Starting phenix.real_space_refine on Sat Jul 20 19:42:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi6_16887/07_2024/8oi6_16887_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi6_16887/07_2024/8oi6_16887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi6_16887/07_2024/8oi6_16887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi6_16887/07_2024/8oi6_16887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi6_16887/07_2024/8oi6_16887_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi6_16887/07_2024/8oi6_16887_neut.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.214 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 83 5.16 5 C 7304 2.51 5 N 1945 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 80": "OD1" <-> "OD2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D ASP 286": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11573 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2843 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2843 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2843 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2767 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 18, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.13, per 1000 atoms: 0.62 Number of scatterers: 11573 At special positions: 0 Unit cell: (94.38, 89.54, 165.77, 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 83 16.00 P 8 15.00 Mg 4 11.99 O 2229 8.00 N 1945 7.00 C 7304 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=0, symmetry=0 Time building additional restraints: 4.84 Conformation dependent library (CDL) restraints added in 2.1 seconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 2722 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 22 sheets defined 49.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.569A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.864A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.699A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 214 removed outlier: 4.041A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.783A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.599A pdb=" N ILE A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 4.050A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.007A 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 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.531A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.570A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.293A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.518A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.678A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.797A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.518A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.165A pdb=" N LYS B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.958A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.568A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.908A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.680A pdb=" N SER B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.500A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.691A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.810A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.507A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.549A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.733A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.430A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.501A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 3.980A 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 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.916A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.585A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.567A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.652A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.585A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.746A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.513A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.851A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.550A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.658A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.602A pdb=" N MET D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.019A 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 349 Processing helix chain 'D' and resid 350 through 354 removed outlier: 4.011A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.565A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.839A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 7.171A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (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: 3.667A pdb=" N PHE B 31 " --> pdb=" O CYS B 17 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.698A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.574A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (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: 3.654A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR C 106 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.815A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) 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: 3.705A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.071A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR D 133 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 16 through 19 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.755A pdb=" N LYS D 68 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 176 through 178 removed outlier: 5.947A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 241 529 hydrogen bonds defined for protein. 1329 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.15 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3734 1.34 - 1.46: 2694 1.46 - 1.58: 5233 1.58 - 1.70: 18 1.70 - 1.82: 143 Bond restraints: 11822 Sorted by residual: bond pdb=" N HYP I 6 " pdb=" CD HYP I 6 " ideal model delta sigma weight residual 1.473 1.636 -0.163 1.40e-02 5.10e+03 1.36e+02 bond pdb=" N HYP H 6 " pdb=" CD HYP H 6 " ideal model delta sigma weight residual 1.473 1.635 -0.162 1.40e-02 5.10e+03 1.35e+02 bond pdb=" N HYP J 6 " pdb=" CD HYP J 6 " ideal model delta sigma weight residual 1.473 1.635 -0.162 1.40e-02 5.10e+03 1.33e+02 bond pdb=" CG HYP H 6 " pdb=" CD HYP H 6 " ideal model delta sigma weight residual 1.530 1.371 0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" CG HYP J 6 " pdb=" CD HYP J 6 " ideal model delta sigma weight residual 1.530 1.372 0.158 2.00e-02 2.50e+03 6.23e+01 ... (remaining 11817 not shown) Histogram of bond angle deviations from ideal: 98.48 - 106.01: 362 106.01 - 113.55: 6546 113.55 - 121.08: 5903 121.08 - 128.62: 3153 128.62 - 136.15: 81 Bond angle restraints: 16045 Sorted by residual: angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.42 -4.42 1.10e+00 8.26e-01 1.61e+01 angle pdb=" N HYP H 6 " pdb=" CD HYP H 6 " pdb=" CG HYP H 6 " ideal model delta sigma weight residual 103.20 109.04 -5.84 1.50e+00 4.44e-01 1.52e+01 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 116.88 -6.38 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N HYP J 6 " pdb=" CA HYP J 6 " pdb=" CB HYP J 6 " ideal model delta sigma weight residual 103.00 106.86 -3.86 1.10e+00 8.26e-01 1.23e+01 angle pdb=" N HYP I 6 " pdb=" CA HYP I 6 " pdb=" CB HYP I 6 " ideal model delta sigma weight residual 103.00 106.84 -3.84 1.10e+00 8.26e-01 1.22e+01 ... (remaining 16040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.98: 6864 33.98 - 67.96: 220 67.96 - 101.94: 17 101.94 - 135.92: 4 135.92 - 169.90: 3 Dihedral angle restraints: 7108 sinusoidal: 2873 harmonic: 4235 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 130.10 169.90 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 131.78 168.22 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 137.14 162.86 1 2.00e+01 2.50e-03 4.69e+01 ... (remaining 7105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1562 0.061 - 0.122: 226 0.122 - 0.184: 4 0.184 - 0.245: 0 0.245 - 0.306: 3 Chirality restraints: 1795 Sorted by residual: chirality pdb=" CA HYP I 6 " pdb=" N HYP I 6 " pdb=" C HYP I 6 " pdb=" CB HYP I 6 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA HYP J 6 " pdb=" N HYP J 6 " pdb=" C HYP J 6 " pdb=" CB HYP J 6 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA HYP H 6 " pdb=" N HYP H 6 " pdb=" C HYP H 6 " pdb=" CB HYP H 6 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1792 not shown) Planarity restraints: 2031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 117 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" CD GLU A 117 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU A 117 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 117 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 166 " -0.011 2.00e-02 2.50e+03 1.15e-02 2.63e+00 pdb=" CG TYR C 166 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 166 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 166 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR C 166 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 166 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 166 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 166 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 366 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 367 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 367 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 367 " -0.022 5.00e-02 4.00e+02 ... (remaining 2028 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 9 2.03 - 2.75: 1202 2.75 - 3.46: 16351 3.46 - 4.18: 27433 4.18 - 4.90: 49884 Nonbonded interactions: 94879 Sorted by model distance: nonbonded pdb=" N TRP I 1 " pdb=" C ALA I 7 " model vdw 1.310 3.350 nonbonded pdb=" N TRP J 1 " pdb=" C ALA J 7 " model vdw 1.312 3.350 nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.313 3.350 nonbonded pdb=" C ALA J 3 " pdb=" N DTH J 4 " model vdw 1.327 3.350 nonbonded pdb=" C ALA H 3 " pdb=" N DTH H 4 " model vdw 1.327 3.350 ... (remaining 94874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 362 or resid 401 through 402)) selection = (chain 'B' and (resid 6 through 362 or resid 401 through 402)) selection = (chain 'C' and (resid 6 through 362 or resid 401 through 402)) selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 35.930 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 11822 Z= 0.346 Angle : 0.640 8.991 16045 Z= 0.300 Chirality : 0.043 0.306 1795 Planarity : 0.003 0.040 2031 Dihedral : 16.973 169.900 4386 Min Nonbonded Distance : 1.310 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.10 % Rotamer: Outliers : 0.24 % Allowed : 17.74 % Favored : 82.02 % 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: 0.35 (0.23), residues: 1418 helix: 0.06 (0.22), residues: 538 sheet: 0.56 (0.37), residues: 212 loop : 0.49 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 86 HIS 0.011 0.001 HIS B 371 PHE 0.008 0.001 PHE A 124 TYR 0.028 0.001 TYR C 166 ARG 0.003 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 88 average time/residue: 0.1952 time to fit residues: 26.9192 Evaluate side-chains 84 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.0770 chunk 83 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 225 GLN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 11822 Z= 0.457 Angle : 0.709 7.500 16045 Z= 0.347 Chirality : 0.048 0.198 1795 Planarity : 0.004 0.039 2031 Dihedral : 12.138 175.899 1673 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.40 % Favored : 97.53 % Rotamer: Outliers : 2.77 % Allowed : 17.25 % Favored : 79.98 % 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: 0.36 (0.22), residues: 1418 helix: 0.17 (0.22), residues: 577 sheet: 0.58 (0.33), residues: 250 loop : 0.40 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 1 HIS 0.006 0.001 HIS B 101 PHE 0.020 0.002 PHE C 352 TYR 0.016 0.002 TYR B 143 ARG 0.007 0.001 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 76 time to evaluate : 1.398 Fit side-chains REVERT: A 80 ASP cc_start: 0.8018 (t0) cc_final: 0.7696 (t0) REVERT: B 314 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7755 (tt0) REVERT: I 5 CYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7302 (p) outliers start: 34 outliers final: 17 residues processed: 105 average time/residue: 0.1742 time to fit residues: 29.6658 Evaluate side-chains 93 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 104 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11822 Z= 0.158 Angle : 0.555 6.928 16045 Z= 0.261 Chirality : 0.043 0.205 1795 Planarity : 0.004 0.036 2031 Dihedral : 11.178 165.462 1668 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % Rotamer: Outliers : 1.55 % Allowed : 18.39 % Favored : 80.07 % 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: 0.64 (0.23), residues: 1418 helix: 0.51 (0.22), residues: 582 sheet: 0.48 (0.35), residues: 232 loop : 0.56 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.003 0.001 HIS D 87 PHE 0.012 0.001 PHE D 31 TYR 0.015 0.001 TYR B 143 ARG 0.002 0.000 ARG D 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 1.362 Fit side-chains REVERT: A 80 ASP cc_start: 0.7893 (t0) cc_final: 0.7410 (t0) REVERT: B 132 MET cc_start: 0.8169 (ttp) cc_final: 0.7505 (ttp) REVERT: B 269 MET cc_start: 0.7717 (mtp) cc_final: 0.7478 (mtm) REVERT: C 82 MET cc_start: 0.8431 (tpt) cc_final: 0.8199 (tpt) REVERT: D 123 MET cc_start: 0.6680 (mmt) cc_final: 0.6372 (mmt) REVERT: D 305 MET cc_start: 0.8161 (tpp) cc_final: 0.7946 (tpp) REVERT: I 5 CYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7198 (p) outliers start: 19 outliers final: 8 residues processed: 97 average time/residue: 0.1916 time to fit residues: 29.2708 Evaluate side-chains 86 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 67 optimal weight: 0.0770 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS B 12 ASN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11822 Z= 0.350 Angle : 0.630 7.373 16045 Z= 0.299 Chirality : 0.046 0.206 1795 Planarity : 0.004 0.038 2031 Dihedral : 10.532 147.352 1668 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 3.09 % Allowed : 17.49 % Favored : 79.41 % 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: 0.58 (0.23), residues: 1418 helix: 0.50 (0.22), residues: 582 sheet: 0.35 (0.34), residues: 250 loop : 0.52 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.005 0.001 HIS B 101 PHE 0.015 0.002 PHE C 352 TYR 0.014 0.001 TYR B 143 ARG 0.006 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 76 time to evaluate : 1.389 Fit side-chains REVERT: A 80 ASP cc_start: 0.8056 (t0) cc_final: 0.7493 (t0) REVERT: D 180 LEU cc_start: 0.7825 (tp) cc_final: 0.7544 (tp) REVERT: D 305 MET cc_start: 0.8098 (tpp) cc_final: 0.7741 (tpp) REVERT: D 355 MET cc_start: 0.8020 (pmm) cc_final: 0.7424 (pmm) REVERT: I 5 CYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7170 (p) outliers start: 38 outliers final: 25 residues processed: 105 average time/residue: 0.1890 time to fit residues: 31.4393 Evaluate side-chains 99 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 73 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11822 Z= 0.292 Angle : 0.595 6.960 16045 Z= 0.280 Chirality : 0.045 0.196 1795 Planarity : 0.004 0.037 2031 Dihedral : 10.043 142.895 1668 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.33 % Favored : 97.60 % Rotamer: Outliers : 3.25 % Allowed : 17.66 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1418 helix: 0.58 (0.23), residues: 581 sheet: 0.30 (0.34), residues: 252 loop : 0.47 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.004 0.001 HIS B 101 PHE 0.012 0.001 PHE C 352 TYR 0.009 0.001 TYR A 169 ARG 0.005 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 74 time to evaluate : 1.353 Fit side-chains REVERT: A 80 ASP cc_start: 0.8055 (t0) cc_final: 0.7432 (t0) REVERT: B 118 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7932 (tptt) REVERT: B 269 MET cc_start: 0.7771 (mtp) cc_final: 0.7540 (mtm) REVERT: D 180 LEU cc_start: 0.7832 (tp) cc_final: 0.7572 (tp) REVERT: D 305 MET cc_start: 0.8134 (tpp) cc_final: 0.7843 (tpp) REVERT: I 5 CYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6925 (p) outliers start: 40 outliers final: 26 residues processed: 108 average time/residue: 0.1824 time to fit residues: 31.8248 Evaluate side-chains 102 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 74 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 27 optimal weight: 0.0030 chunk 81 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11822 Z= 0.203 Angle : 0.564 7.687 16045 Z= 0.261 Chirality : 0.044 0.197 1795 Planarity : 0.003 0.036 2031 Dihedral : 9.812 140.253 1668 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.26 % Favored : 97.67 % Rotamer: Outliers : 2.12 % Allowed : 19.45 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.70 (0.23), residues: 1418 helix: 0.70 (0.23), residues: 581 sheet: 0.28 (0.34), residues: 250 loop : 0.54 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.003 0.001 HIS D 87 PHE 0.011 0.001 PHE D 31 TYR 0.011 0.001 TYR B 143 ARG 0.003 0.000 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 1.359 Fit side-chains REVERT: A 80 ASP cc_start: 0.8020 (t0) cc_final: 0.7501 (t0) REVERT: A 132 MET cc_start: 0.7181 (ptt) cc_final: 0.6924 (ptt) REVERT: B 118 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7919 (tptt) REVERT: B 269 MET cc_start: 0.7748 (mtp) cc_final: 0.7517 (mtm) REVERT: D 180 LEU cc_start: 0.7773 (tp) cc_final: 0.7515 (tp) REVERT: D 305 MET cc_start: 0.8186 (tpp) cc_final: 0.7792 (tpp) REVERT: I 5 CYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6829 (p) outliers start: 26 outliers final: 21 residues processed: 100 average time/residue: 0.1817 time to fit residues: 29.2536 Evaluate side-chains 100 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11822 Z= 0.246 Angle : 0.585 9.372 16045 Z= 0.271 Chirality : 0.044 0.195 1795 Planarity : 0.003 0.037 2031 Dihedral : 9.463 136.793 1668 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.82 % Favored : 97.11 % Rotamer: Outliers : 2.93 % Allowed : 19.12 % Favored : 77.95 % 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: 0.69 (0.23), residues: 1418 helix: 0.69 (0.22), residues: 589 sheet: 0.26 (0.34), residues: 250 loop : 0.55 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.010 0.001 HIS B 371 PHE 0.011 0.001 PHE D 31 TYR 0.009 0.001 TYR A 169 ARG 0.003 0.000 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 78 time to evaluate : 1.313 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8046 (t0) cc_final: 0.7549 (t0) REVERT: A 82 MET cc_start: 0.8695 (tpp) cc_final: 0.8492 (tpp) REVERT: A 132 MET cc_start: 0.7249 (ptt) cc_final: 0.6987 (ptt) REVERT: B 118 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7851 (tptm) REVERT: B 269 MET cc_start: 0.7757 (mtp) cc_final: 0.7531 (mtm) REVERT: D 44 MET cc_start: 0.6943 (ttp) cc_final: 0.6614 (ttp) REVERT: D 180 LEU cc_start: 0.7752 (tp) cc_final: 0.7455 (tp) REVERT: D 305 MET cc_start: 0.8307 (tpp) cc_final: 0.7936 (tpp) REVERT: D 355 MET cc_start: 0.7981 (pmm) cc_final: 0.7578 (pmm) REVERT: I 5 CYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6775 (p) outliers start: 36 outliers final: 25 residues processed: 109 average time/residue: 0.1820 time to fit residues: 32.1342 Evaluate side-chains 105 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 78 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 0.0370 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 68 optimal weight: 0.0000 chunk 12 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11822 Z= 0.141 Angle : 0.545 10.953 16045 Z= 0.250 Chirality : 0.043 0.197 1795 Planarity : 0.003 0.036 2031 Dihedral : 9.021 143.384 1668 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.05 % Favored : 97.88 % Rotamer: Outliers : 1.55 % Allowed : 20.34 % Favored : 78.11 % 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 (0.23), residues: 1418 helix: 0.81 (0.23), residues: 590 sheet: 0.43 (0.35), residues: 226 loop : 0.67 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 340 HIS 0.008 0.001 HIS B 371 PHE 0.013 0.001 PHE D 31 TYR 0.009 0.001 TYR A 143 ARG 0.001 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7967 (t0) cc_final: 0.7481 (t0) REVERT: A 132 MET cc_start: 0.7094 (ptt) cc_final: 0.6858 (ptt) REVERT: B 118 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7730 (tptm) REVERT: B 269 MET cc_start: 0.7711 (mtp) cc_final: 0.7487 (mtm) REVERT: D 44 MET cc_start: 0.7134 (ttp) cc_final: 0.6565 (ttp) REVERT: D 305 MET cc_start: 0.8263 (tpp) cc_final: 0.7929 (tpp) REVERT: D 355 MET cc_start: 0.8005 (pmm) cc_final: 0.7627 (pmm) REVERT: I 5 CYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6631 (p) outliers start: 19 outliers final: 14 residues processed: 98 average time/residue: 0.1874 time to fit residues: 29.5285 Evaluate side-chains 97 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11822 Z= 0.226 Angle : 0.578 9.428 16045 Z= 0.267 Chirality : 0.044 0.193 1795 Planarity : 0.003 0.036 2031 Dihedral : 8.782 144.207 1668 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 1.79 % Allowed : 19.93 % Favored : 78.28 % 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: 0.83 (0.23), residues: 1418 helix: 0.76 (0.22), residues: 593 sheet: 0.33 (0.35), residues: 232 loop : 0.66 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.008 0.001 HIS B 371 PHE 0.012 0.001 PHE D 31 TYR 0.017 0.001 TYR C 166 ARG 0.002 0.000 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 1.359 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8071 (t0) cc_final: 0.7596 (t0) REVERT: A 132 MET cc_start: 0.7258 (ptt) cc_final: 0.6981 (ptt) REVERT: B 118 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7675 (tptm) REVERT: B 269 MET cc_start: 0.7734 (mtp) cc_final: 0.7507 (mtm) REVERT: D 44 MET cc_start: 0.7132 (ttp) cc_final: 0.6559 (ttp) REVERT: D 305 MET cc_start: 0.8296 (tpp) cc_final: 0.7938 (tpp) REVERT: D 355 MET cc_start: 0.8065 (pmm) cc_final: 0.7594 (pmm) REVERT: I 5 CYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6698 (p) outliers start: 22 outliers final: 19 residues processed: 98 average time/residue: 0.1862 time to fit residues: 29.0563 Evaluate side-chains 99 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 2.9990 chunk 82 optimal weight: 0.0060 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 131 optimal weight: 0.0970 chunk 113 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11822 Z= 0.133 Angle : 0.542 8.428 16045 Z= 0.248 Chirality : 0.043 0.194 1795 Planarity : 0.003 0.040 2031 Dihedral : 8.557 147.745 1668 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.97 % Favored : 97.95 % Rotamer: Outliers : 1.79 % Allowed : 20.02 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.23), residues: 1418 helix: 0.92 (0.22), residues: 587 sheet: 0.57 (0.33), residues: 244 loop : 0.76 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 340 HIS 0.007 0.001 HIS B 371 PHE 0.013 0.001 PHE D 31 TYR 0.009 0.001 TYR A 143 ARG 0.002 0.000 ARG D 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 1.553 Fit side-chains revert: symmetry clash REVERT: A 80 ASP cc_start: 0.8064 (t0) cc_final: 0.7479 (t0) REVERT: A 132 MET cc_start: 0.7057 (ptt) cc_final: 0.6821 (ptt) REVERT: B 118 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7626 (tptm) REVERT: B 132 MET cc_start: 0.7935 (ttp) cc_final: 0.7158 (ttp) REVERT: B 269 MET cc_start: 0.7712 (mtp) cc_final: 0.7480 (mtm) REVERT: D 44 MET cc_start: 0.7066 (ttp) cc_final: 0.6512 (ttp) REVERT: D 132 MET cc_start: 0.6849 (tmm) cc_final: 0.6639 (tmm) REVERT: D 305 MET cc_start: 0.8226 (tpp) cc_final: 0.8016 (tpp) REVERT: D 355 MET cc_start: 0.7999 (pmm) cc_final: 0.7637 (pmm) REVERT: I 5 CYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6855 (m) outliers start: 22 outliers final: 14 residues processed: 98 average time/residue: 0.1897 time to fit residues: 30.0018 Evaluate side-chains 95 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 104 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.073455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062525 restraints weight = 33565.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.064661 restraints weight = 17347.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.066091 restraints weight = 10820.272| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11822 Z= 0.257 Angle : 0.594 10.239 16045 Z= 0.272 Chirality : 0.044 0.192 1795 Planarity : 0.003 0.036 2031 Dihedral : 8.494 143.644 1668 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.47 % Favored : 97.46 % Rotamer: Outliers : 1.63 % Allowed : 19.93 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.23), residues: 1418 helix: 0.85 (0.22), residues: 589 sheet: 0.47 (0.33), residues: 244 loop : 0.69 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 86 HIS 0.008 0.001 HIS B 371 PHE 0.011 0.001 PHE D 31 TYR 0.018 0.001 TYR C 166 ARG 0.002 0.000 ARG D 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2029.43 seconds wall clock time: 37 minutes 38.82 seconds (2258.82 seconds total)