Starting phenix.real_space_refine on Fri Jun 20 17:23:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9az4_44012/06_2025/9az4_44012.cif Found real_map, /net/cci-nas-00/data/ceres_data/9az4_44012/06_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_44012/06_2025/9az4_44012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9az4_44012/06_2025/9az4_44012.map" model { file = "/net/cci-nas-00/data/ceres_data/9az4_44012/06_2025/9az4_44012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9az4_44012/06_2025/9az4_44012.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.68, per 1000 atoms: 0.62 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: 6.02 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 3.46 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: 9.19 Time building geometry restraints manager: 7.10 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 56.400 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.120 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.100 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.004 TRP A 356 HIS 0.017 0.002 HIS G 554 PHE 0.027 0.003 PHE G 920 TYR 0.070 0.003 TYR G 705 ARG 0.008 0.001 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.15725 ( 1207) hydrogen bonds : angle 6.67274 ( 3339) covalent geometry : bond 0.00671 (24340) covalent geometry : angle 1.05715 (32968) 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 : 2.668 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: 0.3394 time to fit residues: 71.0721 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 : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 8.9990 chunk 227 optimal weight: 40.0000 chunk 126 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 272 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.043538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.033022 restraints weight = 255980.335| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 5.96 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24344 Z= 0.245 Angle : 0.662 8.979 32968 Z= 0.328 Chirality : 0.043 0.170 3695 Planarity : 0.004 0.069 4230 Dihedral : 7.603 173.035 3345 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.23 % Allowed : 3.00 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 2973 helix: 0.40 (0.13), residues: 1485 sheet: -0.62 (0.25), residues: 402 loop : -0.43 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 79 HIS 0.005 0.001 HIS F 87 PHE 0.014 0.002 PHE B 127 TYR 0.034 0.001 TYR G 705 ARG 0.004 0.000 ARG H 868 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 1207) hydrogen bonds : angle 4.64181 ( 3339) covalent geometry : bond 0.00527 (24340) covalent geometry : angle 0.66190 (32968) Misc. bond : bond 0.00264 ( 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 127 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 2.728 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: 0.8502 (tmm) cc_final: 0.8022 (tmm) REVERT: A 283 MET cc_start: 0.9115 (mmm) cc_final: 0.8904 (mmm) REVERT: A 355 MET cc_start: 0.8592 (tpp) cc_final: 0.8366 (tpp) REVERT: B 132 MET cc_start: 0.8467 (tmm) cc_final: 0.8064 (tmm) REVERT: B 355 MET cc_start: 0.8524 (tpp) cc_final: 0.8181 (tpp) REVERT: C 119 MET cc_start: 0.8818 (mtm) cc_final: 0.8603 (mtm) REVERT: C 132 MET cc_start: 0.8196 (ppp) cc_final: 0.7839 (tmm) REVERT: C 305 MET cc_start: 0.8134 (mpp) cc_final: 0.7860 (mpp) REVERT: C 355 MET cc_start: 0.5670 (pmm) cc_final: 0.5438 (pmm) REVERT: D 82 MET cc_start: 0.8429 (tpt) cc_final: 0.8185 (tmm) REVERT: D 227 MET cc_start: 0.9065 (mmm) cc_final: 0.8840 (mmm) REVERT: E 123 MET cc_start: 0.9105 (mmp) cc_final: 0.8856 (mmp) REVERT: E 299 MET cc_start: 0.9011 (mtm) cc_final: 0.8772 (mtp) REVERT: F 47 MET cc_start: 0.7394 (pmm) cc_final: 0.7076 (pmm) REVERT: F 82 MET cc_start: 0.8996 (tpt) cc_final: 0.8690 (tpt) REVERT: F 119 MET cc_start: 0.9428 (mtm) cc_final: 0.9133 (mtt) REVERT: F 132 MET cc_start: 0.9160 (ppp) cc_final: 0.8600 (ppp) REVERT: F 227 MET cc_start: 0.8328 (mmp) cc_final: 0.7957 (mmp) REVERT: F 305 MET cc_start: 0.8786 (mmp) cc_final: 0.8334 (mmp) REVERT: F 325 MET cc_start: 0.8565 (pmm) cc_final: 0.8267 (pmm) REVERT: G 564 MET cc_start: 0.7336 (mmp) cc_final: 0.6408 (mmp) REVERT: G 733 MET cc_start: 0.9425 (tmm) cc_final: 0.9194 (tmm) REVERT: H 705 TYR cc_start: 0.9455 (m-10) cc_final: 0.9189 (m-80) outliers start: 6 outliers final: 3 residues processed: 124 average time/residue: 0.3952 time to fit residues: 83.2992 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 : 2.820 ------------------------------------------------------------------------------- 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 57 optimal weight: 3.9990 chunk 267 optimal weight: 40.0000 chunk 69 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 195 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 291 optimal weight: 30.0000 chunk 68 optimal weight: 10.0000 chunk 281 optimal weight: 50.0000 chunk 0 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN D 162 ASN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.043780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.033286 restraints weight = 253197.486| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 5.96 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1535 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= 0.154 Angle : 0.576 8.087 32968 Z= 0.280 Chirality : 0.041 0.167 3695 Planarity : 0.004 0.064 4230 Dihedral : 7.292 170.243 3345 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.47 % Allowed : 4.09 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2973 helix: 1.16 (0.14), residues: 1469 sheet: -0.45 (0.25), residues: 402 loop : -0.17 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.004 0.001 HIS F 87 PHE 0.011 0.001 PHE G 920 TYR 0.030 0.001 TYR G 705 ARG 0.003 0.000 ARG F 177 Details of bonding type rmsd hydrogen bonds : bond 0.03123 ( 1207) hydrogen bonds : angle 4.33733 ( 3339) covalent geometry : bond 0.00334 (24340) covalent geometry : angle 0.57581 (32968) Misc. bond : bond 0.00218 ( 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 130 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 3.965 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: 0.8542 (tmm) cc_final: 0.7964 (tmm) REVERT: A 355 MET cc_start: 0.8740 (tpp) cc_final: 0.8124 (tpt) REVERT: B 44 MET cc_start: 0.2208 (pmm) cc_final: 0.1824 (ptt) REVERT: B 132 MET cc_start: 0.8453 (tmm) cc_final: 0.7987 (tmm) REVERT: B 283 MET cc_start: 0.9059 (mmt) cc_final: 0.8637 (mmp) REVERT: B 355 MET cc_start: 0.8557 (tpp) cc_final: 0.8122 (tpp) REVERT: C 132 MET cc_start: 0.8205 (ppp) cc_final: 0.7800 (tmm) REVERT: C 305 MET cc_start: 0.8172 (mpp) cc_final: 0.7901 (mpp) REVERT: D 47 MET cc_start: 0.4610 (mtt) cc_final: 0.2878 (mmt) REVERT: D 82 MET cc_start: 0.8410 (tpt) cc_final: 0.8121 (tmm) REVERT: D 176 MET cc_start: 0.8142 (pmm) cc_final: 0.7876 (pmm) REVERT: E 123 MET cc_start: 0.9172 (mmp) cc_final: 0.8954 (mmp) REVERT: F 47 MET cc_start: 0.7634 (pmm) cc_final: 0.7290 (pmm) REVERT: F 119 MET cc_start: 0.9413 (mtm) cc_final: 0.9080 (mtt) REVERT: F 132 MET cc_start: 0.9185 (ppp) cc_final: 0.8630 (ppp) REVERT: F 227 MET cc_start: 0.8421 (mmp) cc_final: 0.8003 (mmp) REVERT: F 305 MET cc_start: 0.8780 (mmp) cc_final: 0.8294 (mmp) REVERT: F 313 MET cc_start: 0.9411 (tpt) cc_final: 0.9063 (tpt) REVERT: F 325 MET cc_start: 0.8588 (pmm) cc_final: 0.8238 (pmm) REVERT: G 564 MET cc_start: 0.7015 (mmp) cc_final: 0.6355 (mmp) REVERT: G 733 MET cc_start: 0.9398 (tmm) cc_final: 0.9150 (tmm) REVERT: H 705 TYR cc_start: 0.9430 (m-10) cc_final: 0.9145 (m-80) REVERT: H 721 MET cc_start: 0.9674 (mmt) cc_final: 0.8811 (mmm) outliers start: 12 outliers final: 4 residues processed: 125 average time/residue: 0.4565 time to fit residues: 95.2440 Evaluate side-chains 122 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 5.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLU 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 152 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 273 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 106 optimal weight: 0.0980 chunk 204 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3613 r_free = 0.3613 target = 0.044395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.033847 restraints weight = 254440.862| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 6.25 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 24344 Z= 0.092 Angle : 0.539 10.604 32968 Z= 0.256 Chirality : 0.040 0.162 3695 Planarity : 0.003 0.060 4230 Dihedral : 7.029 169.178 3345 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.43 % Allowed : 4.98 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.16), residues: 2973 helix: 1.42 (0.14), residues: 1476 sheet: -0.20 (0.26), residues: 402 loop : 0.06 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 79 HIS 0.003 0.000 HIS G 554 PHE 0.010 0.001 PHE G 920 TYR 0.026 0.001 TYR G 705 ARG 0.006 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.02739 ( 1207) hydrogen bonds : angle 4.09029 ( 3339) covalent geometry : bond 0.00207 (24340) covalent geometry : angle 0.53862 (32968) Misc. bond : bond 0.00171 ( 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 129 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 2.683 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: 0.8446 (tmm) cc_final: 0.8022 (tmm) REVERT: A 355 MET cc_start: 0.8848 (tpp) cc_final: 0.8158 (tpt) REVERT: B 132 MET cc_start: 0.8506 (tmm) cc_final: 0.8025 (tmm) REVERT: B 283 MET cc_start: 0.9046 (mmt) cc_final: 0.8664 (mmp) REVERT: C 119 MET cc_start: 0.8598 (mtm) cc_final: 0.8347 (mtm) REVERT: C 123 MET cc_start: 0.8815 (mmm) cc_final: 0.8507 (mmm) REVERT: C 132 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7701 (tmm) REVERT: C 305 MET cc_start: 0.8202 (mpp) cc_final: 0.7925 (mpp) REVERT: D 47 MET cc_start: 0.4039 (mtt) cc_final: 0.2531 (mmt) REVERT: D 82 MET cc_start: 0.8392 (tpt) cc_final: 0.8078 (tmm) REVERT: D 305 MET cc_start: 0.8792 (mmp) cc_final: 0.8082 (mmp) REVERT: D 325 MET cc_start: 0.5366 (OUTLIER) cc_final: 0.4992 (ppp) REVERT: E 305 MET cc_start: 0.8399 (mmp) cc_final: 0.8102 (mmp) REVERT: F 47 MET cc_start: 0.7608 (pmm) cc_final: 0.7240 (pmm) REVERT: F 82 MET cc_start: 0.9075 (tpt) cc_final: 0.8411 (tpt) REVERT: F 119 MET cc_start: 0.9342 (mtm) cc_final: 0.9013 (mtt) REVERT: F 132 MET cc_start: 0.9186 (ppp) cc_final: 0.8761 (ppp) REVERT: F 227 MET cc_start: 0.8414 (mmp) cc_final: 0.7988 (mmp) REVERT: F 305 MET cc_start: 0.8781 (mmp) cc_final: 0.8451 (mmp) REVERT: F 325 MET cc_start: 0.8562 (pmm) cc_final: 0.8181 (pmm) REVERT: G 564 MET cc_start: 0.8074 (mmp) cc_final: 0.7597 (mmp) REVERT: G 733 MET cc_start: 0.9456 (tmm) cc_final: 0.9188 (tmm) REVERT: H 705 TYR cc_start: 0.9467 (m-10) cc_final: 0.9190 (m-80) REVERT: H 721 MET cc_start: 0.9679 (mmt) cc_final: 0.8937 (mmm) REVERT: H 913 MET cc_start: 0.7523 (ppp) cc_final: 0.6880 (ppp) outliers start: 11 outliers final: 7 residues processed: 122 average time/residue: 0.3288 time to fit residues: 67.6105 Evaluate side-chains 126 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 325 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 280 optimal weight: 20.0000 chunk 253 optimal weight: 20.0000 chunk 134 optimal weight: 0.1980 chunk 233 optimal weight: 7.9990 chunk 232 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 197 optimal weight: 20.0000 chunk 173 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.043714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.033145 restraints weight = 255159.552| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 6.12 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1915 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= 0.160 Angle : 0.569 8.045 32968 Z= 0.273 Chirality : 0.041 0.163 3695 Planarity : 0.003 0.059 4230 Dihedral : 6.963 170.693 3345 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.47 % Allowed : 5.61 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.16), residues: 2973 helix: 1.61 (0.14), residues: 1478 sheet: -0.15 (0.26), residues: 402 loop : 0.12 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 79 HIS 0.004 0.001 HIS F 87 PHE 0.011 0.001 PHE B 127 TYR 0.021 0.001 TYR G 705 ARG 0.006 0.000 ARG E 254 Details of bonding type rmsd hydrogen bonds : bond 0.02863 ( 1207) hydrogen bonds : angle 4.09914 ( 3339) covalent geometry : bond 0.00352 (24340) covalent geometry : angle 0.56876 (32968) Misc. bond : bond 0.00202 ( 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 129 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8526 (tmm) cc_final: 0.8041 (tmm) REVERT: B 132 MET cc_start: 0.8564 (tmm) cc_final: 0.8080 (tmm) REVERT: B 283 MET cc_start: 0.8910 (mmt) cc_final: 0.8553 (mmp) REVERT: C 123 MET cc_start: 0.8717 (mmm) cc_final: 0.8454 (mmm) REVERT: C 132 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7765 (tmm) REVERT: D 47 MET cc_start: 0.4755 (mtt) cc_final: 0.3431 (mmt) REVERT: D 82 MET cc_start: 0.8470 (tpt) cc_final: 0.8171 (tmm) REVERT: D 176 MET cc_start: 0.8421 (ptp) cc_final: 0.8187 (pmm) REVERT: D 325 MET cc_start: 0.5683 (OUTLIER) cc_final: 0.5287 (ppp) REVERT: E 119 MET cc_start: 0.9441 (mtm) cc_final: 0.9227 (mtm) REVERT: E 305 MET cc_start: 0.8470 (mmp) cc_final: 0.8267 (mmp) REVERT: F 44 MET cc_start: 0.8406 (mmm) cc_final: 0.8184 (mmm) REVERT: F 47 MET cc_start: 0.7895 (pmm) cc_final: 0.7433 (pmm) REVERT: F 82 MET cc_start: 0.9157 (tpt) cc_final: 0.8479 (tpt) REVERT: F 119 MET cc_start: 0.9351 (mtm) cc_final: 0.8926 (mtt) REVERT: F 132 MET cc_start: 0.9164 (ppp) cc_final: 0.8726 (ppp) REVERT: F 305 MET cc_start: 0.8791 (mmp) cc_final: 0.8434 (mmp) REVERT: F 325 MET cc_start: 0.8590 (pmm) cc_final: 0.8069 (pmm) REVERT: G 564 MET cc_start: 0.7128 (mmp) cc_final: 0.6444 (mmp) REVERT: G 733 MET cc_start: 0.9432 (tmm) cc_final: 0.9160 (tmm) outliers start: 12 outliers final: 8 residues processed: 122 average time/residue: 0.3321 time to fit residues: 68.7143 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 : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 325 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 34 optimal weight: 7.9990 chunk 274 optimal weight: 0.9980 chunk 216 optimal weight: 7.9990 chunk 235 optimal weight: 40.0000 chunk 198 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 268 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 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 = 0.3589 r_free = 0.3589 target = 0.043840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.033226 restraints weight = 253453.251| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 6.03 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24344 Z= 0.132 Angle : 0.561 11.108 32968 Z= 0.265 Chirality : 0.041 0.167 3695 Planarity : 0.003 0.058 4230 Dihedral : 6.908 170.161 3345 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.51 % Allowed : 6.19 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 2973 helix: 1.57 (0.14), residues: 1513 sheet: -0.09 (0.26), residues: 402 loop : 0.14 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 79 HIS 0.003 0.001 HIS F 87 PHE 0.010 0.001 PHE G 920 TYR 0.019 0.001 TYR G 705 ARG 0.005 0.000 ARG E 254 Details of bonding type rmsd hydrogen bonds : bond 0.02729 ( 1207) hydrogen bonds : angle 4.02464 ( 3339) covalent geometry : bond 0.00294 (24340) covalent geometry : angle 0.56072 (32968) Misc. bond : bond 0.00196 ( 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 133 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8483 (tmm) cc_final: 0.7998 (tmm) REVERT: B 132 MET cc_start: 0.8564 (tmm) cc_final: 0.8076 (tmm) REVERT: B 283 MET cc_start: 0.8838 (mmt) cc_final: 0.8542 (mmp) REVERT: C 123 MET cc_start: 0.8783 (mmm) cc_final: 0.8487 (mmm) REVERT: C 305 MET cc_start: 0.8187 (mpp) cc_final: 0.7904 (mpp) REVERT: D 47 MET cc_start: 0.4745 (mtt) cc_final: 0.3044 (mmt) REVERT: D 82 MET cc_start: 0.8480 (tpt) cc_final: 0.8175 (tmm) REVERT: D 305 MET cc_start: 0.8651 (mmp) cc_final: 0.8433 (mmp) REVERT: D 325 MET cc_start: 0.5778 (OUTLIER) cc_final: 0.5446 (ppp) REVERT: E 119 MET cc_start: 0.9434 (mtm) cc_final: 0.9208 (mtm) REVERT: F 47 MET cc_start: 0.7976 (pmm) cc_final: 0.7573 (pmm) REVERT: F 82 MET cc_start: 0.9139 (tpt) cc_final: 0.8425 (tpt) REVERT: F 119 MET cc_start: 0.9341 (mtm) cc_final: 0.8956 (mtt) REVERT: F 132 MET cc_start: 0.9190 (ppp) cc_final: 0.8759 (ppp) REVERT: F 227 MET cc_start: 0.8328 (mmp) cc_final: 0.7827 (mmp) REVERT: F 305 MET cc_start: 0.8800 (mmp) cc_final: 0.8443 (mmp) REVERT: F 325 MET cc_start: 0.8582 (pmm) cc_final: 0.8102 (pmm) REVERT: G 564 MET cc_start: 0.6899 (mmp) cc_final: 0.6183 (mmp) REVERT: G 733 MET cc_start: 0.9430 (tmm) cc_final: 0.9178 (tmm) REVERT: H 564 MET cc_start: 0.6886 (mtm) cc_final: 0.6225 (ptt) outliers start: 13 outliers final: 6 residues processed: 124 average time/residue: 0.3279 time to fit residues: 69.0898 Evaluate side-chains 124 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 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 D residue 325 MET 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 43 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 291 optimal weight: 30.0000 chunk 104 optimal weight: 0.6980 chunk 115 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN C 137 GLN C 297 ASN D 137 GLN D 354 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 794 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.043065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.032417 restraints weight = 260351.383| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 6.02 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24344 Z= 0.240 Angle : 0.647 9.953 32968 Z= 0.314 Chirality : 0.043 0.197 3695 Planarity : 0.004 0.057 4230 Dihedral : 7.085 171.627 3345 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.51 % Allowed : 7.20 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.16), residues: 2973 helix: 1.43 (0.14), residues: 1521 sheet: -0.04 (0.26), residues: 408 loop : 0.02 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 79 HIS 0.010 0.001 HIS G 773 PHE 0.021 0.002 PHE G 704 TYR 0.022 0.001 TYR G 705 ARG 0.005 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 1207) hydrogen bonds : angle 4.27182 ( 3339) covalent geometry : bond 0.00522 (24340) covalent geometry : angle 0.64678 (32968) Misc. bond : bond 0.00271 ( 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 130 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.8436 (tmm) cc_final: 0.7970 (tmm) REVERT: B 176 MET cc_start: 0.8893 (mmm) cc_final: 0.8692 (mmp) REVERT: B 283 MET cc_start: 0.8798 (mmt) cc_final: 0.8490 (mmp) REVERT: C 119 MET cc_start: 0.8798 (mtm) cc_final: 0.8506 (mtm) REVERT: C 123 MET cc_start: 0.8761 (mmm) cc_final: 0.8416 (mmm) REVERT: C 305 MET cc_start: 0.8233 (mpp) cc_final: 0.7871 (mpp) REVERT: D 82 MET cc_start: 0.8581 (tpt) cc_final: 0.8247 (tmm) REVERT: D 176 MET cc_start: 0.8512 (ptp) cc_final: 0.8033 (pmm) REVERT: D 305 MET cc_start: 0.8840 (mmp) cc_final: 0.8578 (mmp) REVERT: D 325 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5943 (ppp) REVERT: E 119 MET cc_start: 0.9447 (mtm) cc_final: 0.9228 (mtm) REVERT: E 123 MET cc_start: 0.9071 (mmp) cc_final: 0.8773 (mmp) REVERT: E 305 MET cc_start: 0.8478 (mmp) cc_final: 0.8125 (mmp) REVERT: F 47 MET cc_start: 0.8116 (pmm) cc_final: 0.7754 (pmm) REVERT: F 82 MET cc_start: 0.9168 (tpt) cc_final: 0.8462 (tpt) REVERT: F 119 MET cc_start: 0.9313 (mtm) cc_final: 0.9039 (mtt) REVERT: F 132 MET cc_start: 0.9202 (ppp) cc_final: 0.8721 (ppp) REVERT: F 227 MET cc_start: 0.8453 (mmp) cc_final: 0.7995 (mmp) REVERT: F 305 MET cc_start: 0.8926 (mmp) cc_final: 0.8463 (mmp) REVERT: F 325 MET cc_start: 0.8619 (pmm) cc_final: 0.7985 (pmm) REVERT: G 564 MET cc_start: 0.7236 (mmp) cc_final: 0.6565 (mmp) REVERT: G 733 MET cc_start: 0.9432 (tmm) cc_final: 0.9176 (tmm) REVERT: H 564 MET cc_start: 0.6910 (mtm) cc_final: 0.6251 (ptt) REVERT: H 721 MET cc_start: 0.9738 (mmt) cc_final: 0.9179 (mmm) outliers start: 13 outliers final: 8 residues processed: 123 average time/residue: 0.3243 time to fit residues: 67.4999 Evaluate side-chains 125 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 2.868 ------------------------------------------------------------------------------- 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 313 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 325 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 162 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 227 optimal weight: 50.0000 chunk 106 optimal weight: 0.0970 chunk 80 optimal weight: 1.9990 chunk 286 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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** D 354 GLN ** 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 = 0.3577 r_free = 0.3577 target = 0.043680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.033279 restraints weight = 252581.020| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 5.78 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24344 Z= 0.120 Angle : 0.572 11.092 32968 Z= 0.270 Chirality : 0.041 0.174 3695 Planarity : 0.003 0.059 4230 Dihedral : 7.007 171.414 3345 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.43 % Allowed : 7.63 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.16), residues: 2973 helix: 1.58 (0.14), residues: 1514 sheet: 0.15 (0.28), residues: 372 loop : 0.05 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 79 HIS 0.003 0.001 HIS B 371 PHE 0.010 0.001 PHE G 920 TYR 0.018 0.001 TYR G 705 ARG 0.003 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.02765 ( 1207) hydrogen bonds : angle 4.06807 ( 3339) covalent geometry : bond 0.00268 (24340) covalent geometry : angle 0.57180 (32968) Misc. bond : bond 0.00196 ( 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 127 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8528 (tmm) cc_final: 0.7954 (tmm) REVERT: B 132 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7962 (tmm) REVERT: B 176 MET cc_start: 0.9008 (mmm) cc_final: 0.8803 (mmp) REVERT: B 283 MET cc_start: 0.8769 (mmt) cc_final: 0.8512 (mmp) REVERT: C 119 MET cc_start: 0.8796 (mtm) cc_final: 0.8455 (mtm) REVERT: C 123 MET cc_start: 0.8765 (mmm) cc_final: 0.8476 (mmm) REVERT: C 132 MET cc_start: 0.8039 (tmm) cc_final: 0.7566 (tmm) REVERT: C 325 MET cc_start: 0.8050 (ptp) cc_final: 0.7728 (pmm) REVERT: D 47 MET cc_start: 0.2456 (mtm) cc_final: 0.0249 (mmt) REVERT: D 82 MET cc_start: 0.8534 (tpt) cc_final: 0.8205 (tmm) REVERT: D 176 MET cc_start: 0.8457 (ptp) cc_final: 0.8019 (pmm) REVERT: D 305 MET cc_start: 0.8815 (mmp) cc_final: 0.8305 (mmp) REVERT: D 325 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5897 (ppp) REVERT: E 123 MET cc_start: 0.9100 (mmp) cc_final: 0.8768 (mmp) REVERT: E 305 MET cc_start: 0.8471 (mmp) cc_final: 0.8100 (mmp) REVERT: F 47 MET cc_start: 0.8213 (pmm) cc_final: 0.7831 (pmm) REVERT: F 82 MET cc_start: 0.9142 (tpt) cc_final: 0.8426 (tpt) REVERT: F 119 MET cc_start: 0.9372 (mtm) cc_final: 0.9005 (mtt) REVERT: F 132 MET cc_start: 0.9241 (ppp) cc_final: 0.8753 (ppp) REVERT: F 227 MET cc_start: 0.8376 (mmp) cc_final: 0.7966 (mmp) REVERT: F 299 MET cc_start: 0.8387 (mmt) cc_final: 0.8168 (mmm) REVERT: F 305 MET cc_start: 0.8896 (mmp) cc_final: 0.8411 (mmp) REVERT: F 325 MET cc_start: 0.8552 (pmm) cc_final: 0.7949 (pmm) REVERT: G 564 MET cc_start: 0.6578 (mmp) cc_final: 0.5786 (mmp) REVERT: G 733 MET cc_start: 0.9383 (tmm) cc_final: 0.9137 (tmm) REVERT: H 721 MET cc_start: 0.9689 (mmt) cc_final: 0.9048 (mmm) outliers start: 11 outliers final: 6 residues processed: 119 average time/residue: 0.3263 time to fit residues: 65.8398 Evaluate side-chains 124 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 305 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 D residue 325 MET Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain G residue 812 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 120 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 296 optimal weight: 7.9990 chunk 222 optimal weight: 20.0000 chunk 195 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 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 49 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 554 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 = 0.3545 r_free = 0.3545 target = 0.042929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.032536 restraints weight = 257087.963| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 6.13 r_work: 0.2906 rms_B_bonded: 6.12 restraints_weight: 2.0000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 24344 Z= 0.258 Angle : 0.671 12.270 32968 Z= 0.323 Chirality : 0.043 0.366 3695 Planarity : 0.004 0.058 4230 Dihedral : 7.138 173.857 3345 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.43 % Allowed : 7.71 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.16), residues: 2973 helix: 1.51 (0.14), residues: 1514 sheet: -0.13 (0.26), residues: 402 loop : 0.00 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 79 HIS 0.006 0.001 HIS F 87 PHE 0.016 0.002 PHE G 704 TYR 0.014 0.001 TYR D 143 ARG 0.004 0.000 ARG G 981 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 1207) hydrogen bonds : angle 4.30018 ( 3339) covalent geometry : bond 0.00561 (24340) covalent geometry : angle 0.67115 (32968) Misc. bond : bond 0.00280 ( 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 127 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8810 (tmm) cc_final: 0.8502 (tmm) REVERT: B 132 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8421 (tmm) REVERT: B 283 MET cc_start: 0.8882 (mmt) cc_final: 0.8601 (mmp) REVERT: C 119 MET cc_start: 0.9131 (mtm) cc_final: 0.8850 (mtm) REVERT: C 123 MET cc_start: 0.8952 (mmm) cc_final: 0.8687 (mmm) REVERT: D 47 MET cc_start: 0.3595 (mtm) cc_final: 0.1195 (mmp) REVERT: D 82 MET cc_start: 0.8734 (tpt) cc_final: 0.8487 (tmm) REVERT: D 176 MET cc_start: 0.8410 (ptp) cc_final: 0.8107 (pmm) REVERT: D 325 MET cc_start: 0.6544 (OUTLIER) cc_final: 0.6247 (ppp) REVERT: E 123 MET cc_start: 0.9178 (mmp) cc_final: 0.8967 (mmp) REVERT: E 305 MET cc_start: 0.9010 (mmp) cc_final: 0.8676 (mmp) REVERT: F 47 MET cc_start: 0.8584 (pmm) cc_final: 0.8020 (pmm) REVERT: F 82 MET cc_start: 0.9171 (tpt) cc_final: 0.8498 (tpt) REVERT: F 132 MET cc_start: 0.9271 (ppp) cc_final: 0.8792 (ppp) REVERT: F 227 MET cc_start: 0.8599 (mmp) cc_final: 0.8127 (mmp) REVERT: F 305 MET cc_start: 0.9034 (mmp) cc_final: 0.8628 (mmp) REVERT: G 564 MET cc_start: 0.7409 (mmp) cc_final: 0.6978 (mmp) REVERT: G 733 MET cc_start: 0.9448 (tmm) cc_final: 0.9196 (tmm) REVERT: H 705 TYR cc_start: 0.9521 (m-80) cc_final: 0.9176 (m-80) REVERT: H 721 MET cc_start: 0.9710 (mmt) cc_final: 0.9308 (mmm) REVERT: H 733 MET cc_start: 0.9277 (ptp) cc_final: 0.9016 (mpp) outliers start: 11 outliers final: 7 residues processed: 120 average time/residue: 0.3630 time to fit residues: 73.3766 Evaluate side-chains 125 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 325 MET Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain G residue 812 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 238 optimal weight: 20.0000 chunk 241 optimal weight: 30.0000 chunk 81 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 263 optimal weight: 20.0000 chunk 243 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 0.0980 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN E 49 GLN ** G 554 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 = 0.3550 r_free = 0.3550 target = 0.042904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.033602 restraints weight = 292147.267| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 5.02 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2823 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= 0.203 Angle : 0.638 12.529 32968 Z= 0.304 Chirality : 0.043 0.231 3695 Planarity : 0.003 0.058 4230 Dihedral : 7.149 175.051 3345 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.58 % Allowed : 7.63 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.16), residues: 2973 helix: 1.52 (0.14), residues: 1514 sheet: -0.12 (0.26), residues: 402 loop : 0.02 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 79 HIS 0.005 0.001 HIS E 161 PHE 0.013 0.001 PHE G 704 TYR 0.017 0.001 TYR G 705 ARG 0.008 0.000 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.03006 ( 1207) hydrogen bonds : angle 4.22997 ( 3339) covalent geometry : bond 0.00446 (24340) covalent geometry : angle 0.63798 (32968) Misc. bond : bond 0.00231 ( 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 131 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8580 (tmm) cc_final: 0.8332 (tmm) REVERT: A 283 MET cc_start: 0.8963 (mmm) cc_final: 0.8746 (mmm) REVERT: B 132 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7945 (tmm) REVERT: B 283 MET cc_start: 0.8767 (mmt) cc_final: 0.8491 (mmp) REVERT: C 119 MET cc_start: 0.8887 (mtm) cc_final: 0.8588 (mtm) REVERT: C 123 MET cc_start: 0.8830 (mmm) cc_final: 0.8489 (mmm) REVERT: C 132 MET cc_start: 0.8026 (tmm) cc_final: 0.7571 (tmm) REVERT: D 47 MET cc_start: 0.2254 (mtm) cc_final: 0.0414 (mmp) REVERT: D 82 MET cc_start: 0.8616 (tpt) cc_final: 0.8307 (tmm) REVERT: D 123 MET cc_start: 0.8400 (tmm) cc_final: 0.8196 (tmm) REVERT: D 176 MET cc_start: 0.8502 (ptp) cc_final: 0.7958 (pmm) REVERT: D 325 MET cc_start: 0.6494 (OUTLIER) cc_final: 0.6274 (ppp) REVERT: E 49 GLN cc_start: 0.5297 (OUTLIER) cc_final: 0.4588 (mp10) REVERT: E 305 MET cc_start: 0.8538 (mmp) cc_final: 0.8036 (mmp) REVERT: F 47 MET cc_start: 0.8228 (pmm) cc_final: 0.7739 (pmm) REVERT: F 82 MET cc_start: 0.9255 (tpt) cc_final: 0.8567 (tpt) REVERT: F 132 MET cc_start: 0.9147 (ppp) cc_final: 0.8520 (ppp) REVERT: F 227 MET cc_start: 0.8391 (mmp) cc_final: 0.8085 (mmp) REVERT: F 305 MET cc_start: 0.8879 (mmp) cc_final: 0.8473 (mmp) REVERT: F 325 MET cc_start: 0.8657 (pmm) cc_final: 0.8329 (pmm) REVERT: G 564 MET cc_start: 0.5955 (mmp) cc_final: 0.5300 (mmp) REVERT: G 733 MET cc_start: 0.9191 (tmm) cc_final: 0.8942 (tmm) REVERT: H 705 TYR cc_start: 0.9040 (m-80) cc_final: 0.8816 (m-80) REVERT: H 721 MET cc_start: 0.9639 (mmt) cc_final: 0.9076 (mmm) REVERT: H 733 MET cc_start: 0.8982 (ptp) cc_final: 0.8668 (mpp) outliers start: 15 outliers final: 7 residues processed: 122 average time/residue: 0.3433 time to fit residues: 70.8110 Evaluate side-chains 126 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 325 MET Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain G residue 812 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 80 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 283 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 554 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 = 0.3548 r_free = 0.3548 target = 0.042824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.033594 restraints weight = 291607.553| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.99 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24344 Z= 0.199 Angle : 0.641 12.486 32968 Z= 0.306 Chirality : 0.042 0.221 3695 Planarity : 0.003 0.057 4230 Dihedral : 7.127 175.712 3345 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.39 % Allowed : 7.75 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.16), residues: 2973 helix: 1.50 (0.14), residues: 1519 sheet: -0.13 (0.26), residues: 402 loop : 0.10 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.004 0.001 HIS F 87 PHE 0.014 0.001 PHE G 704 TYR 0.015 0.001 TYR G 705 ARG 0.003 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.03008 ( 1207) hydrogen bonds : angle 4.23963 ( 3339) covalent geometry : bond 0.00438 (24340) covalent geometry : angle 0.64092 (32968) Misc. bond : bond 0.00230 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11480.67 seconds wall clock time: 203 minutes 13.27 seconds (12193.27 seconds total)