Starting phenix.real_space_refine on Mon Apr 6 16:24:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q7m_72307/04_2026/9q7m_72307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q7m_72307/04_2026/9q7m_72307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q7m_72307/04_2026/9q7m_72307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q7m_72307/04_2026/9q7m_72307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q7m_72307/04_2026/9q7m_72307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q7m_72307/04_2026/9q7m_72307.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 10 5.49 5 Mg 5 5.21 5 S 115 5.16 5 C 12417 2.51 5 N 3275 2.21 5 O 3791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19613 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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: 2842 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 Conformer: "B" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 bond proxies already assigned to first conformer: 2896 Chain: "C" Number of atoms: 2846 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 Conformer: "B" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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 bond proxies already assigned to first conformer: 2891 Chain: "D" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 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: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "b" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "c" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "d" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.66, per 1000 atoms: 0.29 Number of scatterers: 19613 At special positions: 0 Unit cell: (111.696, 124.584, 185.802, 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 115 16.00 P 10 15.00 Mg 5 11.99 O 3791 8.00 N 3275 7.00 C 12417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4630 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 32 sheets defined 45.8% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.737A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.672A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.956A 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 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.670A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 195 removed outlier: 4.004A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.668A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.606A pdb=" N ARG A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.681A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.600A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.580A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 306' Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.630A pdb=" N PHE A 352 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.699A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.610A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.693A 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 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.846A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.772A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.562A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.687A pdb=" N THR B 260 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.560A pdb=" N PHE B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 removed outlier: 4.217A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.614A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.874A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.979A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.873A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.710A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.536A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.758A pdb=" N THR C 260 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.534A pdb=" N PHE C 266 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.651A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.561A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 57 through 61 removed outlier: 3.713A pdb=" N SER D 60 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS D 61 " --> pdb=" O ALA D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 61' Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.549A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.977A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.659A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.897A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.852A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.698A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.615A pdb=" N THR D 260 " --> pdb=" O CYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.552A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 352 through 356 removed outlier: 3.633A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 112 through 126 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.690A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 197 removed outlier: 3.750A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.810A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 251 through 256 removed outlier: 3.638A pdb=" N ARG E 254 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 removed outlier: 3.583A pdb=" N THR E 260 " --> pdb=" O CYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 removed outlier: 4.038A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.271A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.729A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 366 through 368 No H-bonds generated for 'chain 'E' and resid 366 through 368' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'a' and resid 8 through 20 removed outlier: 3.888A pdb=" N ILE a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL a 20 " --> pdb=" O ASN a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 31 Processing helix chain 'a' and resid 58 through 60 No H-bonds generated for 'chain 'a' and resid 58 through 60' Processing helix chain 'a' and resid 66 through 74 Processing helix chain 'a' and resid 110 through 120 Processing helix chain 'a' and resid 120 through 127 removed outlier: 3.810A pdb=" N ILE a 124 " --> pdb=" O SER a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 143 removed outlier: 3.732A pdb=" N ASP a 142 " --> pdb=" O GLY a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 146 through 153 Processing helix chain 'b' and resid 8 through 20 removed outlier: 3.858A pdb=" N ILE b 12 " --> pdb=" O ASN b 8 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL b 20 " --> pdb=" O ASN b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 31 Processing helix chain 'b' and resid 58 through 60 No H-bonds generated for 'chain 'b' and resid 58 through 60' Processing helix chain 'b' and resid 66 through 74 Processing helix chain 'b' and resid 110 through 128 removed outlier: 5.066A pdb=" N ASP b 122 " --> pdb=" O ALA b 118 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ALA b 123 " --> pdb=" O SER b 119 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE b 124 " --> pdb=" O SER b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 143 removed outlier: 3.639A pdb=" N ASP b 142 " --> pdb=" O GLY b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 153 removed outlier: 4.170A pdb=" N LEU b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 154 through 156 No H-bonds generated for 'chain 'b' and resid 154 through 156' Processing helix chain 'c' and resid 8 through 20 removed outlier: 3.887A pdb=" N ILE c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL c 20 " --> pdb=" O ASN c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 58 through 60 No H-bonds generated for 'chain 'c' and resid 58 through 60' Processing helix chain 'c' and resid 66 through 74 removed outlier: 3.518A pdb=" N SER c 70 " --> pdb=" O ASP c 66 " (cutoff:3.500A) Processing helix chain 'c' and resid 110 through 120 Processing helix chain 'c' and resid 120 through 128 removed outlier: 3.911A pdb=" N ILE c 124 " --> pdb=" O SER c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 143 removed outlier: 3.711A pdb=" N ASP c 142 " --> pdb=" O GLY c 139 " (cutoff:3.500A) Processing helix chain 'c' and resid 145 through 153 removed outlier: 4.207A pdb=" N LEU c 149 " --> pdb=" O ASP c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 154 through 156 No H-bonds generated for 'chain 'c' and resid 154 through 156' Processing helix chain 'd' and resid 8 through 20 removed outlier: 3.548A pdb=" N ILE d 12 " --> pdb=" O ASN d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 31 Processing helix chain 'd' and resid 58 through 60 No H-bonds generated for 'chain 'd' and resid 58 through 60' Processing helix chain 'd' and resid 66 through 75 removed outlier: 3.590A pdb=" N SER d 70 " --> pdb=" O ASP d 66 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU d 75 " --> pdb=" O PHE d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 128 removed outlier: 5.251A pdb=" N ASP d 122 " --> pdb=" O ALA d 118 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA d 123 " --> pdb=" O SER d 119 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE d 124 " --> pdb=" O SER d 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 143 removed outlier: 3.564A pdb=" N ASP d 142 " --> pdb=" O GLY d 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 145 through 153 removed outlier: 4.169A pdb=" N LEU d 149 " --> pdb=" O ASP d 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.815A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.231A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.867A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.373A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.867A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.582A pdb=" N TYR C 169 " --> pdb=" O TYR C 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.582A pdb=" N TYR C 169 " --> pdb=" O TYR C 166 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB6, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.814A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB8, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB9, first strand: chain 'D' and resid 169 through 170 removed outlier: 7.800A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC2, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.021A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.196A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.542A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU a 37 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ALA a 52 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N ALA a 35 " --> pdb=" O ALA a 52 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N GLN a 54 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N LYS a 33 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HIS a 133 " --> pdb=" O LEU a 99 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.542A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU a 37 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ALA a 52 " --> pdb=" O ALA a 35 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N ALA a 35 " --> pdb=" O ALA a 52 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N GLN a 54 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N LYS a 33 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.742A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU b 37 " --> pdb=" O GLU b 50 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N ALA b 52 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ALA b 35 " --> pdb=" O ALA b 52 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N GLN b 54 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N LYS b 33 " --> pdb=" O GLN b 54 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N HIS b 133 " --> pdb=" O LEU b 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.742A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU b 37 " --> pdb=" O GLU b 50 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N ALA b 52 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N ALA b 35 " --> pdb=" O ALA b 52 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N GLN b 54 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N LYS b 33 " --> pdb=" O GLN b 54 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.878A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.755A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL c 49 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU c 40 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N GLU c 51 " --> pdb=" O PHE c 38 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N PHE c 38 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LYS c 53 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL c 36 " --> pdb=" O LYS c 53 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE c 55 " --> pdb=" O LYS c 34 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS c 133 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.878A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.755A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL c 49 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU c 40 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N GLU c 51 " --> pdb=" O PHE c 38 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N PHE c 38 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LYS c 53 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL c 36 " --> pdb=" O LYS c 53 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE c 55 " --> pdb=" O LYS c 34 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.437A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU d 50 " --> pdb=" O LEU d 37 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU d 37 " --> pdb=" O GLU d 50 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N ALA d 52 " --> pdb=" O ALA d 35 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N ALA d 35 " --> pdb=" O ALA d 52 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N GLN d 54 " --> pdb=" O LYS d 33 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N LYS d 33 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N HIS d 133 " --> pdb=" O LEU d 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.437A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU d 50 " --> pdb=" O LEU d 37 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU d 37 " --> pdb=" O GLU d 50 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N ALA d 52 " --> pdb=" O ALA d 35 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N ALA d 35 " --> pdb=" O ALA d 52 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N GLN d 54 " --> pdb=" O LYS d 33 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N LYS d 33 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2472 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: 4.03 Time building geometry restraints manager: 2.26 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: 6014 1.34 - 1.46: 4330 1.46 - 1.58: 9450 1.58 - 1.71: 15 1.71 - 1.83: 197 Bond restraints: 20006 Sorted by residual: bond pdb=" CB ASN A 128 " pdb=" CG ASN A 128 " ideal model delta sigma weight residual 1.516 1.572 -0.056 2.50e-02 1.60e+03 5.08e+00 bond pdb=" CA THR a 63 " pdb=" C THR a 63 " ideal model delta sigma weight residual 1.525 1.559 -0.034 1.63e-02 3.76e+03 4.46e+00 bond pdb=" N THR a 63 " pdb=" CA THR a 63 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.48e-02 4.57e+03 4.09e+00 bond pdb=" CB GLU d 65 " pdb=" CG GLU d 65 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 3.96e+00 bond pdb=" CB GLN B 353 " pdb=" CG GLN B 353 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 3.96e+00 ... (remaining 20001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 26447 3.09 - 6.18: 573 6.18 - 9.27: 52 9.27 - 12.36: 12 12.36 - 15.45: 5 Bond angle restraints: 27089 Sorted by residual: angle pdb=" C VAL d 137 " pdb=" N ASN d 138 " pdb=" CA ASN d 138 " ideal model delta sigma weight residual 122.82 132.27 -9.45 1.42e+00 4.96e-01 4.43e+01 angle pdb=" C ASP c 62 " pdb=" N THR c 63 " pdb=" CA THR c 63 " ideal model delta sigma weight residual 121.54 132.88 -11.34 1.91e+00 2.74e-01 3.52e+01 angle pdb=" C ASP b 62 " pdb=" N THR b 63 " pdb=" CA THR b 63 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 angle pdb=" CA GLN C 59 " pdb=" CB GLN C 59 " pdb=" CG GLN C 59 " ideal model delta sigma weight residual 114.10 125.61 -11.51 2.00e+00 2.50e-01 3.31e+01 angle pdb=" C ASP a 62 " pdb=" N THR a 63 " pdb=" CA THR a 63 " ideal model delta sigma weight residual 122.61 131.42 -8.81 1.56e+00 4.11e-01 3.19e+01 ... (remaining 27084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11163 17.99 - 35.98: 790 35.98 - 53.96: 161 53.96 - 71.95: 18 71.95 - 89.94: 19 Dihedral angle restraints: 12151 sinusoidal: 4957 harmonic: 7194 Sorted by residual: dihedral pdb=" CA ARG d 45 " pdb=" C ARG d 45 " pdb=" N GLN d 46 " pdb=" CA GLN d 46 " ideal model delta harmonic sigma weight residual 180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLN d 136 " pdb=" C GLN d 136 " pdb=" N VAL d 137 " pdb=" CA VAL d 137 " ideal model delta harmonic sigma weight residual 180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ARG c 81 " pdb=" C ARG c 81 " pdb=" N TYR c 82 " pdb=" CA TYR c 82 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 12148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2446 0.071 - 0.142: 526 0.142 - 0.213: 47 0.213 - 0.283: 14 0.283 - 0.354: 4 Chirality restraints: 3037 Sorted by residual: chirality pdb=" CB ILE B 287 " pdb=" CA ILE B 287 " pdb=" CG1 ILE B 287 " pdb=" CG2 ILE B 287 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CB ILE A 287 " pdb=" CA ILE A 287 " pdb=" CG1 ILE A 287 " pdb=" CG2 ILE A 287 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB VAL b 57 " pdb=" CA VAL b 57 " pdb=" CG1 VAL b 57 " pdb=" CG2 VAL b 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 3034 not shown) Planarity restraints: 3442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 370 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C VAL B 370 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL B 370 " -0.019 2.00e-02 2.50e+03 pdb=" N HIS B 371 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 370 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.73e+00 pdb=" C VAL D 370 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL D 370 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS D 371 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 370 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.44e+00 pdb=" C VAL E 370 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL E 370 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS E 371 " -0.016 2.00e-02 2.50e+03 ... (remaining 3439 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 63 2.67 - 3.23: 16668 3.23 - 3.79: 29094 3.79 - 4.34: 40952 4.34 - 4.90: 66767 Nonbonded interactions: 153544 Sorted by model distance: nonbonded pdb=" O1B ADP D 400 " pdb="MG MG D 401 " model vdw 2.116 2.170 nonbonded pdb=" O1B ADP A 400 " pdb="MG MG A 401 " model vdw 2.117 2.170 nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.124 2.170 nonbonded pdb=" O1B ADP B 400 " pdb="MG MG B 401 " model vdw 2.133 2.170 nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.137 2.170 ... (remaining 153539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 172 or resid 174 through 270 or resid 272 throug \ h 401)) selection = (chain 'B' and (resid 4 through 172 or resid 174 through 270 or resid 272 throug \ h 401)) selection = (chain 'C' and (resid 4 through 172 or resid 174 through 270 or resid 272 throug \ h 401)) selection = (chain 'D' and (resid 4 through 172 or resid 174 through 270 or resid 272 throug \ h 401)) selection = (chain 'E' and (resid 4 through 172 or resid 174 through 270 or resid 272 throug \ h 401)) } ncs_group { reference = chain 'a' selection = chain 'b' 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 7.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.680 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20006 Z= 0.255 Angle : 1.047 15.450 27089 Z= 0.556 Chirality : 0.059 0.354 3037 Planarity : 0.008 0.068 3442 Dihedral : 13.410 89.941 7521 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.15), residues: 2433 helix: -2.48 (0.12), residues: 914 sheet: 0.01 (0.23), residues: 472 loop : -0.38 (0.19), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 62 TYR 0.034 0.002 TYR D 279 PHE 0.036 0.003 PHE C 90 TRP 0.036 0.002 TRP D 86 HIS 0.012 0.002 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00516 (20006) covalent geometry : angle 1.04673 (27089) hydrogen bonds : bond 0.16338 ( 890) hydrogen bonds : angle 7.25408 ( 2472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8504 (tpt) cc_final: 0.7815 (tmm) REVERT: B 176 MET cc_start: 0.8162 (mmm) cc_final: 0.7699 (mmt) REVERT: C 132 MET cc_start: 0.8655 (tmm) cc_final: 0.8357 (tmm) REVERT: C 305 MET cc_start: 0.9057 (mmm) cc_final: 0.8650 (tpp) REVERT: D 184 ASP cc_start: 0.8955 (m-30) cc_final: 0.8732 (m-30) REVERT: D 305 MET cc_start: 0.9021 (mmt) cc_final: 0.8630 (tpp) REVERT: D 325 MET cc_start: 0.6612 (mpp) cc_final: 0.6262 (mpp) REVERT: E 82 MET cc_start: 0.9254 (tpp) cc_final: 0.8646 (mmm) REVERT: E 123 MET cc_start: 0.9443 (mmp) cc_final: 0.9202 (mmp) REVERT: E 205 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8295 (mt-10) REVERT: E 355 MET cc_start: 0.8866 (mmp) cc_final: 0.8644 (mmt) REVERT: a 26 GLN cc_start: 0.8195 (pp30) cc_final: 0.7992 (pp30) REVERT: a 115 MET cc_start: 0.9067 (tpt) cc_final: 0.8585 (tpt) REVERT: b 115 MET cc_start: 0.8829 (tpp) cc_final: 0.8537 (tpp) REVERT: c 31 LYS cc_start: 0.8970 (mmpt) cc_final: 0.8561 (ttpp) REVERT: c 46 GLN cc_start: 0.8913 (mm110) cc_final: 0.8647 (mm110) REVERT: c 115 MET cc_start: 0.8684 (mmm) cc_final: 0.8259 (tpp) REVERT: d 16 ASN cc_start: 0.9325 (m110) cc_final: 0.9114 (p0) REVERT: d 18 MET cc_start: 0.6989 (mmp) cc_final: 0.6683 (mmm) REVERT: d 115 MET cc_start: 0.9127 (tpt) cc_final: 0.8459 (tpp) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1200 time to fit residues: 29.9300 Evaluate side-chains 133 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 101 HIS C 360 GLN D 173 HIS E 59 GLN E 162 ASN E 314 GLN E 353 GLN c 136 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.065366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.046118 restraints weight = 129657.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048104 restraints weight = 49810.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049401 restraints weight = 28316.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.050300 restraints weight = 19979.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.050865 restraints weight = 15944.890| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20006 Z= 0.109 Angle : 0.564 7.246 27089 Z= 0.286 Chirality : 0.043 0.146 3037 Planarity : 0.005 0.056 3442 Dihedral : 5.323 42.625 2743 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.47 % Favored : 97.45 % Rotamer: Outliers : 0.38 % Allowed : 3.24 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2433 helix: -0.52 (0.16), residues: 932 sheet: 0.08 (0.24), residues: 507 loop : 0.05 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 116 TYR 0.026 0.001 TYR D 279 PHE 0.018 0.001 PHE D 223 TRP 0.011 0.001 TRP B 79 HIS 0.002 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00237 (20006) covalent geometry : angle 0.56390 (27089) hydrogen bonds : bond 0.03691 ( 890) hydrogen bonds : angle 5.00185 ( 2472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: B 82 MET cc_start: 0.8677 (tpt) cc_final: 0.8278 (tmm) REVERT: C 132 MET cc_start: 0.8235 (tmm) cc_final: 0.7926 (tmm) REVERT: D 325 MET cc_start: 0.6719 (mpp) cc_final: 0.6369 (mpp) REVERT: E 82 MET cc_start: 0.9291 (tpp) cc_final: 0.8686 (tmm) REVERT: E 119 MET cc_start: 0.9031 (ttm) cc_final: 0.8013 (tmm) REVERT: E 123 MET cc_start: 0.9399 (mmp) cc_final: 0.8877 (mmp) REVERT: E 205 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8284 (mt-10) REVERT: a 115 MET cc_start: 0.9261 (tpt) cc_final: 0.8815 (tpp) REVERT: c 31 LYS cc_start: 0.8916 (mmpt) cc_final: 0.8552 (ttpp) REVERT: c 82 TYR cc_start: 0.7767 (m-80) cc_final: 0.7109 (m-80) REVERT: c 115 MET cc_start: 0.9122 (mmm) cc_final: 0.8678 (tpp) REVERT: d 18 MET cc_start: 0.7190 (mmp) cc_final: 0.6711 (mmm) REVERT: d 115 MET cc_start: 0.9222 (tpt) cc_final: 0.8619 (tpp) outliers start: 8 outliers final: 4 residues processed: 143 average time/residue: 0.1215 time to fit residues: 28.2355 Evaluate side-chains 133 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain d residue 80 CYS Chi-restraints excluded: chain d residue 142 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 164 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS D 101 HIS d 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.064380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.045631 restraints weight = 93481.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.047377 restraints weight = 41948.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048569 restraints weight = 25637.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049347 restraints weight = 18818.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.049826 restraints weight = 15451.411| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20006 Z= 0.119 Angle : 0.544 6.663 27089 Z= 0.272 Chirality : 0.043 0.141 3037 Planarity : 0.004 0.064 3442 Dihedral : 4.912 38.269 2743 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 0.61 % Allowed : 4.37 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.17), residues: 2433 helix: 0.47 (0.17), residues: 947 sheet: 0.10 (0.24), residues: 507 loop : 0.47 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.016 0.001 TYR D 279 PHE 0.012 0.001 PHE d 71 TRP 0.013 0.001 TRP B 79 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00268 (20006) covalent geometry : angle 0.54442 (27089) hydrogen bonds : bond 0.03374 ( 890) hydrogen bonds : angle 4.46190 ( 2472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8726 (tpt) cc_final: 0.8157 (tmm) REVERT: C 132 MET cc_start: 0.8324 (tmm) cc_final: 0.7951 (tmm) REVERT: D 82 MET cc_start: 0.8355 (tpp) cc_final: 0.7815 (tpp) REVERT: D 325 MET cc_start: 0.7225 (mpp) cc_final: 0.6843 (mpp) REVERT: E 82 MET cc_start: 0.9290 (tpp) cc_final: 0.8685 (tmm) REVERT: E 119 MET cc_start: 0.9084 (ttm) cc_final: 0.7989 (tmm) REVERT: E 123 MET cc_start: 0.9452 (mmp) cc_final: 0.8900 (mmm) REVERT: E 205 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8209 (mt-10) REVERT: E 355 MET cc_start: 0.8642 (mmm) cc_final: 0.8432 (mmm) REVERT: a 115 MET cc_start: 0.9268 (tpt) cc_final: 0.8772 (tpp) REVERT: c 31 LYS cc_start: 0.8938 (mmpt) cc_final: 0.8579 (ttpp) REVERT: c 59 ASP cc_start: 0.8707 (m-30) cc_final: 0.8350 (t70) REVERT: c 115 MET cc_start: 0.9098 (mmm) cc_final: 0.8853 (tpp) REVERT: d 18 MET cc_start: 0.7212 (mmp) cc_final: 0.6872 (mmm) REVERT: d 54 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8137 (mp-120) REVERT: d 115 MET cc_start: 0.9299 (tpt) cc_final: 0.8650 (tpp) outliers start: 13 outliers final: 7 residues processed: 144 average time/residue: 0.1171 time to fit residues: 28.1846 Evaluate side-chains 139 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 80 CYS Chi-restraints excluded: chain d residue 142 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 39 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 74 optimal weight: 0.0570 chunk 91 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN C 314 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.062772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.043761 restraints weight = 116899.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045625 restraints weight = 47605.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046841 restraints weight = 27868.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047661 restraints weight = 19903.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.048156 restraints weight = 16058.792| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20006 Z= 0.159 Angle : 0.567 7.991 27089 Z= 0.284 Chirality : 0.044 0.139 3037 Planarity : 0.004 0.051 3442 Dihedral : 4.904 40.846 2743 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.29 % Favored : 96.63 % Rotamer: Outliers : 0.70 % Allowed : 5.59 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.18), residues: 2433 helix: 1.13 (0.18), residues: 912 sheet: 0.08 (0.23), residues: 528 loop : 0.62 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 62 TYR 0.017 0.001 TYR d 68 PHE 0.011 0.001 PHE C 223 TRP 0.013 0.001 TRP B 79 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00365 (20006) covalent geometry : angle 0.56671 (27089) hydrogen bonds : bond 0.03549 ( 890) hydrogen bonds : angle 4.33899 ( 2472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8766 (tpt) cc_final: 0.8316 (tmm) REVERT: B 176 MET cc_start: 0.8011 (tpp) cc_final: 0.7467 (mpp) REVERT: D 82 MET cc_start: 0.8488 (tpp) cc_final: 0.7950 (tpp) REVERT: D 325 MET cc_start: 0.7045 (mpp) cc_final: 0.6613 (mpp) REVERT: E 119 MET cc_start: 0.9064 (ttm) cc_final: 0.7969 (tmm) REVERT: E 123 MET cc_start: 0.9469 (mmp) cc_final: 0.8882 (mmm) REVERT: E 205 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8220 (mt-10) REVERT: a 115 MET cc_start: 0.9282 (tpt) cc_final: 0.8851 (tpp) REVERT: c 31 LYS cc_start: 0.8966 (mmpt) cc_final: 0.8538 (ttpp) REVERT: c 59 ASP cc_start: 0.8651 (m-30) cc_final: 0.8311 (t70) REVERT: c 115 MET cc_start: 0.9184 (mmm) cc_final: 0.8934 (tpp) REVERT: d 54 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8161 (mp-120) REVERT: d 115 MET cc_start: 0.9375 (tpt) cc_final: 0.8723 (tpp) outliers start: 15 outliers final: 9 residues processed: 142 average time/residue: 0.1130 time to fit residues: 26.8719 Evaluate side-chains 137 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain a residue 6 THR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 80 CYS Chi-restraints excluded: chain d residue 142 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 128 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 187 optimal weight: 0.0970 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 243 optimal weight: 0.0570 chunk 117 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.064164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.045016 restraints weight = 130396.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.046913 restraints weight = 51745.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.048208 restraints weight = 29943.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.049068 restraints weight = 21202.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049614 restraints weight = 17011.162| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20006 Z= 0.086 Angle : 0.519 9.290 27089 Z= 0.254 Chirality : 0.042 0.150 3037 Planarity : 0.003 0.050 3442 Dihedral : 4.705 41.455 2743 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.88 % Favored : 97.04 % Rotamer: Outliers : 0.85 % Allowed : 6.39 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.18), residues: 2433 helix: 1.32 (0.19), residues: 917 sheet: 0.08 (0.23), residues: 528 loop : 0.76 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 290 TYR 0.019 0.001 TYR d 68 PHE 0.011 0.001 PHE C 223 TRP 0.011 0.001 TRP B 340 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00187 (20006) covalent geometry : angle 0.51893 (27089) hydrogen bonds : bond 0.02864 ( 890) hydrogen bonds : angle 4.12484 ( 2472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: B 82 MET cc_start: 0.8753 (tpt) cc_final: 0.8241 (tmm) REVERT: B 176 MET cc_start: 0.8012 (tpp) cc_final: 0.7532 (mpp) REVERT: D 82 MET cc_start: 0.8422 (tpp) cc_final: 0.8183 (tpp) REVERT: D 325 MET cc_start: 0.7103 (mpp) cc_final: 0.6686 (mpp) REVERT: E 82 MET cc_start: 0.9296 (tpp) cc_final: 0.8840 (mmm) REVERT: E 119 MET cc_start: 0.9054 (ttm) cc_final: 0.7968 (tmm) REVERT: E 123 MET cc_start: 0.9435 (mmp) cc_final: 0.8844 (mmm) REVERT: E 205 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8181 (mt-10) REVERT: E 325 MET cc_start: 0.2860 (mtm) cc_final: 0.2636 (pmm) REVERT: E 355 MET cc_start: 0.8674 (mmm) cc_final: 0.8295 (mmt) REVERT: a 115 MET cc_start: 0.9248 (tpt) cc_final: 0.8879 (tpp) REVERT: c 31 LYS cc_start: 0.8979 (mmpt) cc_final: 0.8604 (ttpp) REVERT: c 115 MET cc_start: 0.9174 (mmm) cc_final: 0.8682 (tpp) REVERT: d 54 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8267 (mp-120) REVERT: d 115 MET cc_start: 0.9350 (tpt) cc_final: 0.8714 (tpp) outliers start: 18 outliers final: 11 residues processed: 147 average time/residue: 0.1173 time to fit residues: 28.4549 Evaluate side-chains 139 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain c residue 143 ILE Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 142 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 36 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 202 optimal weight: 0.0020 chunk 241 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 overall best weight: 3.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.061124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.042956 restraints weight = 94769.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.044609 restraints weight = 43095.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.045702 restraints weight = 26584.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046412 restraints weight = 19501.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.046864 restraints weight = 16026.254| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20006 Z= 0.245 Angle : 0.641 9.267 27089 Z= 0.320 Chirality : 0.046 0.155 3037 Planarity : 0.004 0.050 3442 Dihedral : 5.025 43.485 2743 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 0.80 % Allowed : 6.43 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.18), residues: 2433 helix: 1.22 (0.18), residues: 921 sheet: -0.09 (0.23), residues: 552 loop : 0.84 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 147 TYR 0.013 0.001 TYR b 117 PHE 0.011 0.002 PHE b 101 TRP 0.016 0.001 TRP B 79 HIS 0.006 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00559 (20006) covalent geometry : angle 0.64098 (27089) hydrogen bonds : bond 0.04144 ( 890) hydrogen bonds : angle 4.47885 ( 2472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8817 (tpt) cc_final: 0.8271 (tmm) REVERT: D 283 MET cc_start: 0.7485 (tpp) cc_final: 0.6853 (mpp) REVERT: D 305 MET cc_start: 0.8902 (mmm) cc_final: 0.8564 (mmm) REVERT: D 325 MET cc_start: 0.7028 (mpp) cc_final: 0.6504 (mpp) REVERT: E 119 MET cc_start: 0.9067 (ttm) cc_final: 0.7972 (tmm) REVERT: E 123 MET cc_start: 0.9515 (mmp) cc_final: 0.8945 (mmm) REVERT: E 325 MET cc_start: 0.3081 (mtm) cc_final: 0.2798 (pmm) REVERT: a 115 MET cc_start: 0.9314 (tpt) cc_final: 0.8883 (tpp) REVERT: c 31 LYS cc_start: 0.8979 (mmpt) cc_final: 0.8621 (ttpp) REVERT: d 54 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8238 (mp-120) REVERT: d 103 PHE cc_start: 0.8789 (t80) cc_final: 0.8520 (t80) REVERT: d 115 MET cc_start: 0.9459 (tpt) cc_final: 0.8782 (tpp) outliers start: 17 outliers final: 11 residues processed: 137 average time/residue: 0.1225 time to fit residues: 28.1166 Evaluate side-chains 137 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 25 THR Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 12 ILE Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 80 CYS Chi-restraints excluded: chain d residue 142 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 105 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 186 optimal weight: 0.0070 chunk 121 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN c 54 GLN d 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.063354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.044152 restraints weight = 134216.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.046122 restraints weight = 53216.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047402 restraints weight = 30557.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048281 restraints weight = 21553.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048809 restraints weight = 17164.058| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20006 Z= 0.092 Angle : 0.534 9.871 27089 Z= 0.262 Chirality : 0.043 0.142 3037 Planarity : 0.003 0.050 3442 Dihedral : 4.757 44.661 2743 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 0.70 % Allowed : 6.76 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.18), residues: 2433 helix: 1.34 (0.19), residues: 936 sheet: 0.04 (0.23), residues: 543 loop : 0.95 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 116 TYR 0.012 0.001 TYR d 68 PHE 0.017 0.001 PHE C 223 TRP 0.013 0.001 TRP B 340 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00202 (20006) covalent geometry : angle 0.53422 (27089) hydrogen bonds : bond 0.02936 ( 890) hydrogen bonds : angle 4.09699 ( 2472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8745 (tpt) cc_final: 0.8176 (tmm) REVERT: B 313 MET cc_start: 0.9102 (tpp) cc_final: 0.8754 (tpp) REVERT: D 305 MET cc_start: 0.8796 (mmm) cc_final: 0.8451 (mmm) REVERT: D 325 MET cc_start: 0.7130 (mpp) cc_final: 0.6785 (mpp) REVERT: E 82 MET cc_start: 0.9230 (tpp) cc_final: 0.8419 (mmm) REVERT: E 119 MET cc_start: 0.9034 (ttm) cc_final: 0.7957 (tmm) REVERT: E 123 MET cc_start: 0.9398 (mmp) cc_final: 0.8815 (mmm) REVERT: E 325 MET cc_start: 0.2907 (mtm) cc_final: 0.2604 (pmm) REVERT: a 115 MET cc_start: 0.9229 (tpt) cc_final: 0.8899 (tpp) REVERT: c 31 LYS cc_start: 0.9057 (mmpt) cc_final: 0.8658 (ttpp) REVERT: c 115 MET cc_start: 0.9066 (mmm) cc_final: 0.8709 (tpp) REVERT: d 18 MET cc_start: 0.6981 (mmm) cc_final: 0.6726 (mmm) REVERT: d 54 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8288 (mp-120) REVERT: d 115 MET cc_start: 0.9389 (tpt) cc_final: 0.8733 (tpp) outliers start: 15 outliers final: 11 residues processed: 137 average time/residue: 0.1169 time to fit residues: 26.7173 Evaluate side-chains 140 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 80 CYS Chi-restraints excluded: chain d residue 138 ASN Chi-restraints excluded: chain d residue 142 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 53 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 228 optimal weight: 0.0060 chunk 216 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.062238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.043549 restraints weight = 116653.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045387 restraints weight = 48420.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046577 restraints weight = 28379.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047371 restraints weight = 20379.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.047892 restraints weight = 16450.963| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20006 Z= 0.145 Angle : 0.555 10.326 27089 Z= 0.274 Chirality : 0.044 0.139 3037 Planarity : 0.003 0.050 3442 Dihedral : 4.745 44.975 2743 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 0.75 % Allowed : 6.81 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.18), residues: 2433 helix: 1.37 (0.18), residues: 936 sheet: 0.03 (0.23), residues: 543 loop : 0.95 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 290 TYR 0.013 0.001 TYR d 85 PHE 0.019 0.001 PHE d 71 TRP 0.012 0.001 TRP B 79 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00334 (20006) covalent geometry : angle 0.55510 (27089) hydrogen bonds : bond 0.03249 ( 890) hydrogen bonds : angle 4.14965 ( 2472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8838 (tpt) cc_final: 0.8359 (mmm) REVERT: D 305 MET cc_start: 0.8847 (mmm) cc_final: 0.8610 (mmm) REVERT: D 325 MET cc_start: 0.7105 (mpp) cc_final: 0.6703 (mpp) REVERT: E 82 MET cc_start: 0.9231 (tpp) cc_final: 0.8431 (mmm) REVERT: E 119 MET cc_start: 0.9039 (ttm) cc_final: 0.7950 (tmm) REVERT: E 123 MET cc_start: 0.9468 (mmp) cc_final: 0.8853 (mmm) REVERT: E 325 MET cc_start: 0.3059 (mtm) cc_final: 0.2797 (pmm) REVERT: a 115 MET cc_start: 0.9278 (tpt) cc_final: 0.8876 (tpp) REVERT: c 31 LYS cc_start: 0.9047 (mmpt) cc_final: 0.8658 (ttpp) REVERT: c 115 MET cc_start: 0.9097 (mmm) cc_final: 0.8637 (tpp) REVERT: d 18 MET cc_start: 0.7051 (mmm) cc_final: 0.6776 (mmm) REVERT: d 54 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8323 (mp-120) REVERT: d 115 MET cc_start: 0.9426 (tpt) cc_final: 0.8761 (tpp) outliers start: 16 outliers final: 14 residues processed: 137 average time/residue: 0.1193 time to fit residues: 27.3823 Evaluate side-chains 143 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain a residue 6 THR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 12 ILE Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 80 CYS Chi-restraints excluded: chain d residue 138 ASN Chi-restraints excluded: chain d residue 142 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 119 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 187 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.062362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.043769 restraints weight = 114140.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.045577 restraints weight = 47661.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046796 restraints weight = 28090.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.047600 restraints weight = 20015.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048092 restraints weight = 16111.900| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20006 Z= 0.136 Angle : 0.554 9.981 27089 Z= 0.274 Chirality : 0.044 0.161 3037 Planarity : 0.003 0.051 3442 Dihedral : 4.745 44.934 2743 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 0.75 % Allowed : 6.81 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.18), residues: 2433 helix: 1.33 (0.18), residues: 941 sheet: -0.01 (0.23), residues: 533 loop : 0.96 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 116 TYR 0.017 0.001 TYR d 85 PHE 0.019 0.001 PHE d 71 TRP 0.011 0.001 TRP B 79 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00315 (20006) covalent geometry : angle 0.55447 (27089) hydrogen bonds : bond 0.03207 ( 890) hydrogen bonds : angle 4.11694 ( 2472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8837 (tpt) cc_final: 0.8349 (mmm) REVERT: D 305 MET cc_start: 0.8825 (mmm) cc_final: 0.8595 (mmm) REVERT: D 325 MET cc_start: 0.7097 (mpp) cc_final: 0.6709 (mpp) REVERT: E 82 MET cc_start: 0.9217 (tpp) cc_final: 0.8422 (mmm) REVERT: E 119 MET cc_start: 0.9042 (ttm) cc_final: 0.7964 (tmm) REVERT: E 123 MET cc_start: 0.9460 (mmp) cc_final: 0.8854 (mmm) REVERT: a 115 MET cc_start: 0.9264 (tpt) cc_final: 0.8876 (tpp) REVERT: c 31 LYS cc_start: 0.9052 (mmpt) cc_final: 0.8669 (ttpp) REVERT: c 115 MET cc_start: 0.9091 (mmm) cc_final: 0.8629 (tpp) REVERT: d 18 MET cc_start: 0.7113 (mmm) cc_final: 0.6840 (mmm) REVERT: d 54 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8310 (mp-120) REVERT: d 115 MET cc_start: 0.9420 (tpt) cc_final: 0.8769 (tpp) outliers start: 16 outliers final: 13 residues processed: 138 average time/residue: 0.1219 time to fit residues: 27.4617 Evaluate side-chains 142 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain a residue 6 THR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 12 ILE Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 80 CYS Chi-restraints excluded: chain d residue 138 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 237 optimal weight: 20.0000 chunk 199 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 224 optimal weight: 2.9990 chunk 213 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 203 optimal weight: 0.2980 chunk 11 optimal weight: 0.0980 chunk 122 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.062002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.043935 restraints weight = 93934.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.045601 restraints weight = 42625.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.046720 restraints weight = 26140.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.047448 restraints weight = 19109.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.047915 restraints weight = 15652.408| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20006 Z= 0.162 Angle : 0.573 9.761 27089 Z= 0.283 Chirality : 0.044 0.177 3037 Planarity : 0.003 0.051 3442 Dihedral : 4.784 45.379 2743 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 0.75 % Allowed : 6.76 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 2433 helix: 1.43 (0.18), residues: 926 sheet: -0.01 (0.23), residues: 547 loop : 0.95 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 290 TYR 0.017 0.001 TYR d 85 PHE 0.013 0.001 PHE C 223 TRP 0.012 0.001 TRP B 79 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00375 (20006) covalent geometry : angle 0.57301 (27089) hydrogen bonds : bond 0.03352 ( 890) hydrogen bonds : angle 4.15943 ( 2472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4866 Ramachandran restraints generated. 2433 Oldfield, 0 Emsley, 2433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8838 (tpt) cc_final: 0.8349 (mmm) REVERT: D 86 TRP cc_start: 0.9197 (m-10) cc_final: 0.8328 (m-90) REVERT: D 305 MET cc_start: 0.8845 (mmm) cc_final: 0.8615 (mmm) REVERT: D 325 MET cc_start: 0.7040 (mpp) cc_final: 0.6586 (mpp) REVERT: E 82 MET cc_start: 0.9209 (tpp) cc_final: 0.8420 (mmm) REVERT: E 119 MET cc_start: 0.9041 (ttm) cc_final: 0.7957 (tmm) REVERT: E 123 MET cc_start: 0.9465 (mmp) cc_final: 0.8860 (mmm) REVERT: E 325 MET cc_start: 0.3243 (mtm) cc_final: 0.3008 (pmm) REVERT: a 115 MET cc_start: 0.9286 (tpt) cc_final: 0.8877 (tpp) REVERT: c 31 LYS cc_start: 0.9030 (mmpt) cc_final: 0.8658 (ttpp) REVERT: c 115 MET cc_start: 0.9067 (mmm) cc_final: 0.8566 (tpp) REVERT: d 18 MET cc_start: 0.7059 (mmm) cc_final: 0.6795 (mmm) REVERT: d 54 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8321 (mp-120) REVERT: d 115 MET cc_start: 0.9442 (tpt) cc_final: 0.8800 (tpp) outliers start: 16 outliers final: 15 residues processed: 138 average time/residue: 0.1182 time to fit residues: 27.3636 Evaluate side-chains 146 residues out of total 2125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain a residue 6 THR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 12 ILE Chi-restraints excluded: chain d residue 54 GLN Chi-restraints excluded: chain d residue 80 CYS Chi-restraints excluded: chain d residue 138 ASN Chi-restraints excluded: chain d residue 142 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 85 optimal weight: 3.9990 chunk 170 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 187 optimal weight: 0.3980 chunk 125 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 133 HIS d 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.062900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.044485 restraints weight = 109380.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046318 restraints weight = 45308.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047527 restraints weight = 26513.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048327 restraints weight = 18876.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048808 restraints weight = 15181.902| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20006 Z= 0.099 Angle : 0.540 9.099 27089 Z= 0.265 Chirality : 0.043 0.177 3037 Planarity : 0.003 0.049 3442 Dihedral : 4.679 45.159 2743 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.61 % Allowed : 6.90 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.18), residues: 2433 helix: 1.43 (0.19), residues: 936 sheet: -0.01 (0.23), residues: 533 loop : 0.96 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 116 TYR 0.014 0.001 TYR d 85 PHE 0.015 0.001 PHE C 223 TRP 0.012 0.001 TRP B 340 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00224 (20006) covalent geometry : angle 0.54043 (27089) hydrogen bonds : bond 0.02966 ( 890) hydrogen bonds : angle 4.03313 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3673.83 seconds wall clock time: 64 minutes 5.28 seconds (3845.28 seconds total)