Starting phenix.real_space_refine on Sat Nov 16 19:17:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fjm_50506/11_2024/9fjm_50506.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fjm_50506/11_2024/9fjm_50506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fjm_50506/11_2024/9fjm_50506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fjm_50506/11_2024/9fjm_50506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fjm_50506/11_2024/9fjm_50506.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fjm_50506/11_2024/9fjm_50506.cif" } resolution = 3.65 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= -0.001 sd= 0.051 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 4 5.21 5 S 84 5.16 5 C 7417 2.51 5 N 1975 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11772 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2803 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} 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: 2847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2847 Classifications: {'peptide': 364} Modifications used: {'COO': 1} 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: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "K" 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: "K" 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.18, per 1000 atoms: 0.78 Number of scatterers: 11772 At special positions: 0 Unit cell: (97.68, 80.08, 154.88, 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 84 16.00 P 12 15.00 Mg 4 11.99 O 2280 8.00 N 1975 7.00 C 7417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " " TRP K 1 " - " ALA K 7 " " DTH K 4 " - " ALA K 3 " Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 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 K 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 24 sheets defined 49.7% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.596A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.736A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.621A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.614A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.618A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.614A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.708A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.635A pdb=" N MET A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.367A pdb=" N LYS A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.522A 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 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.763A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 removed outlier: 3.648A pdb=" N ASP A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.708A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.715A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.696A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.034A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.504A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.844A 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 197 removed outlier: 3.729A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.989A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.585A pdb=" N MET B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.797A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix removed outlier: 4.755A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.533A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.533A 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 removed outlier: 3.552A pdb=" N ILE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.636A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.985A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.546A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.544A pdb=" N LEU C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.829A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.971A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.658A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 4.063A pdb=" N ALA C 174 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.535A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.652A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 232 removed outlier: 3.569A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.726A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.517A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.232A 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 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.717A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 366 removed outlier: 3.784A pdb=" N SER C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.529A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.589A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.579A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.000A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.633A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.940A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.805A 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: 3.802A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.073A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.249A pdb=" N LYS D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.796A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.594A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.524A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 366 removed outlier: 3.527A pdb=" N ASP D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.363A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.585A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 106 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.856A 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 176 through 178 removed outlier: 3.865A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 165 through 166 removed outlier: 3.907A pdb=" N TYR A 166 " --> pdb=" O TYR A 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.547A pdb=" N LYS A 238 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.622A pdb=" N PHE B 31 " --> pdb=" O CYS B 17 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 133 " --> pdb=" O VAL B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 36 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: 3.502A pdb=" N LEU B 176 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.685A pdb=" N TYR B 166 " --> pdb=" O TYR B 169 " (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: 3.886A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR C 106 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 36 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 Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.530A pdb=" N ILE C 250 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 10 removed outlier: 3.819A pdb=" N THR D 106 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.562A 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 removed outlier: 3.812A pdb=" N PHE D 31 " --> pdb=" O CYS D 17 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.628A pdb=" N LYS D 68 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) 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 169 through 170 removed outlier: 3.637A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 176 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.637A pdb=" N TYR D 166 " --> pdb=" O TYR D 169 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 removed outlier: 3.653A pdb=" N LYS D 238 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE D 250 " --> pdb=" O LYS D 238 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1230 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: 3.65 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3806 1.35 - 1.46: 2759 1.46 - 1.58: 5303 1.58 - 1.70: 12 1.70 - 1.82: 144 Bond restraints: 12024 Sorted by residual: bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.00e+00 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.00e+00 bond pdb=" CB LYS B 291 " pdb=" CG LYS B 291 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.02e-01 ... (remaining 12019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 16032 1.85 - 3.70: 227 3.70 - 5.55: 42 5.55 - 7.40: 14 7.40 - 9.25: 5 Bond angle restraints: 16320 Sorted by residual: angle pdb=" CB MET A 355 " pdb=" CG MET A 355 " pdb=" SD MET A 355 " ideal model delta sigma weight residual 112.70 121.95 -9.25 3.00e+00 1.11e-01 9.51e+00 angle pdb=" CB LYS B 291 " pdb=" CG LYS B 291 " pdb=" CD LYS B 291 " ideal model delta sigma weight residual 111.30 118.00 -6.70 2.30e+00 1.89e-01 8.48e+00 angle pdb=" CA LEU A 242 " pdb=" CB LEU A 242 " pdb=" CG LEU A 242 " ideal model delta sigma weight residual 116.30 125.30 -9.00 3.50e+00 8.16e-02 6.62e+00 angle pdb=" CB MET D 325 " pdb=" CG MET D 325 " pdb=" SD MET D 325 " ideal model delta sigma weight residual 112.70 105.04 7.66 3.00e+00 1.11e-01 6.51e+00 angle pdb=" CB MET C 355 " pdb=" CG MET C 355 " pdb=" SD MET C 355 " ideal model delta sigma weight residual 112.70 120.27 -7.57 3.00e+00 1.11e-01 6.37e+00 ... (remaining 16315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.20: 6392 20.20 - 40.40: 684 40.40 - 60.60: 127 60.60 - 80.80: 29 80.80 - 101.00: 10 Dihedral angle restraints: 7242 sinusoidal: 2937 harmonic: 4305 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 41.00 -101.00 1 2.00e+01 2.50e-03 2.86e+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 -60.00 39.71 -99.71 1 2.00e+01 2.50e-03 2.80e+01 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 -60.00 8.07 -68.07 1 2.00e+01 2.50e-03 1.50e+01 ... (remaining 7239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1263 0.037 - 0.074: 382 0.074 - 0.110: 148 0.110 - 0.147: 18 0.147 - 0.184: 5 Chirality restraints: 1816 Sorted by residual: 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 2.53 0.18 2.00e-01 2.50e+01 8.47e-01 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 2.54 0.18 2.00e-01 2.50e+01 7.81e-01 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 2.55 0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 1813 not shown) Planarity restraints: 2072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N TRP J 1 " -0.025 2.00e-02 2.50e+03 4.27e-02 1.83e+01 pdb=" CA ALA J 7 " -0.021 2.00e-02 2.50e+03 pdb=" C ALA J 7 " 0.074 2.00e-02 2.50e+03 pdb=" O ALA J 7 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 129 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO C 130 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 130 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 130 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 257 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO D 258 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 258 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 258 " 0.025 5.00e-02 4.00e+02 ... (remaining 2069 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 37 2.39 - 3.02: 6454 3.02 - 3.65: 17430 3.65 - 4.27: 25917 4.27 - 4.90: 44047 Nonbonded interactions: 93885 Sorted by model distance: nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.766 3.620 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.782 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.785 3.620 nonbonded pdb=" CD1 TRP K 1 " pdb=" SG CYS K 5 " model vdw 1.808 3.620 nonbonded pdb="MG MG B 402 " pdb=" O2 PO4 B 403 " model vdw 2.050 2.170 ... (remaining 93880 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' and (resid 6 through 39 or resid 50 through 374 or resid 401 through \ 403)) selection = (chain 'C' and (resid 6 through 39 or resid 50 through 374 or resid 401 through \ 403)) selection = (chain 'D' and (resid 6 through 39 or resid 50 through 374 or resid 401 through \ 403)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 31.070 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.002 0.031 12024 Z= 0.150 Angle : 0.574 9.252 16320 Z= 0.267 Chirality : 0.042 0.184 1816 Planarity : 0.004 0.051 2064 Dihedral : 16.752 100.999 4458 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.24 % Allowed : 22.26 % Favored : 77.50 % 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: -0.30 (0.23), residues: 1439 helix: -0.69 (0.22), residues: 521 sheet: -0.73 (0.39), residues: 193 loop : 0.58 (0.25), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 86 HIS 0.003 0.001 HIS A 87 PHE 0.006 0.001 PHE B 223 TYR 0.012 0.001 TYR D 362 ARG 0.009 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: D 132 MET cc_start: 0.6366 (ttt) cc_final: 0.6127 (ttt) REVERT: D 325 MET cc_start: 0.7436 (ttp) cc_final: 0.6949 (ttp) outliers start: 3 outliers final: 1 residues processed: 139 average time/residue: 0.2124 time to fit residues: 45.1288 Evaluate side-chains 131 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 12 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12024 Z= 0.342 Angle : 0.666 7.549 16320 Z= 0.323 Chirality : 0.048 0.225 1816 Planarity : 0.005 0.052 2064 Dihedral : 8.067 110.618 1709 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.44 % Allowed : 19.92 % Favored : 75.65 % 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: -0.19 (0.22), residues: 1439 helix: -0.04 (0.21), residues: 567 sheet: -0.65 (0.34), residues: 242 loop : 0.28 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 1 HIS 0.006 0.001 HIS B 101 PHE 0.012 0.002 PHE D 90 TYR 0.014 0.001 TYR C 362 ARG 0.004 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 1.442 Fit side-chains REVERT: C 283 MET cc_start: 0.8259 (tpp) cc_final: 0.6933 (mpp) REVERT: C 292 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7614 (t0) REVERT: D 9 VAL cc_start: 0.9016 (t) cc_final: 0.8746 (m) outliers start: 55 outliers final: 33 residues processed: 174 average time/residue: 0.1932 time to fit residues: 52.1806 Evaluate side-chains 161 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 0.0970 chunk 89 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 142 optimal weight: 0.3980 chunk 117 optimal weight: 0.0270 chunk 130 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN B 101 HIS C 12 ASN D 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12024 Z= 0.169 Angle : 0.586 8.406 16320 Z= 0.275 Chirality : 0.044 0.206 1816 Planarity : 0.004 0.048 2064 Dihedral : 7.865 108.881 1708 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.03 % Allowed : 20.40 % Favored : 75.56 % 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: 0.09 (0.23), residues: 1439 helix: 0.31 (0.22), residues: 563 sheet: -0.64 (0.33), residues: 250 loop : 0.37 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 1 HIS 0.007 0.001 HIS B 101 PHE 0.010 0.001 PHE A 223 TYR 0.013 0.001 TYR D 294 ARG 0.005 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 1.352 Fit side-chains REVERT: A 123 MET cc_start: 0.7842 (mtp) cc_final: 0.7621 (mtp) REVERT: A 202 THR cc_start: 0.7644 (t) cc_final: 0.7172 (p) REVERT: A 207 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6728 (tm-30) REVERT: B 153 MET cc_start: 0.7601 (tmm) cc_final: 0.7170 (tmt) REVERT: C 283 MET cc_start: 0.8159 (tpp) cc_final: 0.6845 (mpp) REVERT: D 9 VAL cc_start: 0.8964 (t) cc_final: 0.8726 (m) REVERT: D 132 MET cc_start: 0.6620 (ttt) cc_final: 0.6384 (ttt) REVERT: D 294 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.6570 (t80) REVERT: D 346 LEU cc_start: 0.8637 (tp) cc_final: 0.8321 (tt) outliers start: 50 outliers final: 32 residues processed: 174 average time/residue: 0.2128 time to fit residues: 55.7661 Evaluate side-chains 157 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 101 HIS C 12 ASN C 49 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12024 Z= 0.401 Angle : 0.684 7.891 16320 Z= 0.327 Chirality : 0.049 0.226 1816 Planarity : 0.005 0.049 2064 Dihedral : 8.154 116.203 1708 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.24 % Allowed : 19.52 % Favored : 75.24 % 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: -0.10 (0.23), residues: 1439 helix: 0.25 (0.22), residues: 560 sheet: -0.86 (0.33), residues: 244 loop : 0.21 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 86 HIS 0.006 0.001 HIS B 101 PHE 0.021 0.002 PHE A 223 TYR 0.011 0.002 TYR B 143 ARG 0.006 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 134 time to evaluate : 1.441 Fit side-chains REVERT: A 104 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8434 (tt) REVERT: A 207 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6838 (tm-30) REVERT: A 353 GLN cc_start: 0.8257 (mm110) cc_final: 0.7599 (tm-30) REVERT: B 167 GLU cc_start: 0.7904 (tp30) cc_final: 0.7668 (tp30) REVERT: B 328 LYS cc_start: 0.7947 (tptt) cc_final: 0.7679 (tttp) REVERT: C 125 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6573 (mt-10) REVERT: D 9 VAL cc_start: 0.9071 (t) cc_final: 0.8777 (m) REVERT: D 132 MET cc_start: 0.6789 (ttt) cc_final: 0.6507 (ttt) REVERT: D 294 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.6463 (t80) REVERT: D 355 MET cc_start: 0.7624 (tpt) cc_final: 0.7333 (tpt) outliers start: 65 outliers final: 47 residues processed: 180 average time/residue: 0.2066 time to fit residues: 56.8269 Evaluate side-chains 171 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 128 ASN B 101 HIS C 12 ASN C 246 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12024 Z= 0.236 Angle : 0.609 8.612 16320 Z= 0.286 Chirality : 0.045 0.227 1816 Planarity : 0.004 0.048 2064 Dihedral : 7.992 112.565 1708 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.16 % Allowed : 20.00 % Favored : 74.84 % 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: -0.00 (0.23), residues: 1439 helix: 0.41 (0.23), residues: 559 sheet: -0.86 (0.33), residues: 248 loop : 0.21 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 340 HIS 0.006 0.001 HIS B 101 PHE 0.018 0.001 PHE A 223 TYR 0.013 0.001 TYR D 294 ARG 0.006 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 129 time to evaluate : 1.297 Fit side-chains REVERT: A 104 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8424 (tt) REVERT: A 190 MET cc_start: 0.7199 (tpp) cc_final: 0.6812 (tpp) REVERT: A 207 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6814 (tm-30) REVERT: A 259 GLU cc_start: 0.7089 (tp30) cc_final: 0.6841 (tp30) REVERT: A 353 GLN cc_start: 0.8233 (mm110) cc_final: 0.7623 (tm-30) REVERT: B 16 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7824 (ptp) REVERT: B 153 MET cc_start: 0.7623 (tmm) cc_final: 0.7148 (tmt) REVERT: B 167 GLU cc_start: 0.7889 (tp30) cc_final: 0.7664 (tp30) REVERT: B 328 LYS cc_start: 0.7963 (tptt) cc_final: 0.7702 (tttp) REVERT: C 123 MET cc_start: 0.7072 (tpp) cc_final: 0.6769 (mtt) REVERT: C 125 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6548 (mt-10) REVERT: D 9 VAL cc_start: 0.9038 (t) cc_final: 0.8768 (m) REVERT: D 151 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7856 (pt) REVERT: D 294 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.6408 (t80) outliers start: 64 outliers final: 47 residues processed: 179 average time/residue: 0.2003 time to fit residues: 56.0542 Evaluate side-chains 177 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 12 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12024 Z= 0.276 Angle : 0.623 9.485 16320 Z= 0.292 Chirality : 0.046 0.235 1816 Planarity : 0.004 0.047 2064 Dihedral : 8.029 115.674 1708 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.56 % Allowed : 20.65 % Favored : 73.79 % 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: -0.12 (0.23), residues: 1439 helix: 0.42 (0.23), residues: 562 sheet: -1.06 (0.31), residues: 265 loop : 0.13 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 86 HIS 0.007 0.001 HIS A 101 PHE 0.017 0.001 PHE A 223 TYR 0.012 0.001 TYR D 294 ARG 0.007 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 125 time to evaluate : 1.219 Fit side-chains REVERT: A 205 GLU cc_start: 0.6933 (mp0) cc_final: 0.6359 (pm20) REVERT: A 207 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6799 (tm-30) REVERT: A 353 GLN cc_start: 0.8197 (mm110) cc_final: 0.7659 (tm-30) REVERT: B 153 MET cc_start: 0.7617 (tmm) cc_final: 0.7105 (tmt) REVERT: B 167 GLU cc_start: 0.7911 (tp30) cc_final: 0.7682 (tp30) REVERT: B 328 LYS cc_start: 0.7979 (tptt) cc_final: 0.7733 (tttp) REVERT: C 125 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6562 (mt-10) REVERT: D 9 VAL cc_start: 0.9039 (t) cc_final: 0.8765 (m) REVERT: D 151 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7872 (pt) REVERT: D 256 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7796 (ttt180) REVERT: D 294 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.6328 (t80) outliers start: 69 outliers final: 52 residues processed: 179 average time/residue: 0.1598 time to fit residues: 43.9983 Evaluate side-chains 177 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 85 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS B 101 HIS C 12 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12024 Z= 0.187 Angle : 0.586 9.856 16320 Z= 0.272 Chirality : 0.044 0.232 1816 Planarity : 0.004 0.045 2064 Dihedral : 7.847 113.371 1708 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.92 % Allowed : 21.37 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.23), residues: 1439 helix: 0.64 (0.23), residues: 562 sheet: -0.93 (0.32), residues: 259 loop : 0.22 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 86 HIS 0.007 0.001 HIS B 101 PHE 0.022 0.001 PHE A 223 TYR 0.014 0.001 TYR D 294 ARG 0.007 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 126 time to evaluate : 1.463 Fit side-chains REVERT: A 104 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8443 (tt) REVERT: A 205 GLU cc_start: 0.6876 (mp0) cc_final: 0.6355 (pm20) REVERT: A 207 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6721 (tm-30) REVERT: A 353 GLN cc_start: 0.8161 (mm110) cc_final: 0.7664 (tm-30) REVERT: B 100 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6352 (pm20) REVERT: B 132 MET cc_start: 0.7729 (tpp) cc_final: 0.7450 (tpt) REVERT: B 153 MET cc_start: 0.7578 (tmm) cc_final: 0.7106 (tmt) REVERT: B 167 GLU cc_start: 0.7887 (tp30) cc_final: 0.7669 (tp30) REVERT: B 259 GLU cc_start: 0.7796 (tp30) cc_final: 0.7419 (tp30) REVERT: B 328 LYS cc_start: 0.7967 (tptt) cc_final: 0.7725 (tttp) REVERT: D 9 VAL cc_start: 0.8962 (t) cc_final: 0.8749 (m) REVERT: D 151 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7801 (pt) REVERT: D 256 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7747 (ttt180) REVERT: D 294 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.6209 (t80) outliers start: 61 outliers final: 48 residues processed: 175 average time/residue: 0.2027 time to fit residues: 54.5846 Evaluate side-chains 175 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 122 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 0.0010 chunk 13 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 12 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12024 Z= 0.208 Angle : 0.598 10.039 16320 Z= 0.277 Chirality : 0.045 0.233 1816 Planarity : 0.004 0.044 2064 Dihedral : 7.813 113.736 1708 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.84 % Allowed : 21.69 % Favored : 73.47 % 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: 0.12 (0.23), residues: 1439 helix: 0.67 (0.23), residues: 562 sheet: -0.97 (0.31), residues: 270 loop : 0.25 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 86 HIS 0.009 0.001 HIS A 101 PHE 0.019 0.001 PHE A 223 TYR 0.013 0.001 TYR D 294 ARG 0.009 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 126 time to evaluate : 1.441 Fit side-chains REVERT: A 207 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6729 (tm-30) REVERT: A 353 GLN cc_start: 0.8126 (mm110) cc_final: 0.7671 (tm-30) REVERT: B 100 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6359 (pm20) REVERT: B 132 MET cc_start: 0.7753 (tpp) cc_final: 0.7533 (tpt) REVERT: B 153 MET cc_start: 0.7583 (tmm) cc_final: 0.7109 (tmt) REVERT: B 259 GLU cc_start: 0.7818 (tp30) cc_final: 0.7456 (tp30) REVERT: B 328 LYS cc_start: 0.7987 (tptt) cc_final: 0.7751 (tttp) REVERT: C 292 ASP cc_start: 0.7880 (t0) cc_final: 0.7677 (t0) REVERT: D 9 VAL cc_start: 0.9007 (t) cc_final: 0.8776 (m) REVERT: D 151 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7826 (pt) REVERT: D 256 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7765 (ttt180) REVERT: D 294 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6193 (t80) outliers start: 60 outliers final: 47 residues processed: 174 average time/residue: 0.2084 time to fit residues: 56.3132 Evaluate side-chains 174 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 123 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.0770 chunk 130 optimal weight: 0.9990 chunk 133 optimal weight: 0.0370 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 129 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 101 HIS C 12 ASN D 252 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12024 Z= 0.162 Angle : 0.590 11.730 16320 Z= 0.272 Chirality : 0.044 0.229 1816 Planarity : 0.004 0.043 2064 Dihedral : 7.633 110.677 1708 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.79 % Allowed : 22.82 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.24 (0.23), residues: 1439 helix: 0.89 (0.23), residues: 550 sheet: -1.08 (0.30), residues: 289 loop : 0.36 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 86 HIS 0.008 0.001 HIS B 101 PHE 0.016 0.001 PHE A 223 TYR 0.015 0.001 TYR D 294 ARG 0.009 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 1.448 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6675 (tm-30) REVERT: A 353 GLN cc_start: 0.8092 (mm110) cc_final: 0.7606 (tm-30) REVERT: B 100 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6304 (pm20) REVERT: B 132 MET cc_start: 0.7641 (tpp) cc_final: 0.7435 (tpt) REVERT: B 153 MET cc_start: 0.7567 (tmm) cc_final: 0.7106 (tmt) REVERT: B 259 GLU cc_start: 0.7789 (tp30) cc_final: 0.7450 (tp30) REVERT: B 328 LYS cc_start: 0.8044 (tptt) cc_final: 0.7813 (tttp) REVERT: C 82 MET cc_start: 0.8088 (tpt) cc_final: 0.7579 (tpt) REVERT: C 292 ASP cc_start: 0.7918 (t0) cc_final: 0.7701 (t0) REVERT: D 151 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7738 (pt) REVERT: D 294 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.6208 (t80) outliers start: 47 outliers final: 37 residues processed: 170 average time/residue: 0.2033 time to fit residues: 53.1302 Evaluate side-chains 165 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 0.0970 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 144 optimal weight: 0.0570 chunk 132 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 0.0770 chunk 91 optimal weight: 0.6980 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS B 115 ASN C 12 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12024 Z= 0.158 Angle : 0.598 10.878 16320 Z= 0.275 Chirality : 0.044 0.230 1816 Planarity : 0.004 0.042 2064 Dihedral : 7.549 109.615 1708 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.55 % Allowed : 22.82 % Favored : 73.63 % 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: 0.28 (0.23), residues: 1439 helix: 0.89 (0.23), residues: 560 sheet: -1.06 (0.30), residues: 288 loop : 0.40 (0.28), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 86 HIS 0.008 0.001 HIS B 101 PHE 0.014 0.001 PHE A 223 TYR 0.015 0.001 TYR D 294 ARG 0.010 0.000 ARG B 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.6979 (tpp) cc_final: 0.6681 (tpp) REVERT: A 207 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6497 (tm-30) REVERT: A 353 GLN cc_start: 0.8063 (mm110) cc_final: 0.7613 (tm-30) REVERT: B 100 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6333 (pm20) REVERT: B 132 MET cc_start: 0.7636 (tpp) cc_final: 0.7423 (tpt) REVERT: B 153 MET cc_start: 0.7599 (tmm) cc_final: 0.7168 (tmt) REVERT: B 259 GLU cc_start: 0.7812 (tp30) cc_final: 0.7507 (tp30) REVERT: B 291 LYS cc_start: 0.8432 (tppt) cc_final: 0.7861 (pttm) REVERT: B 328 LYS cc_start: 0.8056 (tptt) cc_final: 0.7831 (tttp) REVERT: C 82 MET cc_start: 0.8124 (tpt) cc_final: 0.7615 (tpt) REVERT: C 292 ASP cc_start: 0.7933 (t0) cc_final: 0.7714 (t0) REVERT: D 151 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7693 (pt) REVERT: D 256 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7752 (ttt180) REVERT: D 294 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.6195 (t80) REVERT: D 297 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8437 (p) outliers start: 44 outliers final: 35 residues processed: 167 average time/residue: 0.2035 time to fit residues: 52.1178 Evaluate side-chains 165 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 17 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.0870 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 101 HIS B 115 ASN C 12 ASN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107885 restraints weight = 18419.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111040 restraints weight = 11211.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113403 restraints weight = 7773.117| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12024 Z= 0.321 Angle : 0.663 10.627 16320 Z= 0.312 Chirality : 0.047 0.241 1816 Planarity : 0.004 0.044 2064 Dihedral : 7.792 114.287 1708 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.87 % Allowed : 22.58 % Favored : 73.55 % 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: 0.01 (0.23), residues: 1439 helix: 0.63 (0.23), residues: 564 sheet: -1.18 (0.30), residues: 286 loop : 0.27 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 86 HIS 0.007 0.001 HIS B 101 PHE 0.028 0.002 PHE A 223 TYR 0.011 0.001 TYR D 294 ARG 0.009 0.000 ARG B 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2391.25 seconds wall clock time: 50 minutes 34.08 seconds (3034.08 seconds total)