Starting phenix.real_space_refine on Thu Aug 8 19:59:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9az4_44012/08_2024/9az4_44012.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9az4_44012/08_2024/9az4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9az4_44012/08_2024/9az4_44012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9az4_44012/08_2024/9az4_44012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9az4_44012/08_2024/9az4_44012.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9az4_44012/08_2024/9az4_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 Residue "B ASP 80": "OD1" <-> "OD2" Residue "E GLU 364": "OE1" <-> "OE2" Residue "G TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 947": "OE1" <-> "OE2" Residue "H TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 12.61, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 8.93 Conformation dependent library (CDL) restraints added in 4.2 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: 3.60 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: 9.60 Time building geometry restraints manager: 9.81 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: 87.70 - 97.38: 12 97.38 - 107.06: 916 107.06 - 116.74: 15987 116.74 - 126.41: 15711 126.41 - 136.09: 342 Bond angle restraints: 32968 Sorted by residual: angle pdb=" CB MET D 325 " pdb=" CG MET D 325 " pdb=" SD MET D 325 " ideal model delta sigma weight residual 112.70 133.49 -20.79 3.00e+00 1.11e-01 4.80e+01 angle pdb=" CG MET D 325 " pdb=" SD MET D 325 " pdb=" CE MET D 325 " ideal model delta sigma weight residual 100.90 87.70 13.20 2.20e+00 2.07e-01 3.60e+01 angle pdb=" C GLY C 46 " pdb=" N MET C 47 " pdb=" CA MET C 47 " ideal model delta sigma weight residual 121.54 132.55 -11.01 1.91e+00 2.74e-01 3.32e+01 angle pdb=" CA MET C 47 " pdb=" CB MET C 47 " pdb=" CG MET C 47 " ideal model delta sigma weight residual 114.10 125.59 -11.49 2.00e+00 2.50e-01 3.30e+01 angle pdb=" CA MET A 355 " pdb=" CB MET A 355 " pdb=" CG MET A 355 " ideal model delta sigma weight residual 114.10 125.51 -11.41 2.00e+00 2.50e-01 3.25e+01 ... (remaining 32963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 14586 35.76 - 71.52: 211 71.52 - 107.28: 12 107.28 - 143.04: 2 143.04 - 178.80: 1 Dihedral angle restraints: 14812 sinusoidal: 6041 harmonic: 8771 Sorted by residual: dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 118.80 -178.80 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 157.95 142.05 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O2A ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PA ADP F 401 " pdb=" PB ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 174.50 125.50 1 2.00e+01 2.50e-03 3.79e+01 ... (remaining 14809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2954 0.068 - 0.136: 628 0.136 - 0.205: 86 0.205 - 0.273: 17 0.273 - 0.341: 10 Chirality restraints: 3695 Sorted by residual: chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE B 287 " pdb=" CA ILE B 287 " pdb=" CG1 ILE B 287 " pdb=" CG2 ILE B 287 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 3692 not shown) Planarity restraints: 4230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 364 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" CD GLU E 364 " 0.073 2.00e-02 2.50e+03 pdb=" OE1 GLU E 364 " -0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU E 364 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 705 " -0.021 2.00e-02 2.50e+03 2.86e-02 1.64e+01 pdb=" CG TYR G 705 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR G 705 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR G 705 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR G 705 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 705 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR G 705 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR G 705 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 824 " -0.056 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO H 825 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO H 825 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO H 825 " -0.047 5.00e-02 4.00e+02 ... (remaining 4227 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 296 2.63 - 3.20: 19868 3.20 - 3.77: 38305 3.77 - 4.33: 52733 4.33 - 4.90: 85935 Nonbonded interactions: 197137 Sorted by model distance: nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 2.069 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.086 2.170 nonbonded pdb=" O1A ADP B 401 " pdb="MG MG B 402 " model vdw 2.087 2.170 nonbonded pdb=" O1A ADP A 401 " pdb="MG MG A 402 " model vdw 2.088 2.170 nonbonded pdb=" O3A ADP D 401 " pdb="MG MG D 402 " model vdw 2.095 2.170 ... (remaining 197132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and (resid 551 through 608 or resid 626 through 983)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 65.810 Find NCS groups from input model: 1.060 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.280 ------------------------------------------------------------------------------- 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 24340 Z= 0.437 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.888 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: 0.3486 time to fit residues: 72.6652 Evaluate side-chains 120 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.878 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 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 24340 Z= 0.345 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9099 (tpt) cc_final: 0.8899 (tpt) REVERT: A 132 MET cc_start: 0.8487 (tmm) cc_final: 0.7988 (tmm) REVERT: A 283 MET cc_start: 0.9149 (mmm) cc_final: 0.8933 (mmm) REVERT: A 355 MET cc_start: 0.8611 (tpp) cc_final: 0.8368 (tpp) REVERT: B 132 MET cc_start: 0.8489 (tmm) cc_final: 0.8057 (tmm) REVERT: B 355 MET cc_start: 0.8589 (tpp) cc_final: 0.8174 (tpp) REVERT: C 119 MET cc_start: 0.8858 (mtm) cc_final: 0.8646 (mtm) REVERT: C 132 MET cc_start: 0.8229 (ppp) cc_final: 0.7859 (tmm) REVERT: C 305 MET cc_start: 0.8209 (mpp) cc_final: 0.7956 (mpp) REVERT: C 355 MET cc_start: 0.5870 (pmm) cc_final: 0.5530 (pmm) REVERT: D 82 MET cc_start: 0.8473 (tpt) cc_final: 0.8211 (tmm) REVERT: D 227 MET cc_start: 0.9070 (mmm) cc_final: 0.8840 (mmm) REVERT: E 123 MET cc_start: 0.9197 (mmp) cc_final: 0.8929 (mmp) REVERT: E 299 MET cc_start: 0.9012 (mtm) cc_final: 0.8777 (mtp) REVERT: E 313 MET cc_start: 0.9231 (tpp) cc_final: 0.9022 (mmm) REVERT: F 47 MET cc_start: 0.7525 (pmm) cc_final: 0.7206 (pmm) REVERT: F 82 MET cc_start: 0.8990 (tpt) cc_final: 0.8684 (tpt) REVERT: F 119 MET cc_start: 0.9437 (mtm) cc_final: 0.9131 (mtt) REVERT: F 132 MET cc_start: 0.9178 (ppp) cc_final: 0.8586 (ppp) REVERT: F 227 MET cc_start: 0.8321 (mmp) cc_final: 0.7952 (mmp) REVERT: F 305 MET cc_start: 0.8841 (mmp) cc_final: 0.8349 (mmp) REVERT: F 325 MET cc_start: 0.8558 (pmm) cc_final: 0.8259 (pmm) REVERT: G 564 MET cc_start: 0.6518 (mmp) cc_final: 0.5512 (mmp) REVERT: G 733 MET cc_start: 0.9371 (tmm) cc_final: 0.9142 (tmm) REVERT: H 705 TYR cc_start: 0.9414 (m-10) cc_final: 0.9158 (m-80) outliers start: 6 outliers final: 3 residues processed: 124 average time/residue: 0.3361 time to fit residues: 69.8265 Evaluate side-chains 121 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 3.073 ------------------------------------------------------------------------------- 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 151 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 185 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 chunk 294 optimal weight: 40.0000 chunk 243 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24340 Z= 0.226 Angle : 0.573 8.127 32968 Z= 0.279 Chirality : 0.042 0.164 3695 Planarity : 0.004 0.064 4230 Dihedral : 7.276 170.222 3345 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.51 % Allowed : 4.09 % Favored : 95.41 % 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: 0.61 (0.16), residues: 2973 helix: 1.17 (0.14), residues: 1470 sheet: -0.44 (0.25), residues: 402 loop : -0.16 (0.19), residues: 1101 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 0.012 0.001 PHE G 920 TYR 0.031 0.001 TYR G 705 ARG 0.003 0.000 ARG F 177 *********************** 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 131 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9079 (tpt) cc_final: 0.8860 (tpt) REVERT: A 132 MET cc_start: 0.8553 (tmm) cc_final: 0.7954 (tmm) REVERT: A 355 MET cc_start: 0.8756 (tpp) cc_final: 0.8111 (tpt) REVERT: B 132 MET cc_start: 0.8505 (tmm) cc_final: 0.8000 (tmm) REVERT: B 283 MET cc_start: 0.9072 (mmt) cc_final: 0.8661 (mmp) REVERT: B 355 MET cc_start: 0.8616 (tpp) cc_final: 0.8112 (tpp) REVERT: C 132 MET cc_start: 0.8217 (ppp) cc_final: 0.7779 (tmm) REVERT: C 305 MET cc_start: 0.8250 (mpp) cc_final: 0.7951 (mpp) REVERT: D 47 MET cc_start: 0.4672 (mtt) cc_final: 0.2927 (mmt) REVERT: D 82 MET cc_start: 0.8436 (tpt) cc_final: 0.8135 (tmm) REVERT: D 176 MET cc_start: 0.8088 (pmm) cc_final: 0.7813 (pmm) REVERT: E 119 MET cc_start: 0.9425 (mtm) cc_final: 0.9144 (mtm) REVERT: E 123 MET cc_start: 0.9231 (mmp) cc_final: 0.9011 (mmp) REVERT: E 299 MET cc_start: 0.8955 (mtm) cc_final: 0.8743 (mtp) REVERT: F 47 MET cc_start: 0.7740 (pmm) cc_final: 0.7392 (pmm) REVERT: F 119 MET cc_start: 0.9418 (mtm) cc_final: 0.9067 (mtt) REVERT: F 132 MET cc_start: 0.9200 (ppp) cc_final: 0.8639 (ppp) REVERT: F 227 MET cc_start: 0.8412 (mmp) cc_final: 0.7999 (mmp) REVERT: F 305 MET cc_start: 0.8828 (mmp) cc_final: 0.8329 (mmp) REVERT: F 313 MET cc_start: 0.9421 (tpt) cc_final: 0.9079 (tpt) REVERT: F 325 MET cc_start: 0.8592 (pmm) cc_final: 0.8227 (pmm) REVERT: G 564 MET cc_start: 0.6638 (mmp) cc_final: 0.5967 (mmp) REVERT: G 733 MET cc_start: 0.9371 (tmm) cc_final: 0.9120 (tmm) REVERT: H 705 TYR cc_start: 0.9364 (m-10) cc_final: 0.9100 (m-80) REVERT: H 721 MET cc_start: 0.9657 (mmt) cc_final: 0.8772 (mmm) outliers start: 13 outliers final: 5 residues processed: 126 average time/residue: 0.3883 time to fit residues: 82.2912 Evaluate side-chains 123 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 126 THR 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 269 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 273 optimal weight: 7.9990 chunk 289 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 259 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN C 137 GLN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN H 794 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 24340 Z= 0.312 Angle : 0.617 10.789 32968 Z= 0.300 Chirality : 0.042 0.165 3695 Planarity : 0.004 0.060 4230 Dihedral : 7.205 170.973 3345 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.66 % Allowed : 5.45 % Favored : 93.89 % 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: 0.89 (0.16), residues: 2973 helix: 1.42 (0.14), residues: 1472 sheet: -0.35 (0.26), residues: 402 loop : -0.06 (0.19), residues: 1099 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 0.013 0.001 PHE B 127 TYR 0.024 0.001 TYR G 705 ARG 0.003 0.000 ARG D 290 *********************** 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 135 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9121 (tpt) cc_final: 0.8910 (tpt) REVERT: A 132 MET cc_start: 0.8565 (tmm) cc_final: 0.7997 (tmm) REVERT: B 132 MET cc_start: 0.8483 (tmm) cc_final: 0.8014 (tmm) REVERT: B 355 MET cc_start: 0.8774 (tpp) cc_final: 0.8506 (mmm) REVERT: C 123 MET cc_start: 0.8939 (mmm) cc_final: 0.8668 (mmm) REVERT: C 132 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7809 (tmm) REVERT: C 305 MET cc_start: 0.8288 (mpp) cc_final: 0.7988 (mpp) REVERT: D 47 MET cc_start: 0.4960 (mtt) cc_final: 0.3375 (mmt) REVERT: D 82 MET cc_start: 0.8508 (tpt) cc_final: 0.8217 (tmm) REVERT: D 119 MET cc_start: 0.8832 (mtm) cc_final: 0.8421 (mtm) REVERT: D 305 MET cc_start: 0.8904 (mmp) cc_final: 0.8673 (mmp) REVERT: D 325 MET cc_start: 0.5987 (OUTLIER) cc_final: 0.5536 (ppp) REVERT: F 47 MET cc_start: 0.7992 (pmm) cc_final: 0.7682 (pmm) REVERT: F 82 MET cc_start: 0.9155 (tpt) cc_final: 0.8461 (tpt) REVERT: F 119 MET cc_start: 0.9363 (mtm) cc_final: 0.8973 (mtt) REVERT: F 132 MET cc_start: 0.9216 (ppp) cc_final: 0.8644 (ppp) REVERT: F 162 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8332 (m-40) REVERT: F 305 MET cc_start: 0.8891 (mmp) cc_final: 0.8510 (mmp) REVERT: F 325 MET cc_start: 0.8589 (pmm) cc_final: 0.8128 (pmm) REVERT: G 564 MET cc_start: 0.6748 (mmp) cc_final: 0.6071 (mmp) REVERT: G 733 MET cc_start: 0.9381 (tmm) cc_final: 0.9117 (tmm) REVERT: H 721 MET cc_start: 0.9723 (mmt) cc_final: 0.8960 (mmm) outliers start: 17 outliers final: 10 residues processed: 126 average time/residue: 0.3245 time to fit residues: 68.3863 Evaluate side-chains 131 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 2.650 ------------------------------------------------------------------------------- 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 151 ILE 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 E residue 294 TYR Chi-restraints excluded: chain F residue 87 HIS Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain G residue 803 HIS Chi-restraints excluded: chain G residue 812 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 30.0000 chunk 164 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 247 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 260 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24340 Z= 0.207 Angle : 0.566 8.091 32968 Z= 0.271 Chirality : 0.041 0.157 3695 Planarity : 0.003 0.060 4230 Dihedral : 7.138 170.893 3345 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.39 % Allowed : 6.38 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.16), residues: 2973 helix: 1.58 (0.14), residues: 1470 sheet: -0.24 (0.26), residues: 402 loop : 0.07 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 79 HIS 0.006 0.001 HIS F 161 PHE 0.011 0.001 PHE G 920 TYR 0.022 0.001 TYR G 705 ARG 0.002 0.000 ARG D 177 *********************** 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 128 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9061 (tpt) cc_final: 0.8824 (tpt) REVERT: A 132 MET cc_start: 0.8512 (tmm) cc_final: 0.7989 (tmm) REVERT: B 132 MET cc_start: 0.8460 (tmm) cc_final: 0.7975 (tmm) REVERT: B 283 MET cc_start: 0.8851 (mmt) cc_final: 0.8544 (mmp) REVERT: B 355 MET cc_start: 0.8842 (tpp) cc_final: 0.8588 (mmm) REVERT: C 123 MET cc_start: 0.8852 (mmm) cc_final: 0.8343 (mmm) REVERT: D 47 MET cc_start: 0.5047 (mtt) cc_final: 0.3859 (mmt) REVERT: D 82 MET cc_start: 0.8502 (tpt) cc_final: 0.8195 (tmm) REVERT: D 176 MET cc_start: 0.8396 (ptp) cc_final: 0.8033 (pmm) REVERT: D 325 MET cc_start: 0.5997 (OUTLIER) cc_final: 0.5707 (ppp) REVERT: E 123 MET cc_start: 0.9157 (mmm) cc_final: 0.8802 (mmm) REVERT: E 305 MET cc_start: 0.8502 (mmp) cc_final: 0.8175 (mmp) REVERT: F 47 MET cc_start: 0.8137 (pmm) cc_final: 0.7739 (pmm) REVERT: F 82 MET cc_start: 0.9133 (tpt) cc_final: 0.8396 (tpt) REVERT: F 119 MET cc_start: 0.9357 (mtm) cc_final: 0.8940 (mtt) REVERT: F 132 MET cc_start: 0.9207 (ppp) cc_final: 0.8654 (ppp) REVERT: F 227 MET cc_start: 0.8387 (mmp) cc_final: 0.7897 (mmp) REVERT: F 305 MET cc_start: 0.8891 (mmp) cc_final: 0.8520 (mmp) REVERT: F 325 MET cc_start: 0.8670 (pmm) cc_final: 0.8245 (pmm) REVERT: G 564 MET cc_start: 0.6537 (mmp) cc_final: 0.5837 (mmp) REVERT: G 733 MET cc_start: 0.9375 (tmm) cc_final: 0.9124 (tmm) outliers start: 10 outliers final: 5 residues processed: 121 average time/residue: 0.3123 time to fit residues: 63.1332 Evaluate side-chains 124 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 2.612 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 10.0000 chunk 261 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 290 optimal weight: 9.9990 chunk 240 optimal weight: 30.0000 chunk 134 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 152 optimal weight: 0.0270 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24340 Z= 0.128 Angle : 0.536 9.662 32968 Z= 0.253 Chirality : 0.041 0.182 3695 Planarity : 0.003 0.059 4230 Dihedral : 6.935 169.601 3345 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.47 % Allowed : 6.70 % Favored : 92.84 % 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: 1.16 (0.16), residues: 2973 helix: 1.53 (0.14), residues: 1513 sheet: -0.05 (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 0.000 HIS F 161 PHE 0.010 0.001 PHE G 920 TYR 0.020 0.001 TYR G 705 ARG 0.003 0.000 ARG A 290 *********************** 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 fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9039 (tpt) cc_final: 0.8807 (tpt) REVERT: A 132 MET cc_start: 0.8457 (tmm) cc_final: 0.7980 (tmm) REVERT: B 47 MET cc_start: 0.9195 (pmm) cc_final: 0.8907 (pmm) REVERT: B 132 MET cc_start: 0.8543 (tmm) cc_final: 0.8001 (tmm) REVERT: B 355 MET cc_start: 0.8858 (tpp) cc_final: 0.8608 (mmm) REVERT: C 119 MET cc_start: 0.8983 (mtm) cc_final: 0.8693 (mtm) REVERT: C 123 MET cc_start: 0.8751 (mmm) cc_final: 0.8473 (mmm) REVERT: C 132 MET cc_start: 0.8151 (tmm) cc_final: 0.7758 (tmm) REVERT: C 305 MET cc_start: 0.8319 (mpp) cc_final: 0.7968 (mpp) REVERT: D 47 MET cc_start: 0.4441 (mtt) cc_final: 0.2889 (mmt) REVERT: D 82 MET cc_start: 0.8478 (tpt) cc_final: 0.8151 (tmm) REVERT: D 305 MET cc_start: 0.8924 (mmp) cc_final: 0.8362 (mmm) REVERT: D 325 MET cc_start: 0.5778 (OUTLIER) cc_final: 0.5558 (ppp) REVERT: D 355 MET cc_start: 0.8964 (pmm) cc_final: 0.8745 (pmm) REVERT: E 123 MET cc_start: 0.9241 (mmm) cc_final: 0.8992 (mmm) REVERT: E 305 MET cc_start: 0.8476 (mmp) cc_final: 0.8195 (mmp) REVERT: F 47 MET cc_start: 0.8076 (pmm) cc_final: 0.7615 (pmm) REVERT: F 82 MET cc_start: 0.9075 (tpt) cc_final: 0.8562 (mmm) REVERT: F 119 MET cc_start: 0.9361 (mtm) cc_final: 0.9014 (mtt) REVERT: F 132 MET cc_start: 0.9132 (ppp) cc_final: 0.8661 (ppp) REVERT: F 227 MET cc_start: 0.8340 (mmp) cc_final: 0.7893 (mmp) REVERT: F 305 MET cc_start: 0.8853 (mmp) cc_final: 0.8463 (mmp) REVERT: F 325 MET cc_start: 0.8602 (pmm) cc_final: 0.8190 (pmm) REVERT: G 564 MET cc_start: 0.6561 (mmp) cc_final: 0.5831 (mmp) REVERT: G 733 MET cc_start: 0.9372 (tmm) cc_final: 0.9139 (tmm) REVERT: H 721 MET cc_start: 0.9619 (mmt) cc_final: 0.8794 (mmm) outliers start: 12 outliers final: 6 residues processed: 127 average time/residue: 0.3376 time to fit residues: 72.1565 Evaluate side-chains 125 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 2.872 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 9.9990 chunk 32 optimal weight: 0.0870 chunk 165 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 289 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 176 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24340 Z= 0.169 Angle : 0.544 8.814 32968 Z= 0.258 Chirality : 0.040 0.162 3695 Planarity : 0.003 0.058 4230 Dihedral : 6.852 170.650 3345 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.43 % Allowed : 7.40 % Favored : 92.18 % 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: 1.25 (0.16), residues: 2973 helix: 1.58 (0.14), residues: 1520 sheet: -0.02 (0.26), residues: 402 loop : 0.22 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 79 HIS 0.003 0.001 HIS G 703 PHE 0.012 0.001 PHE G 704 TYR 0.043 0.001 TYR G 705 ARG 0.003 0.000 ARG D 177 *********************** 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 129 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9074 (tpt) cc_final: 0.8863 (tpt) REVERT: A 132 MET cc_start: 0.8501 (tmm) cc_final: 0.7981 (tmm) REVERT: B 47 MET cc_start: 0.9164 (pmm) cc_final: 0.8928 (pmm) REVERT: B 132 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8048 (tmm) REVERT: B 355 MET cc_start: 0.8909 (tpp) cc_final: 0.8629 (mmm) REVERT: C 119 MET cc_start: 0.8993 (mtm) cc_final: 0.8682 (mtm) REVERT: C 123 MET cc_start: 0.8788 (mmm) cc_final: 0.8528 (mmm) REVERT: C 132 MET cc_start: 0.8187 (tmm) cc_final: 0.7907 (tmm) REVERT: C 325 MET cc_start: 0.8001 (ptp) cc_final: 0.7689 (pmm) REVERT: D 47 MET cc_start: 0.4633 (mtt) cc_final: 0.3098 (mmt) REVERT: D 82 MET cc_start: 0.8509 (tpt) cc_final: 0.8168 (tmm) REVERT: D 176 MET cc_start: 0.8459 (ptp) cc_final: 0.8026 (pmm) REVERT: D 325 MET cc_start: 0.5816 (OUTLIER) cc_final: 0.5556 (ppp) REVERT: E 119 MET cc_start: 0.9394 (mtm) cc_final: 0.9153 (mtm) REVERT: E 123 MET cc_start: 0.9235 (mmm) cc_final: 0.9009 (mmm) REVERT: E 305 MET cc_start: 0.8526 (mmp) cc_final: 0.8216 (mmp) REVERT: F 47 MET cc_start: 0.8115 (pmm) cc_final: 0.7704 (pmm) REVERT: F 82 MET cc_start: 0.9097 (tpt) cc_final: 0.8593 (mmm) REVERT: F 119 MET cc_start: 0.9359 (mtm) cc_final: 0.8768 (mtm) REVERT: F 132 MET cc_start: 0.9105 (ppp) cc_final: 0.8684 (ppp) REVERT: F 227 MET cc_start: 0.8436 (mmp) cc_final: 0.8057 (mmp) REVERT: F 299 MET cc_start: 0.8642 (mmt) cc_final: 0.8358 (mmm) REVERT: F 305 MET cc_start: 0.8856 (mmp) cc_final: 0.8482 (mmp) REVERT: F 313 MET cc_start: 0.9430 (tpp) cc_final: 0.9100 (tpt) REVERT: F 325 MET cc_start: 0.8619 (pmm) cc_final: 0.8140 (pmm) REVERT: G 564 MET cc_start: 0.6810 (mmp) cc_final: 0.6070 (mmp) REVERT: G 733 MET cc_start: 0.9380 (tmm) cc_final: 0.9139 (tmm) REVERT: H 564 MET cc_start: 0.7156 (mtm) cc_final: 0.6368 (ptt) outliers start: 11 outliers final: 7 residues processed: 122 average time/residue: 0.3370 time to fit residues: 68.8129 Evaluate side-chains 126 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 2.840 ------------------------------------------------------------------------------- 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 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 178 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 227 optimal weight: 50.0000 chunk 263 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24340 Z= 0.175 Angle : 0.550 12.371 32968 Z= 0.260 Chirality : 0.040 0.180 3695 Planarity : 0.003 0.058 4230 Dihedral : 6.799 170.598 3345 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.47 % Allowed : 7.51 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.34 (0.16), residues: 2973 helix: 1.65 (0.14), residues: 1520 sheet: 0.02 (0.26), residues: 402 loop : 0.27 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 79 HIS 0.002 0.001 HIS F 87 PHE 0.010 0.001 PHE G 920 TYR 0.041 0.001 TYR G 705 ARG 0.004 0.000 ARG A 335 *********************** 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 129 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9073 (tpt) cc_final: 0.8862 (tpt) REVERT: A 132 MET cc_start: 0.8526 (tmm) cc_final: 0.7977 (tmm) REVERT: A 283 MET cc_start: 0.8932 (mmm) cc_final: 0.8713 (mmm) REVERT: B 47 MET cc_start: 0.9137 (pmm) cc_final: 0.8865 (pmm) REVERT: B 132 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8045 (tmm) REVERT: B 355 MET cc_start: 0.8952 (tpp) cc_final: 0.8668 (mmm) REVERT: C 119 MET cc_start: 0.8976 (mtm) cc_final: 0.8646 (mtm) REVERT: C 123 MET cc_start: 0.8795 (mmm) cc_final: 0.8530 (mmm) REVERT: C 132 MET cc_start: 0.8175 (tmm) cc_final: 0.7867 (tmm) REVERT: C 325 MET cc_start: 0.7959 (ptp) cc_final: 0.7679 (pmm) REVERT: D 47 MET cc_start: 0.4844 (mtt) cc_final: 0.3241 (mmt) REVERT: D 82 MET cc_start: 0.8521 (tpt) cc_final: 0.8178 (tmm) REVERT: D 176 MET cc_start: 0.8441 (ptp) cc_final: 0.7972 (pmm) REVERT: D 305 MET cc_start: 0.9033 (mmm) cc_final: 0.8796 (mmp) REVERT: D 325 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.5623 (ppp) REVERT: E 123 MET cc_start: 0.9253 (mmm) cc_final: 0.8998 (mmm) REVERT: E 305 MET cc_start: 0.8563 (mmp) cc_final: 0.8207 (mmp) REVERT: F 44 MET cc_start: 0.8410 (mmm) cc_final: 0.8090 (mmm) REVERT: F 47 MET cc_start: 0.8160 (pmm) cc_final: 0.7681 (pmm) REVERT: F 82 MET cc_start: 0.9111 (tpt) cc_final: 0.8610 (mmm) REVERT: F 119 MET cc_start: 0.9302 (mtm) cc_final: 0.8773 (mtm) REVERT: F 132 MET cc_start: 0.9110 (ppp) cc_final: 0.8695 (ppp) REVERT: F 227 MET cc_start: 0.8505 (mmp) cc_final: 0.8159 (mmp) REVERT: F 299 MET cc_start: 0.8551 (mmt) cc_final: 0.8208 (mmm) REVERT: F 305 MET cc_start: 0.8858 (mmp) cc_final: 0.8489 (mmp) REVERT: F 313 MET cc_start: 0.9394 (tpp) cc_final: 0.9084 (tpt) REVERT: F 325 MET cc_start: 0.8527 (pmm) cc_final: 0.7980 (pmm) REVERT: G 564 MET cc_start: 0.6479 (mmp) cc_final: 0.5676 (mmp) REVERT: G 733 MET cc_start: 0.9356 (tmm) cc_final: 0.9129 (tmm) REVERT: H 564 MET cc_start: 0.7092 (mtm) cc_final: 0.6345 (ptt) outliers start: 12 outliers final: 8 residues processed: 123 average time/residue: 0.3305 time to fit residues: 68.2194 Evaluate side-chains 127 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 2.789 ------------------------------------------------------------------------------- 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 151 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 269 optimal weight: 0.8980 chunk 276 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 243 optimal weight: 40.0000 chunk 254 optimal weight: 20.0000 chunk 268 optimal weight: 5.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN D 137 GLN H 652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 24340 Z= 0.387 Angle : 0.685 11.777 32968 Z= 0.334 Chirality : 0.043 0.157 3695 Planarity : 0.004 0.056 4230 Dihedral : 7.130 172.041 3345 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.54 % Allowed : 7.47 % Favored : 91.98 % 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: 1.05 (0.16), residues: 2973 helix: 1.43 (0.14), residues: 1519 sheet: -0.10 (0.26), residues: 402 loop : 0.10 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 86 HIS 0.007 0.001 HIS F 87 PHE 0.017 0.002 PHE G 704 TYR 0.042 0.002 TYR G 705 ARG 0.006 0.001 ARG G 981 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9117 (tpt) cc_final: 0.8912 (tpt) REVERT: A 132 MET cc_start: 0.8541 (tmm) cc_final: 0.7979 (tmm) REVERT: B 47 MET cc_start: 0.9140 (pmm) cc_final: 0.8801 (pmm) REVERT: B 132 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7918 (tmm) REVERT: B 355 MET cc_start: 0.8992 (tpp) cc_final: 0.8607 (mmm) REVERT: C 119 MET cc_start: 0.9068 (mtm) cc_final: 0.8756 (mtm) REVERT: C 123 MET cc_start: 0.8874 (mmm) cc_final: 0.8639 (mmm) REVERT: D 47 MET cc_start: 0.5412 (mtt) cc_final: 0.4498 (mmt) REVERT: D 82 MET cc_start: 0.8596 (tpt) cc_final: 0.8283 (tmm) REVERT: D 176 MET cc_start: 0.8517 (ptp) cc_final: 0.7961 (pmm) REVERT: D 325 MET cc_start: 0.6341 (OUTLIER) cc_final: 0.6000 (ppp) REVERT: D 355 MET cc_start: 0.9021 (pmm) cc_final: 0.8814 (pmm) REVERT: E 119 MET cc_start: 0.9449 (mtm) cc_final: 0.9178 (mtm) REVERT: E 123 MET cc_start: 0.9261 (mmm) cc_final: 0.8947 (mmm) REVERT: E 305 MET cc_start: 0.8593 (mmp) cc_final: 0.8287 (mmp) REVERT: F 47 MET cc_start: 0.8508 (pmm) cc_final: 0.8029 (pmm) REVERT: F 82 MET cc_start: 0.9168 (tpt) cc_final: 0.8483 (tpt) REVERT: F 119 MET cc_start: 0.9260 (mtm) cc_final: 0.8941 (mtm) REVERT: F 132 MET cc_start: 0.9253 (ppp) cc_final: 0.8735 (ppp) REVERT: F 227 MET cc_start: 0.8598 (mmp) cc_final: 0.8233 (mmp) REVERT: F 305 MET cc_start: 0.8918 (mmp) cc_final: 0.8478 (mmp) REVERT: F 313 MET cc_start: 0.9404 (tpp) cc_final: 0.9154 (tpt) REVERT: F 325 MET cc_start: 0.8724 (pmm) cc_final: 0.8083 (pmm) REVERT: G 564 MET cc_start: 0.6718 (mmp) cc_final: 0.5953 (mmp) REVERT: G 733 MET cc_start: 0.9362 (tmm) cc_final: 0.9121 (tmm) REVERT: H 564 MET cc_start: 0.7130 (mtm) cc_final: 0.6382 (ptt) REVERT: H 721 MET cc_start: 0.9774 (mmt) cc_final: 0.9225 (mmm) outliers start: 14 outliers final: 7 residues processed: 122 average time/residue: 0.3352 time to fit residues: 68.9956 Evaluate side-chains 125 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 2.941 ------------------------------------------------------------------------------- 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 176 optimal weight: 0.8980 chunk 284 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 275 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 652 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24340 Z= 0.213 Angle : 0.599 10.927 32968 Z= 0.283 Chirality : 0.042 0.349 3695 Planarity : 0.003 0.057 4230 Dihedral : 7.065 172.283 3345 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.35 % Allowed : 7.75 % Favored : 91.90 % 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: 1.22 (0.16), residues: 2973 helix: 1.57 (0.14), residues: 1515 sheet: -0.02 (0.26), residues: 401 loop : 0.18 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 79 HIS 0.003 0.001 HIS B 371 PHE 0.012 0.001 PHE G 704 TYR 0.038 0.001 TYR G 705 ARG 0.002 0.000 ARG D 177 ********************** 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 126 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 3.031 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: 0.8511 (tmm) cc_final: 0.8240 (tmm) REVERT: A 283 MET cc_start: 0.9000 (mmm) cc_final: 0.8749 (mmm) REVERT: B 47 MET cc_start: 0.9124 (pmm) cc_final: 0.8777 (pmm) REVERT: B 132 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7927 (tmm) REVERT: B 355 MET cc_start: 0.8956 (tpp) cc_final: 0.8621 (mmm) REVERT: C 119 MET cc_start: 0.9043 (mtm) cc_final: 0.8710 (mtm) REVERT: C 123 MET cc_start: 0.8792 (mmm) cc_final: 0.8549 (mmm) REVERT: C 132 MET cc_start: 0.8101 (tmm) cc_final: 0.7530 (tmm) REVERT: D 82 MET cc_start: 0.8594 (tpt) cc_final: 0.8273 (tmm) REVERT: D 123 MET cc_start: 0.8401 (tmm) cc_final: 0.8159 (tmm) REVERT: D 176 MET cc_start: 0.8497 (ptp) cc_final: 0.7995 (pmm) REVERT: D 355 MET cc_start: 0.9021 (pmm) cc_final: 0.8791 (pmm) REVERT: E 123 MET cc_start: 0.9237 (mmm) cc_final: 0.8903 (mmm) REVERT: E 305 MET cc_start: 0.8603 (mmp) cc_final: 0.8224 (mmp) REVERT: F 47 MET cc_start: 0.8447 (pmm) cc_final: 0.7981 (pmm) REVERT: F 82 MET cc_start: 0.9150 (tpt) cc_final: 0.8457 (tpt) REVERT: F 132 MET cc_start: 0.9234 (ppp) cc_final: 0.8725 (ppp) REVERT: F 227 MET cc_start: 0.8646 (mmp) cc_final: 0.8343 (mmp) REVERT: F 299 MET cc_start: 0.8625 (mmm) cc_final: 0.8122 (mtt) REVERT: F 305 MET cc_start: 0.8953 (mmp) cc_final: 0.8521 (mmp) REVERT: G 564 MET cc_start: 0.6192 (mmp) cc_final: 0.5441 (mmp) REVERT: H 564 MET cc_start: 0.7052 (mtm) cc_final: 0.6341 (ptt) REVERT: H 705 TYR cc_start: 0.9352 (m-80) cc_final: 0.9005 (m-80) REVERT: H 721 MET cc_start: 0.9732 (mmt) cc_final: 0.9205 (mmm) outliers start: 9 outliers final: 6 residues processed: 120 average time/residue: 0.3332 time to fit residues: 66.8350 Evaluate side-chains 124 residues out of total 2569 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain 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 189 optimal weight: 0.7980 chunk 253 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 219 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 238 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 244 optimal weight: 30.0000 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.043727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.033363 restraints weight = 253096.235| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 6.05 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24340 Z= 0.165 Angle : 0.576 10.527 32968 Z= 0.270 Chirality : 0.041 0.245 3695 Planarity : 0.003 0.058 4230 Dihedral : 6.930 172.609 3345 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.35 % Allowed : 7.86 % 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: 1.34 (0.16), residues: 2973 helix: 1.64 (0.14), residues: 1519 sheet: -0.05 (0.26), residues: 396 loop : 0.32 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 79 HIS 0.003 0.001 HIS E 161 PHE 0.011 0.001 PHE G 704 TYR 0.037 0.001 TYR G 705 ARG 0.003 0.000 ARG E 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3620.09 seconds wall clock time: 67 minutes 5.35 seconds (4025.35 seconds total)