Starting phenix.real_space_refine on Mon Aug 25 00:14:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9az4_44012/08_2025/9az4_44012.cif Found real_map, /net/cci-nas-00/data/ceres_data/9az4_44012/08_2025/9az4_44012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9az4_44012/08_2025/9az4_44012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9az4_44012/08_2025/9az4_44012.map" model { file = "/net/cci-nas-00/data/ceres_data/9az4_44012/08_2025/9az4_44012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9az4_44012/08_2025/9az4_44012.cif" } resolution = 3.37 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= 0.012 sd= 0.030 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 12 5.49 5 Mg 6 5.21 5 S 154 5.16 5 C 15053 2.51 5 N 4069 2.21 5 O 4571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23865 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3140 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 14, 'TRANS': 378} Chain breaks: 2 Chain: "H" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3157 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.78, per 1000 atoms: 0.20 Number of scatterers: 23865 At special positions: 0 Unit cell: (132.84, 125.28, 230.04, 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 154 16.00 P 12 15.00 Mg 6 11.99 O 4571 8.00 N 4069 7.00 C 15053 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 991.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5662 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 36 sheets defined 56.0% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.837A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.524A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 202 through 217 removed outlier: 4.060A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.654A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.697A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.503A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.539A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.510A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.094A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.962A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.510A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.847A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.535A pdb=" N LEU B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.695A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.811A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.888A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.546A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.717A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.538A 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 289 through 295 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.566A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.623A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.088A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.559A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.755A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.523A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.776A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 4.038A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.589A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.008A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.875A pdb=" N MET C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.536A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.694A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.520A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.675A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 203 through 216 removed outlier: 4.201A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.519A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 289 through 296 removed outlier: 3.650A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.532A pdb=" N MET D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.707A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.933A 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 368 through 374 removed outlier: 4.041A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.638A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.822A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.529A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.864A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.619A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 removed outlier: 3.915A pdb=" N PHE E 262 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 removed outlier: 4.004A pdb=" N LEU E 293 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.570A pdb=" N MET E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 349 through 356 removed outlier: 3.618A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 369 No H-bonds generated for 'chain 'E' and resid 367 through 369' Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 79 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.760A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.594A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 181 through 194 removed outlier: 3.869A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.969A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.665A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.572A pdb=" N LEU F 293 " --> pdb=" O ILE F 289 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.314A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.613A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 removed outlier: 3.817A pdb=" N SER F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 354 removed outlier: 3.648A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.133A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 578 Processing helix chain 'G' and resid 584 through 589 removed outlier: 3.931A pdb=" N SER G 589 " --> pdb=" O ALA G 585 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 606 Processing helix chain 'G' and resid 634 through 646 Processing helix chain 'G' and resid 651 through 661 Processing helix chain 'G' and resid 668 through 678 Processing helix chain 'G' and resid 681 through 691 Processing helix chain 'G' and resid 694 through 698 removed outlier: 3.880A pdb=" N LYS G 697 " --> pdb=" O GLU G 694 " (cutoff:3.500A) Processing helix chain 'G' and resid 699 through 710 Processing helix chain 'G' and resid 713 through 750 removed outlier: 3.686A pdb=" N ARG G 717 " --> pdb=" O CYS G 713 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG G 735 " --> pdb=" O LEU G 731 " (cutoff:3.500A) Proline residue: G 736 - end of helix Processing helix chain 'G' and resid 752 through 769 removed outlier: 3.807A pdb=" N ILE G 756 " --> pdb=" O ARG G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 781 through 785 removed outlier: 3.677A pdb=" N THR G 784 " --> pdb=" O LYS G 781 " (cutoff:3.500A) Processing helix chain 'G' and resid 799 through 812 removed outlier: 3.806A pdb=" N LYS G 810 " --> pdb=" O GLU G 806 " (cutoff:3.500A) Processing helix chain 'G' and resid 813 through 816 Processing helix chain 'G' and resid 817 through 822 removed outlier: 3.526A pdb=" N LEU G 822 " --> pdb=" O LEU G 818 " (cutoff:3.500A) Processing helix chain 'G' and resid 822 through 829 Processing helix chain 'G' and resid 832 through 856 removed outlier: 3.647A pdb=" N ILE G 836 " --> pdb=" O ASN G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 858 through 898 removed outlier: 5.709A pdb=" N GLU G 867 " --> pdb=" O GLU G 863 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ARG G 868 " --> pdb=" O GLN G 864 " (cutoff:3.500A) Processing helix chain 'G' and resid 905 through 947 Processing helix chain 'G' and resid 972 through 983 Processing helix chain 'H' and resid 573 through 578 Processing helix chain 'H' and resid 582 through 588 removed outlier: 3.949A pdb=" N SER H 586 " --> pdb=" O SER H 582 " (cutoff:3.500A) Processing helix chain 'H' and resid 598 through 606 Processing helix chain 'H' and resid 634 through 647 removed outlier: 3.842A pdb=" N GLN H 647 " --> pdb=" O ILE H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 651 through 662 removed outlier: 3.564A pdb=" N VAL H 655 " --> pdb=" O SER H 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 668 through 678 Processing helix chain 'H' and resid 681 through 690 Processing helix chain 'H' and resid 699 through 711 Processing helix chain 'H' and resid 713 through 750 Proline residue: H 736 - end of helix removed outlier: 3.627A pdb=" N THR H 750 " --> pdb=" O GLU H 746 " (cutoff:3.500A) Processing helix chain 'H' and resid 752 through 769 removed outlier: 4.405A pdb=" N ILE H 756 " --> pdb=" O ARG H 752 " (cutoff:3.500A) Processing helix chain 'H' and resid 781 through 785 Processing helix chain 'H' and resid 786 through 790 removed outlier: 3.939A pdb=" N THR H 789 " --> pdb=" O LEU H 786 " (cutoff:3.500A) Processing helix chain 'H' and resid 799 through 811 removed outlier: 4.060A pdb=" N LYS H 810 " --> pdb=" O GLU H 806 " (cutoff:3.500A) Processing helix chain 'H' and resid 812 through 816 Processing helix chain 'H' and resid 817 through 822 removed outlier: 3.989A pdb=" N ASP H 821 " --> pdb=" O GLN H 817 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU H 822 " --> pdb=" O LEU H 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 817 through 822' Processing helix chain 'H' and resid 832 through 856 removed outlier: 3.844A pdb=" N ILE H 836 " --> pdb=" O ASN H 832 " (cutoff:3.500A) Processing helix chain 'H' and resid 858 through 897 removed outlier: 5.601A pdb=" N GLU H 867 " --> pdb=" O GLU H 863 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ARG H 868 " --> pdb=" O GLN H 864 " (cutoff:3.500A) Processing helix chain 'H' and resid 906 through 947 Processing helix chain 'H' and resid 972 through 983 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.137A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.086A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.964A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.343A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.515A pdb=" N SER B 155 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.910A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.279A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.165A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 4.086A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.026A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.267A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.938A pdb=" N GLN F 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.716A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR E 103 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR E 133 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.252A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.447A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR F 133 " --> pdb=" O THR F 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.203A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 1227 hydrogen bonds defined for protein. 3339 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: 4.52 Time building geometry restraints manager: 1.75 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: 7444 1.34 - 1.46: 5419 1.46 - 1.58: 11195 1.58 - 1.71: 20 1.71 - 1.83: 262 Bond restraints: 24340 Sorted by residual: bond pdb=" CA VAL G 551 " pdb=" C VAL G 551 " ideal model delta sigma weight residual 1.525 1.592 -0.067 2.10e-02 2.27e+03 1.03e+01 bond pdb=" CG MET D 325 " pdb=" SD MET D 325 " ideal model delta sigma weight residual 1.803 1.733 0.070 2.50e-02 1.60e+03 7.74e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.64e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" CB MET D 325 " pdb=" CG MET D 325 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.21e+00 ... (remaining 24335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 32642 4.16 - 8.31: 284 8.31 - 12.47: 37 12.47 - 16.63: 4 16.63 - 20.79: 1 Bond angle restraints: 32968 Sorted by residual: angle pdb=" CB MET D 325 " pdb=" CG MET D 325 " pdb=" SD MET D 325 " ideal model delta sigma weight residual 112.70 133.49 -20.79 3.00e+00 1.11e-01 4.80e+01 angle pdb=" CG MET D 325 " pdb=" SD MET D 325 " pdb=" CE MET D 325 " ideal model delta sigma weight residual 100.90 87.70 13.20 2.20e+00 2.07e-01 3.60e+01 angle pdb=" C GLY C 46 " pdb=" N MET C 47 " pdb=" CA MET C 47 " ideal model delta sigma weight residual 121.54 132.55 -11.01 1.91e+00 2.74e-01 3.32e+01 angle pdb=" CA MET C 47 " pdb=" CB MET C 47 " pdb=" CG MET C 47 " ideal model delta sigma weight residual 114.10 125.59 -11.49 2.00e+00 2.50e-01 3.30e+01 angle pdb=" CA MET A 355 " pdb=" CB MET A 355 " pdb=" CG MET A 355 " ideal model delta sigma weight residual 114.10 125.51 -11.41 2.00e+00 2.50e-01 3.25e+01 ... (remaining 32963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 14586 35.76 - 71.52: 211 71.52 - 107.28: 12 107.28 - 143.04: 2 143.04 - 178.80: 1 Dihedral angle restraints: 14812 sinusoidal: 6041 harmonic: 8771 Sorted by residual: dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 118.80 -178.80 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 157.95 142.05 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O2A ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PA ADP F 401 " pdb=" PB ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 174.50 125.50 1 2.00e+01 2.50e-03 3.79e+01 ... (remaining 14809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2954 0.068 - 0.136: 628 0.136 - 0.205: 86 0.205 - 0.273: 17 0.273 - 0.341: 10 Chirality restraints: 3695 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 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 2.30 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 3692 not shown) Planarity restraints: 4230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 364 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" CD GLU E 364 " 0.073 2.00e-02 2.50e+03 pdb=" OE1 GLU E 364 " -0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU E 364 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 705 " -0.021 2.00e-02 2.50e+03 2.86e-02 1.64e+01 pdb=" CG TYR G 705 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR G 705 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR G 705 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR G 705 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 705 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR G 705 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR G 705 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 824 " -0.056 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO H 825 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO H 825 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO H 825 " -0.047 5.00e-02 4.00e+02 ... (remaining 4227 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 296 2.63 - 3.20: 19868 3.20 - 3.77: 38305 3.77 - 4.33: 52733 4.33 - 4.90: 85935 Nonbonded interactions: 197137 Sorted by model distance: nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 2.069 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.086 2.170 nonbonded pdb=" O1A ADP B 401 " pdb="MG MG B 402 " model vdw 2.087 2.170 nonbonded pdb=" O1A ADP A 401 " pdb="MG MG A 402 " model vdw 2.088 2.170 nonbonded pdb=" O3A ADP D 401 " pdb="MG MG D 402 " model vdw 2.095 2.170 ... (remaining 197132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and (resid 551 through 608 or resid 626 through 983)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.410 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.007 0.092 24344 Z= 0.297 Angle : 1.057 20.786 32968 Z= 0.551 Chirality : 0.059 0.341 3695 Planarity : 0.007 0.083 4230 Dihedral : 13.816 178.803 9150 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.43 % 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 aren not related in a simple way. whole: -2.13 (0.13), residues: 2973 helix: -1.55 (0.11), residues: 1478 sheet: -1.13 (0.24), residues: 384 loop : -1.01 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 28 TYR 0.070 0.003 TYR G 705 PHE 0.027 0.003 PHE G 920 TRP 0.023 0.004 TRP A 356 HIS 0.017 0.002 HIS G 554 Details of bonding type rmsd covalent geometry : bond 0.00671 (24340) covalent geometry : angle 1.05715 (32968) hydrogen bonds : bond 0.15725 ( 1207) hydrogen bonds : angle 6.67274 ( 3339) Misc. bond : bond 0.00320 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.9139 (mmm) cc_final: 0.8878 (mmm) REVERT: A 305 MET cc_start: 0.8452 (mmm) cc_final: 0.8219 (mmt) REVERT: A 313 MET cc_start: 0.9128 (tpp) cc_final: 0.8711 (tmm) REVERT: A 325 MET cc_start: 0.8492 (mmm) cc_final: 0.8195 (mmm) REVERT: D 82 MET cc_start: 0.8220 (tpt) cc_final: 0.7947 (tmm) REVERT: F 82 MET cc_start: 0.8866 (tpt) cc_final: 0.8294 (tpt) REVERT: F 101 HIS cc_start: 0.8569 (m-70) cc_final: 0.8270 (m90) REVERT: F 119 MET cc_start: 0.9449 (mtm) cc_final: 0.9116 (mtm) REVERT: F 305 MET cc_start: 0.8837 (mmp) cc_final: 0.8389 (mmp) REVERT: F 325 MET cc_start: 0.8541 (pmm) cc_final: 0.8278 (pmm) REVERT: G 564 MET cc_start: 0.6342 (mmp) cc_final: 0.5381 (mmp) REVERT: G 733 MET cc_start: 0.9323 (tmm) cc_final: 0.9081 (tmm) REVERT: H 705 TYR cc_start: 0.9347 (m-10) cc_final: 0.9079 (m-80) REVERT: H 721 MET cc_start: 0.9454 (mmm) cc_final: 0.8639 (mmm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1408 time to fit residues: 29.3993 Evaluate side-chains 120 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN B 111 ASN C 59 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN F 111 ASN G 683 HIS G 864 GLN H 832 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.043382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.032894 restraints weight = 255001.984| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 5.90 r_work: 0.2929 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 24344 Z= 0.261 Angle : 0.680 10.127 32968 Z= 0.337 Chirality : 0.043 0.176 3695 Planarity : 0.005 0.069 4230 Dihedral : 7.591 172.707 3345 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.31 % Allowed : 3.08 % Favored : 96.61 % 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 aren not related in a simple way. whole: -0.19 (0.15), residues: 2973 helix: 0.38 (0.13), residues: 1505 sheet: -0.62 (0.25), residues: 402 loop : -0.45 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 981 TYR 0.034 0.002 TYR G 705 PHE 0.015 0.002 PHE G 920 TRP 0.016 0.002 TRP D 79 HIS 0.005 0.001 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00566 (24340) covalent geometry : angle 0.67955 (32968) hydrogen bonds : bond 0.03687 ( 1207) hydrogen bonds : angle 4.64836 ( 3339) Misc. bond : bond 0.00246 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8824 (tmm) cc_final: 0.8356 (tmm) REVERT: A 283 MET cc_start: 0.9248 (mmm) cc_final: 0.8836 (mmm) REVERT: A 355 MET cc_start: 0.8959 (tpp) cc_final: 0.8707 (tpp) REVERT: B 132 MET cc_start: 0.8902 (tmm) cc_final: 0.8556 (tmm) REVERT: B 325 MET cc_start: 0.8757 (tpp) cc_final: 0.8465 (mmt) REVERT: B 355 MET cc_start: 0.8820 (tpp) cc_final: 0.8348 (tpp) REVERT: C 132 MET cc_start: 0.8672 (ppp) cc_final: 0.8323 (tmm) REVERT: C 305 MET cc_start: 0.8459 (mpp) cc_final: 0.8217 (mpp) REVERT: D 82 MET cc_start: 0.8628 (tpt) cc_final: 0.8411 (tmm) REVERT: D 227 MET cc_start: 0.9219 (mmm) cc_final: 0.8984 (mmm) REVERT: E 123 MET cc_start: 0.9239 (mmp) cc_final: 0.9004 (mmp) REVERT: F 47 MET cc_start: 0.7841 (pmm) cc_final: 0.7489 (pmm) REVERT: F 82 MET cc_start: 0.9068 (tpt) cc_final: 0.8743 (tpt) REVERT: F 119 MET cc_start: 0.9411 (mtm) cc_final: 0.9096 (mtt) REVERT: F 132 MET cc_start: 0.9259 (ppp) cc_final: 0.8698 (ppp) REVERT: F 305 MET cc_start: 0.8952 (mmp) cc_final: 0.8479 (mmp) REVERT: F 325 MET cc_start: 0.8542 (pmm) cc_final: 0.8220 (pmm) REVERT: G 564 MET cc_start: 0.7282 (mmp) cc_final: 0.6687 (mmp) REVERT: G 733 MET cc_start: 0.9427 (tmm) cc_final: 0.9193 (tmm) REVERT: H 705 TYR cc_start: 0.9501 (m-10) cc_final: 0.9236 (m-80) REVERT: H 721 MET cc_start: 0.9590 (mmm) cc_final: 0.8883 (mmm) outliers start: 8 outliers final: 3 residues processed: 125 average time/residue: 0.1488 time to fit residues: 31.5238 Evaluate side-chains 121 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 87 HIS Chi-restraints excluded: chain G residue 770 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 275 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 267 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 251 optimal weight: 40.0000 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 ASN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.043500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.032972 restraints weight = 254833.964| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 6.00 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24344 Z= 0.189 Angle : 0.598 8.279 32968 Z= 0.292 Chirality : 0.042 0.174 3695 Planarity : 0.004 0.065 4230 Dihedral : 7.357 170.762 3345 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.39 % Allowed : 4.59 % 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 aren not related in a simple way. whole: 0.56 (0.16), residues: 2973 helix: 1.14 (0.14), residues: 1470 sheet: -0.48 (0.25), residues: 402 loop : -0.20 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 177 TYR 0.030 0.001 TYR G 705 PHE 0.012 0.001 PHE G 920 TRP 0.016 0.002 TRP D 79 HIS 0.004 0.001 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00410 (24340) covalent geometry : angle 0.59820 (32968) hydrogen bonds : bond 0.03229 ( 1207) hydrogen bonds : angle 4.39453 ( 3339) Misc. bond : bond 0.00227 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8586 (tmm) cc_final: 0.8002 (tmm) REVERT: A 355 MET cc_start: 0.8742 (tpp) cc_final: 0.8123 (tpt) REVERT: B 132 MET cc_start: 0.8431 (tmm) cc_final: 0.7982 (tmm) REVERT: B 325 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7977 (mmt) REVERT: B 355 MET cc_start: 0.8620 (tpp) cc_final: 0.8418 (mmm) REVERT: C 305 MET cc_start: 0.8172 (mpp) cc_final: 0.7876 (mpp) REVERT: D 47 MET cc_start: 0.4566 (mtt) cc_final: 0.2726 (mmp) REVERT: D 82 MET cc_start: 0.8423 (tpt) cc_final: 0.8150 (tmm) REVERT: D 176 MET cc_start: 0.8164 (pmm) cc_final: 0.7887 (pmm) REVERT: E 123 MET cc_start: 0.9155 (mmp) cc_final: 0.8935 (mmp) REVERT: F 47 MET cc_start: 0.7647 (pmm) cc_final: 0.7313 (pmm) REVERT: F 119 MET cc_start: 0.9408 (mtm) cc_final: 0.9115 (mtt) REVERT: F 132 MET cc_start: 0.9215 (ppp) cc_final: 0.8656 (ppp) REVERT: F 227 MET cc_start: 0.8362 (mmp) cc_final: 0.7901 (mmp) REVERT: F 305 MET cc_start: 0.8825 (mmp) cc_final: 0.8406 (mmp) REVERT: F 313 MET cc_start: 0.9427 (tpt) cc_final: 0.9148 (tpt) REVERT: F 325 MET cc_start: 0.8640 (pmm) cc_final: 0.8266 (pmm) REVERT: G 564 MET cc_start: 0.7472 (mmp) cc_final: 0.6855 (mmp) REVERT: G 733 MET cc_start: 0.9418 (tmm) cc_final: 0.9156 (tmm) REVERT: H 721 MET cc_start: 0.9709 (mmm) cc_final: 0.8945 (mmm) outliers start: 10 outliers final: 6 residues processed: 125 average time/residue: 0.1521 time to fit residues: 32.1177 Evaluate side-chains 125 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain F residue 87 HIS Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain G residue 812 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 199 optimal weight: 9.9990 chunk 293 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 223 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 137 GLN C 225 ASN C 275 HIS C 297 ASN D 137 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 652 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.042762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.032324 restraints weight = 254811.152| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 5.66 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 24344 Z= 0.294 Angle : 0.695 11.757 32968 Z= 0.342 Chirality : 0.044 0.174 3695 Planarity : 0.004 0.061 4230 Dihedral : 7.425 171.978 3345 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.51 % Allowed : 6.31 % Favored : 93.19 % 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 aren not related in a simple way. whole: 0.66 (0.16), residues: 2973 helix: 1.25 (0.14), residues: 1472 sheet: -0.42 (0.25), residues: 414 loop : -0.19 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 28 TYR 0.026 0.002 TYR G 705 PHE 0.017 0.002 PHE B 127 TRP 0.019 0.002 TRP D 79 HIS 0.007 0.001 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00641 (24340) covalent geometry : angle 0.69525 (32968) hydrogen bonds : bond 0.03507 ( 1207) hydrogen bonds : angle 4.53287 ( 3339) Misc. bond : bond 0.00295 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8581 (tmm) cc_final: 0.7985 (tmm) REVERT: B 123 MET cc_start: 0.9086 (tpp) cc_final: 0.8850 (tpp) REVERT: B 132 MET cc_start: 0.8359 (tmm) cc_final: 0.7918 (tmm) REVERT: B 325 MET cc_start: 0.8222 (tpp) cc_final: 0.7998 (mmt) REVERT: B 355 MET cc_start: 0.8832 (tpp) cc_final: 0.8540 (mmm) REVERT: C 305 MET cc_start: 0.8238 (mpp) cc_final: 0.7887 (mpp) REVERT: D 47 MET cc_start: 0.4992 (mtt) cc_final: 0.3716 (mmt) REVERT: D 82 MET cc_start: 0.8517 (tpt) cc_final: 0.8204 (tmm) REVERT: D 119 MET cc_start: 0.8869 (mtm) cc_final: 0.8456 (mtm) REVERT: D 325 MET cc_start: 0.6026 (ppp) cc_final: 0.5604 (ppp) REVERT: E 119 MET cc_start: 0.9437 (mtm) cc_final: 0.9183 (mtm) REVERT: E 305 MET cc_start: 0.8498 (mmp) cc_final: 0.8151 (mmp) REVERT: F 47 MET cc_start: 0.8084 (pmm) cc_final: 0.7766 (pmm) REVERT: F 119 MET cc_start: 0.9373 (mtm) cc_final: 0.9151 (mtm) REVERT: F 132 MET cc_start: 0.9177 (ppp) cc_final: 0.8539 (ppp) REVERT: F 227 MET cc_start: 0.8531 (mmp) cc_final: 0.8173 (mmp) REVERT: F 305 MET cc_start: 0.8913 (mmp) cc_final: 0.8459 (mmp) REVERT: F 313 MET cc_start: 0.9420 (tpt) cc_final: 0.9115 (tpt) REVERT: F 325 MET cc_start: 0.8634 (pmm) cc_final: 0.8184 (pmm) REVERT: G 564 MET cc_start: 0.6540 (mmp) cc_final: 0.5875 (mmp) REVERT: G 733 MET cc_start: 0.9401 (tmm) cc_final: 0.9136 (tmm) REVERT: H 705 TYR cc_start: 0.9388 (OUTLIER) cc_final: 0.9182 (m-80) REVERT: H 721 MET cc_start: 0.9805 (mmm) cc_final: 0.9204 (mmm) outliers start: 13 outliers final: 9 residues processed: 123 average time/residue: 0.1435 time to fit residues: 30.1982 Evaluate side-chains 127 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain F residue 87 HIS Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain G residue 812 HIS Chi-restraints excluded: chain H residue 705 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 298 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 244 optimal weight: 30.0000 chunk 240 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN D 354 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.043007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.032564 restraints weight = 256719.884| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 5.93 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24344 Z= 0.211 Angle : 0.612 8.523 32968 Z= 0.297 Chirality : 0.042 0.160 3695 Planarity : 0.004 0.060 4230 Dihedral : 7.381 173.865 3345 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.51 % Allowed : 7.28 % Favored : 92.21 % 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 aren not related in a simple way. whole: 0.77 (0.16), residues: 2973 helix: 1.32 (0.14), residues: 1508 sheet: -0.30 (0.26), residues: 414 loop : -0.18 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 177 TYR 0.024 0.001 TYR G 705 PHE 0.012 0.001 PHE G 920 TRP 0.018 0.002 TRP D 79 HIS 0.004 0.001 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00459 (24340) covalent geometry : angle 0.61168 (32968) hydrogen bonds : bond 0.03121 ( 1207) hydrogen bonds : angle 4.34400 ( 3339) Misc. bond : bond 0.00223 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8539 (tmm) cc_final: 0.8337 (tmm) REVERT: B 123 MET cc_start: 0.8951 (tpp) cc_final: 0.8749 (tpp) REVERT: B 132 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7856 (tmm) REVERT: B 355 MET cc_start: 0.8838 (tpp) cc_final: 0.8548 (mmm) REVERT: C 47 MET cc_start: 0.7718 (pmm) cc_final: 0.7358 (pmm) REVERT: C 132 MET cc_start: 0.7945 (tmm) cc_final: 0.7556 (tmm) REVERT: C 305 MET cc_start: 0.8292 (mpp) cc_final: 0.8019 (mpp) REVERT: D 47 MET cc_start: 0.4977 (mtt) cc_final: 0.4161 (mmt) REVERT: D 82 MET cc_start: 0.8527 (tpt) cc_final: 0.8205 (tmm) REVERT: D 162 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8197 (m-40) REVERT: D 176 MET cc_start: 0.8526 (ptp) cc_final: 0.8135 (pmm) REVERT: D 305 MET cc_start: 0.8703 (mmp) cc_final: 0.8502 (mmp) REVERT: E 123 MET cc_start: 0.9097 (mmm) cc_final: 0.8756 (mmm) REVERT: E 305 MET cc_start: 0.8528 (mmp) cc_final: 0.8327 (mmp) REVERT: F 47 MET cc_start: 0.8198 (pmm) cc_final: 0.7794 (pmm) REVERT: F 82 MET cc_start: 0.9147 (tpt) cc_final: 0.8452 (tpt) REVERT: F 119 MET cc_start: 0.9382 (mtm) cc_final: 0.9013 (mtt) REVERT: F 132 MET cc_start: 0.9152 (ppp) cc_final: 0.8538 (ppp) REVERT: F 227 MET cc_start: 0.8618 (mmp) cc_final: 0.8326 (mmp) REVERT: F 305 MET cc_start: 0.8851 (mmp) cc_final: 0.8422 (mmp) REVERT: F 313 MET cc_start: 0.9400 (tpt) cc_final: 0.9109 (tpt) REVERT: F 325 MET cc_start: 0.8609 (pmm) cc_final: 0.8134 (pmm) REVERT: G 564 MET cc_start: 0.7205 (mmp) cc_final: 0.6578 (mmp) REVERT: G 733 MET cc_start: 0.9430 (tmm) cc_final: 0.9175 (tmm) REVERT: H 705 TYR cc_start: 0.9412 (OUTLIER) cc_final: 0.9204 (m-80) REVERT: H 721 MET cc_start: 0.9838 (mmm) cc_final: 0.9303 (mmm) outliers start: 13 outliers final: 6 residues processed: 128 average time/residue: 0.1570 time to fit residues: 33.8405 Evaluate side-chains 127 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain G residue 812 HIS Chi-restraints excluded: chain H residue 705 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 222 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 245 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 189 optimal weight: 0.0030 chunk 199 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 794 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.043039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.033734 restraints weight = 293091.049| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 5.03 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24344 Z= 0.154 Angle : 0.587 12.224 32968 Z= 0.280 Chirality : 0.041 0.162 3695 Planarity : 0.003 0.059 4230 Dihedral : 7.285 173.991 3345 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.43 % Allowed : 7.86 % Favored : 91.71 % 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 aren not related in a simple way. whole: 0.97 (0.16), residues: 2973 helix: 1.45 (0.14), residues: 1508 sheet: -0.11 (0.26), residues: 408 loop : -0.11 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 177 TYR 0.021 0.001 TYR G 705 PHE 0.010 0.001 PHE G 920 TRP 0.016 0.002 TRP D 79 HIS 0.003 0.001 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00340 (24340) covalent geometry : angle 0.58652 (32968) hydrogen bonds : bond 0.02936 ( 1207) hydrogen bonds : angle 4.23315 ( 3339) Misc. bond : bond 0.00203 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.8938 (tpp) cc_final: 0.8705 (tpp) REVERT: B 132 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7881 (tmm) REVERT: B 283 MET cc_start: 0.8814 (mmt) cc_final: 0.8520 (mmp) REVERT: B 355 MET cc_start: 0.8877 (tpp) cc_final: 0.8612 (mmm) REVERT: C 47 MET cc_start: 0.7324 (pmm) cc_final: 0.7006 (pmm) REVERT: C 123 MET cc_start: 0.8695 (mmm) cc_final: 0.8390 (mmm) REVERT: D 47 MET cc_start: 0.4265 (mtt) cc_final: 0.2973 (mmt) REVERT: D 82 MET cc_start: 0.8539 (tpt) cc_final: 0.8245 (tmm) REVERT: D 305 MET cc_start: 0.8773 (mmp) cc_final: 0.8563 (mmp) REVERT: D 325 MET cc_start: 0.5750 (ppp) cc_final: 0.5132 (ppp) REVERT: D 355 MET cc_start: 0.8923 (pmm) cc_final: 0.8712 (pmm) REVERT: E 123 MET cc_start: 0.9087 (mmm) cc_final: 0.8840 (mmm) REVERT: E 305 MET cc_start: 0.8571 (mmp) cc_final: 0.8349 (mmp) REVERT: F 47 MET cc_start: 0.7923 (pmm) cc_final: 0.7478 (pmm) REVERT: F 82 MET cc_start: 0.9239 (tpt) cc_final: 0.8540 (tpt) REVERT: F 132 MET cc_start: 0.9002 (ppp) cc_final: 0.8327 (ppp) REVERT: F 162 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.7974 (m110) REVERT: F 305 MET cc_start: 0.8866 (mmp) cc_final: 0.8652 (mmp) REVERT: F 313 MET cc_start: 0.9378 (tpt) cc_final: 0.9014 (tpt) REVERT: F 325 MET cc_start: 0.8620 (pmm) cc_final: 0.8313 (pmm) REVERT: G 564 MET cc_start: 0.6138 (mmp) cc_final: 0.5441 (mmp) REVERT: G 733 MET cc_start: 0.9198 (tmm) cc_final: 0.8944 (tmm) REVERT: H 721 MET cc_start: 0.9682 (mmm) cc_final: 0.9087 (mmm) outliers start: 11 outliers final: 4 residues processed: 125 average time/residue: 0.1579 time to fit residues: 33.3398 Evaluate side-chains 124 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain G residue 812 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 237 optimal weight: 30.0000 chunk 253 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 225 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 291 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 49 GLN B 297 ASN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN F 162 ASN ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 568 ASN H 652 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.042163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.033011 restraints weight = 293667.760| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.96 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 24344 Z= 0.345 Angle : 0.741 12.313 32968 Z= 0.363 Chirality : 0.045 0.168 3695 Planarity : 0.004 0.056 4230 Dihedral : 7.500 176.957 3345 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.74 % Allowed : 8.25 % Favored : 91.01 % 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 aren not related in a simple way. whole: 0.70 (0.16), residues: 2973 helix: 1.29 (0.14), residues: 1491 sheet: -0.41 (0.26), residues: 407 loop : -0.21 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 981 TYR 0.022 0.002 TYR G 705 PHE 0.017 0.002 PHE G 704 TRP 0.018 0.002 TRP D 79 HIS 0.008 0.001 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00748 (24340) covalent geometry : angle 0.74125 (32968) hydrogen bonds : bond 0.03612 ( 1207) hydrogen bonds : angle 4.61649 ( 3339) Misc. bond : bond 0.00326 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7910 (tmm) REVERT: B 283 MET cc_start: 0.8803 (mmt) cc_final: 0.8539 (mmp) REVERT: B 355 MET cc_start: 0.8856 (tpp) cc_final: 0.8492 (mmm) REVERT: C 44 MET cc_start: 0.8347 (mmm) cc_final: 0.7935 (mmm) REVERT: C 123 MET cc_start: 0.8732 (mmm) cc_final: 0.8388 (mmm) REVERT: D 47 MET cc_start: 0.4664 (mtt) cc_final: 0.4112 (mmt) REVERT: D 82 MET cc_start: 0.8604 (tpt) cc_final: 0.8310 (tmm) REVERT: D 162 ASN cc_start: 0.8597 (OUTLIER) cc_final: 0.8289 (m-40) REVERT: D 176 MET cc_start: 0.8625 (ptp) cc_final: 0.8106 (pmm) REVERT: D 305 MET cc_start: 0.8779 (mmp) cc_final: 0.8577 (mmp) REVERT: E 123 MET cc_start: 0.9153 (mmm) cc_final: 0.8868 (mmm) REVERT: E 227 MET cc_start: 0.9127 (mmm) cc_final: 0.8883 (mmm) REVERT: F 47 MET cc_start: 0.8362 (pmm) cc_final: 0.7899 (pmm) REVERT: F 82 MET cc_start: 0.9277 (tpt) cc_final: 0.8596 (tpt) REVERT: F 132 MET cc_start: 0.9032 (ppp) cc_final: 0.8414 (ppp) REVERT: F 162 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8416 (m-40) REVERT: F 305 MET cc_start: 0.8724 (mmp) cc_final: 0.8399 (mmp) REVERT: F 313 MET cc_start: 0.9357 (tpt) cc_final: 0.8884 (tpt) REVERT: G 564 MET cc_start: 0.5876 (mmp) cc_final: 0.5227 (mmp) REVERT: H 721 MET cc_start: 0.9680 (mmm) cc_final: 0.9183 (mmm) outliers start: 19 outliers final: 10 residues processed: 128 average time/residue: 0.1538 time to fit residues: 33.5934 Evaluate side-chains 130 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain G residue 812 HIS Chi-restraints excluded: chain H residue 655 VAL Chi-restraints excluded: chain H residue 803 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 100 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 296 optimal weight: 20.0000 chunk 240 optimal weight: 30.0000 chunk 220 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.042919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.033978 restraints weight = 291185.329| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 5.02 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24344 Z= 0.135 Angle : 0.598 11.737 32968 Z= 0.284 Chirality : 0.042 0.327 3695 Planarity : 0.003 0.057 4230 Dihedral : 7.376 176.313 3345 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.54 % Allowed : 8.45 % Favored : 91.01 % 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 aren not related in a simple way. whole: 0.98 (0.16), residues: 2973 helix: 1.43 (0.14), residues: 1515 sheet: -0.17 (0.26), residues: 401 loop : -0.02 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 177 TYR 0.019 0.001 TYR G 705 PHE 0.010 0.001 PHE G 920 TRP 0.018 0.002 TRP D 79 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00299 (24340) covalent geometry : angle 0.59789 (32968) hydrogen bonds : bond 0.02953 ( 1207) hydrogen bonds : angle 4.25101 ( 3339) Misc. bond : bond 0.00198 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7853 (tmm) REVERT: B 283 MET cc_start: 0.8735 (mmt) cc_final: 0.8505 (mmp) REVERT: B 355 MET cc_start: 0.8899 (tpp) cc_final: 0.8532 (mmm) REVERT: C 123 MET cc_start: 0.8559 (mmm) cc_final: 0.8213 (tpp) REVERT: D 82 MET cc_start: 0.8634 (tpt) cc_final: 0.8341 (tmm) REVERT: D 162 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8117 (m-40) REVERT: D 176 MET cc_start: 0.8483 (ptp) cc_final: 0.7977 (pmm) REVERT: D 325 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.6045 (ppp) REVERT: D 355 MET cc_start: 0.8959 (pmm) cc_final: 0.8759 (pmm) REVERT: E 123 MET cc_start: 0.9125 (mmm) cc_final: 0.8784 (mmm) REVERT: E 305 MET cc_start: 0.8374 (mmp) cc_final: 0.7998 (mmp) REVERT: F 47 MET cc_start: 0.8327 (pmm) cc_final: 0.7937 (pmm) REVERT: F 82 MET cc_start: 0.9238 (tpt) cc_final: 0.8537 (tpt) REVERT: F 132 MET cc_start: 0.9018 (ppp) cc_final: 0.8347 (ppp) REVERT: F 305 MET cc_start: 0.8804 (mmp) cc_final: 0.8600 (mmp) REVERT: F 313 MET cc_start: 0.9357 (tpt) cc_final: 0.9089 (tpt) REVERT: F 325 MET cc_start: 0.8683 (pmm) cc_final: 0.8359 (pmm) REVERT: G 564 MET cc_start: 0.5058 (mmp) cc_final: 0.4586 (mmp) REVERT: H 564 MET cc_start: 0.6430 (ptt) cc_final: 0.5713 (ptt) REVERT: H 721 MET cc_start: 0.9665 (mmm) cc_final: 0.9181 (mmm) outliers start: 14 outliers final: 8 residues processed: 125 average time/residue: 0.1561 time to fit residues: 32.9096 Evaluate side-chains 129 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain G residue 812 HIS Chi-restraints excluded: chain H residue 803 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 132 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 chunk 106 optimal weight: 0.0370 chunk 188 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 overall best weight: 1.8664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 HIS ** 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 = 0.3564 r_free = 0.3564 target = 0.043244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.034900 restraints weight = 293701.469| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 5.18 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24344 Z= 0.120 Angle : 0.585 8.859 32968 Z= 0.277 Chirality : 0.041 0.167 3695 Planarity : 0.003 0.058 4230 Dihedral : 7.204 176.800 3345 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.47 % Allowed : 8.91 % Favored : 90.62 % 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 aren not related in a simple way. whole: 1.14 (0.16), residues: 2973 helix: 1.50 (0.14), residues: 1518 sheet: -0.08 (0.26), residues: 401 loop : 0.15 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 177 TYR 0.028 0.001 TYR H 705 PHE 0.017 0.001 PHE H 704 TRP 0.027 0.002 TRP E 86 HIS 0.003 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00268 (24340) covalent geometry : angle 0.58529 (32968) hydrogen bonds : bond 0.02785 ( 1207) hydrogen bonds : angle 4.15489 ( 3339) Misc. bond : bond 0.00181 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7899 (tmm) REVERT: B 283 MET cc_start: 0.8710 (mmt) cc_final: 0.8465 (mmp) REVERT: B 355 MET cc_start: 0.8873 (tpp) cc_final: 0.8534 (mmm) REVERT: C 119 MET cc_start: 0.9005 (mtm) cc_final: 0.8737 (mtm) REVERT: C 123 MET cc_start: 0.8426 (mmm) cc_final: 0.8029 (tpp) REVERT: D 82 MET cc_start: 0.8618 (tpt) cc_final: 0.8290 (tmm) REVERT: D 162 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8120 (m-40) REVERT: D 176 MET cc_start: 0.8395 (ptp) cc_final: 0.8052 (pmm) REVERT: D 325 MET cc_start: 0.6233 (OUTLIER) cc_final: 0.5939 (ppp) REVERT: D 355 MET cc_start: 0.8903 (pmm) cc_final: 0.8694 (pmm) REVERT: E 176 MET cc_start: 0.8213 (mtp) cc_final: 0.7906 (mtt) REVERT: E 227 MET cc_start: 0.9120 (mmm) cc_final: 0.8890 (mmm) REVERT: E 305 MET cc_start: 0.8384 (mmp) cc_final: 0.7997 (mmp) REVERT: F 47 MET cc_start: 0.8347 (pmm) cc_final: 0.7921 (pmm) REVERT: F 82 MET cc_start: 0.9253 (tpt) cc_final: 0.8502 (tpt) REVERT: F 132 MET cc_start: 0.8974 (ppp) cc_final: 0.8394 (ppp) REVERT: F 227 MET cc_start: 0.8497 (mmp) cc_final: 0.7924 (mmp) REVERT: F 305 MET cc_start: 0.8868 (mmp) cc_final: 0.8629 (mmp) REVERT: F 313 MET cc_start: 0.9430 (tpt) cc_final: 0.8984 (tpt) REVERT: F 325 MET cc_start: 0.8709 (pmm) cc_final: 0.8343 (pmm) REVERT: H 564 MET cc_start: 0.6349 (ptt) cc_final: 0.5654 (ptt) REVERT: H 721 MET cc_start: 0.9610 (mmm) cc_final: 0.9091 (mmm) outliers start: 12 outliers final: 8 residues processed: 123 average time/residue: 0.1556 time to fit residues: 32.3316 Evaluate side-chains 128 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain G residue 812 HIS Chi-restraints excluded: chain H residue 803 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 79 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 209 optimal weight: 0.0170 chunk 260 optimal weight: 7.9990 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.042668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.033422 restraints weight = 294123.052| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 4.99 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24344 Z= 0.199 Angle : 0.637 9.035 32968 Z= 0.303 Chirality : 0.042 0.166 3695 Planarity : 0.004 0.058 4230 Dihedral : 7.189 178.179 3345 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.54 % Allowed : 8.88 % Favored : 90.58 % 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 aren not related in a simple way. whole: 1.10 (0.16), residues: 2973 helix: 1.52 (0.14), residues: 1513 sheet: -0.13 (0.26), residues: 402 loop : 0.06 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 177 TYR 0.043 0.001 TYR H 705 PHE 0.020 0.001 PHE G 704 TRP 0.015 0.001 TRP D 79 HIS 0.004 0.001 HIS G 703 Details of bonding type rmsd covalent geometry : bond 0.00437 (24340) covalent geometry : angle 0.63712 (32968) hydrogen bonds : bond 0.02970 ( 1207) hydrogen bonds : angle 4.26055 ( 3339) Misc. bond : bond 0.00217 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7912 (tmm) REVERT: B 283 MET cc_start: 0.8693 (mmt) cc_final: 0.8436 (mmp) REVERT: B 355 MET cc_start: 0.8870 (tpp) cc_final: 0.8518 (mmm) REVERT: D 47 MET cc_start: 0.1591 (mtm) cc_final: 0.0332 (mmm) REVERT: D 82 MET cc_start: 0.8613 (tpt) cc_final: 0.8284 (tmm) REVERT: D 162 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8147 (m-40) REVERT: D 176 MET cc_start: 0.8518 (ptp) cc_final: 0.8004 (pmm) REVERT: D 325 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.6114 (ppp) REVERT: D 355 MET cc_start: 0.8955 (pmm) cc_final: 0.8743 (pmm) REVERT: E 227 MET cc_start: 0.9120 (mmm) cc_final: 0.8860 (mmm) REVERT: E 305 MET cc_start: 0.8356 (mmp) cc_final: 0.7984 (mmp) REVERT: F 47 MET cc_start: 0.8365 (pmm) cc_final: 0.7971 (pmm) REVERT: F 82 MET cc_start: 0.9234 (tpt) cc_final: 0.8510 (tpt) REVERT: F 132 MET cc_start: 0.8953 (ppp) cc_final: 0.8399 (ppp) REVERT: F 227 MET cc_start: 0.8467 (mmp) cc_final: 0.7948 (mmp) REVERT: F 305 MET cc_start: 0.8845 (mmp) cc_final: 0.8497 (mmp) REVERT: F 313 MET cc_start: 0.9364 (tpt) cc_final: 0.8976 (tpt) REVERT: F 325 MET cc_start: 0.8725 (pmm) cc_final: 0.8467 (pmm) REVERT: H 564 MET cc_start: 0.6539 (ptt) cc_final: 0.5851 (ptt) REVERT: H 721 MET cc_start: 0.9660 (mmm) cc_final: 0.9220 (mmm) outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 0.1574 time to fit residues: 32.6024 Evaluate side-chains 128 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain G residue 564 MET Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain G residue 812 HIS Chi-restraints excluded: chain H residue 803 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 184 optimal weight: 6.9990 chunk 82 optimal weight: 0.3980 chunk 268 optimal weight: 9.9990 chunk 240 optimal weight: 30.0000 chunk 86 optimal weight: 0.7980 chunk 291 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 227 optimal weight: 50.0000 chunk 288 optimal weight: 9.9990 chunk 270 optimal weight: 6.9990 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.042658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.033455 restraints weight = 291703.497| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 4.96 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24344 Z= 0.198 Angle : 0.640 11.814 32968 Z= 0.304 Chirality : 0.043 0.176 3695 Planarity : 0.003 0.058 4230 Dihedral : 7.179 178.500 3345 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.58 % Allowed : 9.03 % Favored : 90.39 % 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 aren not related in a simple way. whole: 1.10 (0.16), residues: 2973 helix: 1.47 (0.14), residues: 1518 sheet: -0.14 (0.26), residues: 402 loop : 0.14 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 177 TYR 0.040 0.001 TYR H 705 PHE 0.015 0.001 PHE B 127 TRP 0.016 0.002 TRP D 79 HIS 0.004 0.001 HIS F 87 Details of bonding type rmsd covalent geometry : bond 0.00434 (24340) covalent geometry : angle 0.63955 (32968) hydrogen bonds : bond 0.02984 ( 1207) hydrogen bonds : angle 4.29157 ( 3339) Misc. bond : bond 0.00225 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5290.86 seconds wall clock time: 92 minutes 4.56 seconds (5524.56 seconds total)