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 151 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 287 ILE 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 178 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 34 ILE 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 334 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 126 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS B 12 ASN C 371 HIS D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107156 restraints weight = 14999.211| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.78 r_work: 0.3139 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12052 Z= 0.153 Angle : 0.590 6.918 16358 Z= 0.289 Chirality : 0.048 0.141 1814 Planarity : 0.005 0.052 2096 Dihedral : 10.637 178.137 1678 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.33 % Allowed : 21.32 % Favored : 75.36 % 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: -0.07 (0.22), residues: 1474 helix: 0.41 (0.24), residues: 538 sheet: 0.46 (0.28), residues: 296 loop : -0.58 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 79 HIS 0.004 0.001 HIS D 161 PHE 0.010 0.001 PHE A 223 TYR 0.023 0.001 TYR B 294 ARG 0.003 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 476) hydrogen bonds : angle 4.41796 ( 1188) covalent geometry : bond 0.00379 (12052) covalent geometry : angle 0.59042 (16358) *********************** 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 176 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 1.439 Fit side-chains REVERT: A 34 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8146 (pt) REVERT: B 65 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8461 (pp) REVERT: B 95 ARG cc_start: 0.7589 (mtm110) cc_final: 0.7236 (mtt90) REVERT: B 326 LYS cc_start: 0.8274 (mttp) cc_final: 0.7395 (tttm) REVERT: C 51 ASP cc_start: 0.7801 (p0) cc_final: 0.7294 (t0) REVERT: C 211 ASP cc_start: 0.8667 (t0) cc_final: 0.8423 (t0) REVERT: D 179 ASP cc_start: 0.7059 (m-30) cc_final: 0.6772 (m-30) REVERT: D 334 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: D 372 ARG cc_start: 0.7349 (ttm170) cc_final: 0.6891 (ttm-80) outliers start: 42 outliers final: 30 residues processed: 165 average time/residue: 0.2306 time to fit residues: 56.1516 Evaluate side-chains 164 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 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 96 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 247 VAL 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 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 178 LEU Chi-restraints excluded: chain C residue 250 ILE 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 151 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 199 SER 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 50 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 chunk 116 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 69 optimal weight: 0.0370 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN C 371 HIS D 12 ASN D 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.127404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107690 restraints weight = 15185.579| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.91 r_work: 0.3140 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12052 Z= 0.123 Angle : 0.552 6.425 16358 Z= 0.269 Chirality : 0.046 0.135 1814 Planarity : 0.004 0.052 2096 Dihedral : 9.951 173.911 1678 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.25 % Allowed : 21.55 % 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: 0.00 (0.22), residues: 1474 helix: 0.49 (0.24), residues: 538 sheet: 0.42 (0.28), residues: 296 loop : -0.51 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 79 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE C 31 TYR 0.014 0.001 TYR B 294 ARG 0.002 0.000 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 476) hydrogen bonds : angle 4.32113 ( 1188) covalent geometry : bond 0.00299 (12052) covalent geometry : angle 0.55219 (16358) *********************** 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 176 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 1.407 Fit side-chains REVERT: A 34 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8136 (pt) REVERT: B 65 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8456 (pp) REVERT: B 95 ARG cc_start: 0.7573 (mtm110) cc_final: 0.7209 (mtt90) REVERT: B 326 LYS cc_start: 0.8284 (mttp) cc_final: 0.7369 (tttm) REVERT: C 51 ASP cc_start: 0.7818 (p0) cc_final: 0.7264 (t0) REVERT: C 211 ASP cc_start: 0.8664 (t0) cc_final: 0.8307 (t0) REVERT: D 34 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.7937 (pt) REVERT: D 179 ASP cc_start: 0.7196 (m-30) cc_final: 0.6928 (m-30) REVERT: D 334 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6960 (pm20) outliers start: 41 outliers final: 34 residues processed: 165 average time/residue: 0.2235 time to fit residues: 54.4389 Evaluate side-chains 171 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 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 269 MET 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 178 LEU 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 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 250 ILE 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 65 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 288 ASP 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 32 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN C 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104144 restraints weight = 15378.857| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.91 r_work: 0.3095 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12052 Z= 0.202 Angle : 0.630 6.290 16358 Z= 0.313 Chirality : 0.050 0.146 1814 Planarity : 0.005 0.053 2096 Dihedral : 9.314 176.628 1678 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.20 % Allowed : 20.76 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1474 helix: 0.28 (0.24), residues: 536 sheet: 0.21 (0.28), residues: 290 loop : -0.64 (0.25), residues: 648 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 0.011 0.001 PHE A 223 TYR 0.014 0.001 TYR B 294 ARG 0.003 0.001 ARG A 254 Details of bonding type rmsd hydrogen bonds : bond 0.05211 ( 476) hydrogen bonds : angle 4.51617 ( 1188) covalent geometry : bond 0.00516 (12052) covalent geometry : angle 0.63023 (16358) *********************** 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 180 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 1.672 Fit side-chains REVERT: B 65 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8466 (pp) REVERT: B 95 ARG cc_start: 0.7595 (mtm110) cc_final: 0.7267 (mtt90) REVERT: B 284 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8043 (mttm) REVERT: B 326 LYS cc_start: 0.8290 (mttp) cc_final: 0.7394 (tttm) REVERT: B 328 LYS cc_start: 0.8289 (ptpp) cc_final: 0.7898 (ptmm) REVERT: C 51 ASP cc_start: 0.7886 (p0) cc_final: 0.7259 (t0) REVERT: C 211 ASP cc_start: 0.8703 (t0) cc_final: 0.8451 (t0) REVERT: D 179 ASP cc_start: 0.7384 (m-30) cc_final: 0.7158 (m-30) REVERT: D 334 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6997 (pm20) outliers start: 53 outliers final: 42 residues processed: 167 average time/residue: 0.2372 time to fit residues: 57.9880 Evaluate side-chains 169 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 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 65 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 178 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 201 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 250 ILE 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 65 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 288 ASP 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 29 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN C 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106391 restraints weight = 15168.853| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.90 r_work: 0.3127 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12052 Z= 0.139 Angle : 0.575 6.500 16358 Z= 0.281 Chirality : 0.047 0.138 1814 Planarity : 0.005 0.054 2096 Dihedral : 8.067 156.150 1678 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.80 % Allowed : 21.47 % 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: -0.17 (0.22), residues: 1474 helix: 0.40 (0.24), residues: 536 sheet: 0.20 (0.28), residues: 288 loop : -0.58 (0.24), residues: 650 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 C 31 TYR 0.013 0.001 TYR B 294 ARG 0.002 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 476) hydrogen bonds : angle 4.40313 ( 1188) covalent geometry : bond 0.00346 (12052) covalent geometry : angle 0.57530 (16358) *********************** 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 181 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 1.407 Fit side-chains REVERT: A 34 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8149 (pt) REVERT: B 65 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8505 (pp) REVERT: B 95 ARG cc_start: 0.7559 (mtm110) cc_final: 0.7204 (mtt90) REVERT: B 284 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7954 (mttm) REVERT: B 326 LYS cc_start: 0.8251 (mttp) cc_final: 0.7464 (tttm) REVERT: C 51 ASP cc_start: 0.7843 (p0) cc_final: 0.7226 (t0) REVERT: C 211 ASP cc_start: 0.8673 (t0) cc_final: 0.8415 (t0) REVERT: D 334 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6958 (pm20) outliers start: 48 outliers final: 39 residues processed: 167 average time/residue: 0.2312 time to fit residues: 56.5618 Evaluate side-chains 174 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 49 GLN 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 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 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 178 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 178 LEU Chi-restraints excluded: chain C residue 250 ILE 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 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 96 VAL 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 325 MET 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 30 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 134 optimal weight: 8.9990 chunk 76 optimal weight: 0.0060 chunk 92 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 overall best weight: 2.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN C 371 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104476 restraints weight = 15317.625| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.78 r_work: 0.3107 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2840 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= 0.196 Angle : 0.637 6.548 16358 Z= 0.314 Chirality : 0.049 0.147 1814 Planarity : 0.005 0.054 2096 Dihedral : 7.627 140.648 1678 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.20 % Allowed : 21.08 % 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: -0.37 (0.22), residues: 1474 helix: 0.23 (0.24), residues: 536 sheet: 0.17 (0.29), residues: 290 loop : -0.74 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 79 HIS 0.005 0.001 HIS D 161 PHE 0.011 0.001 PHE A 223 TYR 0.013 0.001 TYR B 294 ARG 0.003 0.000 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.05115 ( 476) hydrogen bonds : angle 4.51799 ( 1188) covalent geometry : bond 0.00501 (12052) covalent geometry : angle 0.63674 (16358) *********************** 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 178 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 1.298 Fit side-chains REVERT: B 65 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8431 (pp) REVERT: B 95 ARG cc_start: 0.7522 (mtm110) cc_final: 0.7199 (mtt90) REVERT: B 222 ASP cc_start: 0.7664 (t0) cc_final: 0.7050 (t0) REVERT: B 284 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8001 (mttm) REVERT: B 326 LYS cc_start: 0.8244 (mttp) cc_final: 0.7456 (tttm) REVERT: B 328 LYS cc_start: 0.8263 (ptpp) cc_final: 0.7866 (ptmm) REVERT: C 51 ASP cc_start: 0.7869 (p0) cc_final: 0.7243 (t0) REVERT: C 211 ASP cc_start: 0.8619 (t0) cc_final: 0.8349 (t0) REVERT: D 334 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6927 (pm20) outliers start: 53 outliers final: 47 residues processed: 166 average time/residue: 0.2335 time to fit residues: 56.5424 Evaluate side-chains 173 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 49 GLN 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 100 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 190 MET 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 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 6 THR 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 178 LEU 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 288 ASP Chi-restraints excluded: chain C residue 293 LEU 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 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 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 3 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 23 optimal weight: 0.0570 chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108164 restraints weight = 14930.372| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.88 r_work: 0.3149 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12052 Z= 0.106 Angle : 0.555 6.194 16358 Z= 0.269 Chirality : 0.045 0.134 1814 Planarity : 0.005 0.054 2096 Dihedral : 6.914 118.428 1678 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.33 % Allowed : 22.11 % 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: -0.11 (0.22), residues: 1474 helix: 0.51 (0.25), residues: 536 sheet: 0.16 (0.28), residues: 288 loop : -0.58 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE D 223 TYR 0.012 0.001 TYR B 294 ARG 0.002 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 476) hydrogen bonds : angle 4.31683 ( 1188) covalent geometry : bond 0.00250 (12052) covalent geometry : angle 0.55475 (16358) ********************** 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 172 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 1.378 Fit side-chains REVERT: A 34 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8150 (pt) REVERT: B 95 ARG cc_start: 0.7576 (mtm110) cc_final: 0.7228 (mtt90) REVERT: B 284 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7930 (mttm) REVERT: B 326 LYS cc_start: 0.8233 (mttp) cc_final: 0.7550 (tttm) REVERT: C 51 ASP cc_start: 0.7843 (p0) cc_final: 0.7207 (t0) REVERT: C 211 ASP cc_start: 0.8652 (t0) cc_final: 0.8398 (t0) REVERT: D 34 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.7994 (pt) REVERT: D 95 ARG cc_start: 0.7840 (mtm110) cc_final: 0.7634 (mtp-110) REVERT: D 334 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6957 (pm20) outliers start: 42 outliers final: 31 residues processed: 159 average time/residue: 0.2378 time to fit residues: 55.3633 Evaluate side-chains 162 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 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 B residue 54 VAL Chi-restraints excluded: chain B residue 96 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 178 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 250 ILE 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 151 ILE Chi-restraints excluded: chain D residue 163 VAL 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 99 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108998 restraints weight = 15028.287| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.89 r_work: 0.3146 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12052 Z= 0.103 Angle : 0.547 6.322 16358 Z= 0.263 Chirality : 0.045 0.146 1814 Planarity : 0.004 0.054 2096 Dihedral : 6.589 105.455 1678 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.77 % Allowed : 22.74 % Favored : 74.48 % 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: 0.03 (0.22), residues: 1474 helix: 0.60 (0.25), residues: 540 sheet: 0.32 (0.28), residues: 296 loop : -0.52 (0.25), residues: 638 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 0.008 0.001 PHE C 31 TYR 0.011 0.001 TYR B 294 ARG 0.002 0.000 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 476) hydrogen bonds : angle 4.22687 ( 1188) covalent geometry : bond 0.00241 (12052) covalent geometry : angle 0.54709 (16358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5705.02 seconds wall clock time: 99 minutes 54.96 seconds (5994.96 seconds total)