Starting phenix.real_space_refine on Sat May 11 07:28:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtt_19496/05_2024/8rtt_19496_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtt_19496/05_2024/8rtt_19496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtt_19496/05_2024/8rtt_19496.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtt_19496/05_2024/8rtt_19496.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtt_19496/05_2024/8rtt_19496_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rtt_19496/05_2024/8rtt_19496_updated.pdb" } resolution = 3.56 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= 0.000 sd= 0.005 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 11 5.49 5 Mg 4 5.21 5 S 119 5.16 5 C 11460 2.51 5 N 3083 2.21 5 O 3478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C ASP 363": "OD1" <-> "OD2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D ASP 179": "OD1" <-> "OD2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "E ASP 1028": "OD1" <-> "OD2" Residue "E ASP 1051": "OD1" <-> "OD2" Residue "E ASP 1085": "OD1" <-> "OD2" Residue "E PHE 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1359": "OD1" <-> "OD2" Residue "F PHE 1004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1343": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 18155 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" 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: "B" 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: "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: "E" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3173 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 13, 'TRANS': 375} Chain breaks: 1 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3150 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.66, per 1000 atoms: 0.53 Number of scatterers: 18155 At special positions: 0 Unit cell: (113.52, 130.24, 181.28, 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 119 16.00 P 11 15.00 Mg 4 11.99 O 3478 8.00 N 3083 7.00 C 11460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.85 Conformation dependent library (CDL) restraints added in 3.3 seconds 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 4256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 115 helices and 19 sheets defined 50.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.673A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.653A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.535A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.167A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.849A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.535A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.547A pdb=" N PHE A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 4.871A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 292 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA A 295 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.914A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP A 340 " --> pdb=" O TYR A 337 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 341 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.872A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.750A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.512A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.568A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.898A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.979A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.616A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.562A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.765A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.502A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 348 removed outlier: 3.574A pdb=" N SER B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP B 340 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 Processing helix chain 'B' and resid 359 through 365 removed outlier: 3.619A pdb=" N SER B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.589A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.583A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.640A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.531A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.512A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.801A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.540A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.683A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.543A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 276 through 284 Processing helix chain 'C' and resid 287 through 296 removed outlier: 4.333A pdb=" N LYS C 291 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 4.916A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.538A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 373 removed outlier: 3.528A pdb=" N SER C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Proline residue: C 367 - end of helix removed outlier: 5.206A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.779A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 126 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 145 removed outlier: 3.747A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.700A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 215 removed outlier: 3.792A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 removed outlier: 3.533A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 Proline residue: D 258 - end of helix removed outlier: 4.577A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 254 through 261' Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 274 through 284 removed outlier: 3.581A pdb=" N PHE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 removed outlier: 4.068A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 293 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR D 294 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.591A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 removed outlier: 3.539A pdb=" N SER D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.500A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET D 355 " --> pdb=" O PHE D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 removed outlier: 3.667A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 373 removed outlier: 4.031A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 1012 through 1024 Processing helix chain 'E' and resid 1026 through 1033 removed outlier: 3.641A pdb=" N GLU E1032 " --> pdb=" O ASP E1028 " (cutoff:3.500A) Processing helix chain 'E' and resid 1055 through 1064 removed outlier: 3.651A pdb=" N LYS E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) Processing helix chain 'E' and resid 1073 through 1081 Processing helix chain 'E' and resid 1085 through 1094 removed outlier: 4.723A pdb=" N GLU E1089 " --> pdb=" O SER E1086 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS E1090 " --> pdb=" O MET E1087 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL E1091 " --> pdb=" O ASN E1088 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU E1092 " --> pdb=" O GLU E1089 " (cutoff:3.500A) Processing helix chain 'E' and resid 1097 through 1100 No H-bonds generated for 'chain 'E' and resid 1097 through 1100' Processing helix chain 'E' and resid 1103 through 1109 Processing helix chain 'E' and resid 1134 through 1142 Processing helix chain 'E' and resid 1150 through 1185 removed outlier: 3.501A pdb=" N THR E1165 " --> pdb=" O ASN E1161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR E1167 " --> pdb=" O ILE E1163 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLU E1168 " --> pdb=" O GLU E1164 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN E1169 " --> pdb=" O THR E1165 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG E1172 " --> pdb=" O GLU E1168 " (cutoff:3.500A) Processing helix chain 'E' and resid 1188 through 1204 removed outlier: 3.567A pdb=" N MET E1204 " --> pdb=" O LEU E1200 " (cutoff:3.500A) Processing helix chain 'E' and resid 1207 through 1209 No H-bonds generated for 'chain 'E' and resid 1207 through 1209' Processing helix chain 'E' and resid 1216 through 1221 removed outlier: 3.671A pdb=" N GLN E1220 " --> pdb=" O GLY E1217 " (cutoff:3.500A) Processing helix chain 'E' and resid 1234 through 1245 removed outlier: 3.837A pdb=" N ILE E1240 " --> pdb=" O HIS E1236 " (cutoff:3.500A) Processing helix chain 'E' and resid 1247 through 1249 No H-bonds generated for 'chain 'E' and resid 1247 through 1249' Processing helix chain 'E' and resid 1258 through 1264 removed outlier: 4.020A pdb=" N LYS E1264 " --> pdb=" O THR E1260 " (cutoff:3.500A) Processing helix chain 'E' and resid 1267 through 1290 removed outlier: 3.633A pdb=" N LEU E1277 " --> pdb=" O GLU E1273 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE E1278 " --> pdb=" O CYS E1274 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE E1286 " --> pdb=" O GLN E1282 " (cutoff:3.500A) Processing helix chain 'E' and resid 1292 through 1294 No H-bonds generated for 'chain 'E' and resid 1292 through 1294' Processing helix chain 'E' and resid 1305 through 1341 Proline residue: E1311 - end of helix removed outlier: 3.512A pdb=" N MET E1314 " --> pdb=" O LEU E1310 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU E1315 " --> pdb=" O PRO E1311 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE E1322 " --> pdb=" O LYS E1318 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE E1341 " --> pdb=" O ALA E1337 " (cutoff:3.500A) Processing helix chain 'E' and resid 1348 through 1352 Processing helix chain 'E' and resid 1355 through 1384 removed outlier: 3.552A pdb=" N GLU E1378 " --> pdb=" O LYS E1374 " (cutoff:3.500A) Processing helix chain 'F' and resid 1006 through 1008 No H-bonds generated for 'chain 'F' and resid 1006 through 1008' Processing helix chain 'F' and resid 1012 through 1023 removed outlier: 3.672A pdb=" N ILE F1017 " --> pdb=" O GLU F1013 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F1018 " --> pdb=" O ALA F1014 " (cutoff:3.500A) Processing helix chain 'F' and resid 1027 through 1033 removed outlier: 3.592A pdb=" N ASP F1031 " --> pdb=" O LEU F1027 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU F1032 " --> pdb=" O ASP F1028 " (cutoff:3.500A) Processing helix chain 'F' and resid 1055 through 1064 removed outlier: 3.782A pdb=" N LYS F1059 " --> pdb=" O SER F1055 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU F1060 " --> pdb=" O GLU F1056 " (cutoff:3.500A) Processing helix chain 'F' and resid 1066 through 1068 No H-bonds generated for 'chain 'F' and resid 1066 through 1068' Processing helix chain 'F' and resid 1073 through 1082 removed outlier: 3.561A pdb=" N ARG F1078 " --> pdb=" O ASN F1074 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE F1080 " --> pdb=" O ILE F1076 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU F1081 " --> pdb=" O ILE F1077 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS F1082 " --> pdb=" O ARG F1078 " (cutoff:3.500A) Processing helix chain 'F' and resid 1085 through 1087 No H-bonds generated for 'chain 'F' and resid 1085 through 1087' Processing helix chain 'F' and resid 1090 through 1095 removed outlier: 3.553A pdb=" N LEU F1094 " --> pdb=" O CYS F1090 " (cutoff:3.500A) Processing helix chain 'F' and resid 1097 through 1100 No H-bonds generated for 'chain 'F' and resid 1097 through 1100' Processing helix chain 'F' and resid 1103 through 1110 Processing helix chain 'F' and resid 1134 through 1142 removed outlier: 3.626A pdb=" N LEU F1138 " --> pdb=" O ARG F1134 " (cutoff:3.500A) Processing helix chain 'F' and resid 1150 through 1185 removed outlier: 3.634A pdb=" N ILE F1162 " --> pdb=" O LYS F1158 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR F1165 " --> pdb=" O ASN F1161 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU F1168 " --> pdb=" O GLU F1164 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN F1169 " --> pdb=" O THR F1165 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG F1172 " --> pdb=" O GLU F1168 " (cutoff:3.500A) Processing helix chain 'F' and resid 1188 through 1204 removed outlier: 3.762A pdb=" N MET F1204 " --> pdb=" O LEU F1200 " (cutoff:3.500A) Processing helix chain 'F' and resid 1207 through 1209 No H-bonds generated for 'chain 'F' and resid 1207 through 1209' Processing helix chain 'F' and resid 1216 through 1221 removed outlier: 3.925A pdb=" N GLN F1220 " --> pdb=" O GLY F1217 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG F1221 " --> pdb=" O SER F1218 " (cutoff:3.500A) Processing helix chain 'F' and resid 1234 through 1245 removed outlier: 3.519A pdb=" N LEU F1238 " --> pdb=" O LEU F1234 " (cutoff:3.500A) Processing helix chain 'F' and resid 1247 through 1249 No H-bonds generated for 'chain 'F' and resid 1247 through 1249' Processing helix chain 'F' and resid 1258 through 1264 removed outlier: 3.940A pdb=" N LYS F1264 " --> pdb=" O THR F1260 " (cutoff:3.500A) Processing helix chain 'F' and resid 1267 through 1289 removed outlier: 3.606A pdb=" N LEU F1277 " --> pdb=" O GLU F1273 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F1278 " --> pdb=" O CYS F1274 " (cutoff:3.500A) Processing helix chain 'F' and resid 1292 through 1294 No H-bonds generated for 'chain 'F' and resid 1292 through 1294' Processing helix chain 'F' and resid 1305 through 1341 Proline residue: F1311 - end of helix removed outlier: 3.938A pdb=" N MET F1314 " --> pdb=" O LEU F1310 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU F1315 " --> pdb=" O PRO F1311 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS F1318 " --> pdb=" O MET F1314 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP F1321 " --> pdb=" O THR F1317 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE F1341 " --> pdb=" O ALA F1337 " (cutoff:3.500A) Processing helix chain 'F' and resid 1348 through 1352 Processing helix chain 'F' and resid 1355 through 1376 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 11 removed outlier: 3.571A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 52 through 54 removed outlier: 4.168A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'A' and resid 298 through 300 removed outlier: 3.652A pdb=" N VAL A 152 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.881A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B 9 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 31 " --> pdb=" O CYS B 17 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 52 through 54 removed outlier: 4.028A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 298 through 300 Processing sheet with id= I, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= J, first strand: chain 'C' and resid 8 through 11 removed outlier: 3.679A pdb=" N VAL C 9 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 52 through 54 removed outlier: 3.919A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= M, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.305A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N MET C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= O, first strand: chain 'D' and resid 16 through 19 removed outlier: 3.709A pdb=" N PHE D 31 " --> pdb=" O CYS D 17 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 52 through 54 removed outlier: 3.530A pdb=" N LYS D 68 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 103 through 107 removed outlier: 3.636A pdb=" N TYR D 133 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.313A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N MET D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 176 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 238 through 241 680 hydrogen bonds defined for protein. 1770 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: 5.95 Time building geometry restraints manager: 7.49 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: 5938 1.35 - 1.46: 4197 1.46 - 1.58: 8181 1.58 - 1.70: 18 1.70 - 1.82: 205 Bond restraints: 18539 Sorted by residual: bond pdb=" N HYP J 6 " pdb=" CD HYP J 6 " ideal model delta sigma weight residual 1.473 1.636 -0.163 1.40e-02 5.10e+03 1.35e+02 bond pdb=" N HYP H 6 " pdb=" CD HYP H 6 " ideal model delta sigma weight residual 1.473 1.636 -0.163 1.40e-02 5.10e+03 1.35e+02 bond pdb=" N HYP I 6 " pdb=" CD HYP I 6 " ideal model delta sigma weight residual 1.473 1.635 -0.162 1.40e-02 5.10e+03 1.34e+02 bond pdb=" CG HYP J 6 " pdb=" CD HYP J 6 " ideal model delta sigma weight residual 1.530 1.366 0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" CG HYP H 6 " pdb=" CD HYP H 6 " ideal model delta sigma weight residual 1.530 1.367 0.163 2.00e-02 2.50e+03 6.64e+01 ... (remaining 18534 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.56: 608 106.56 - 113.93: 10521 113.93 - 121.30: 9492 121.30 - 128.66: 4355 128.66 - 136.03: 134 Bond angle restraints: 25110 Sorted by residual: angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.87 -4.87 1.10e+00 8.26e-01 1.96e+01 angle pdb=" N HYP J 6 " pdb=" CA HYP J 6 " pdb=" CB HYP J 6 " ideal model delta sigma weight residual 103.00 107.66 -4.66 1.10e+00 8.26e-01 1.79e+01 angle pdb=" N HYP I 6 " pdb=" CA HYP I 6 " pdb=" CB HYP I 6 " ideal model delta sigma weight residual 103.00 107.51 -4.51 1.10e+00 8.26e-01 1.68e+01 angle pdb=" CB MET E1087 " pdb=" CG MET E1087 " pdb=" SD MET E1087 " ideal model delta sigma weight residual 112.70 121.93 -9.23 3.00e+00 1.11e-01 9.46e+00 angle pdb=" CA GLU E1273 " pdb=" CB GLU E1273 " pdb=" CG GLU E1273 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.15e+00 ... (remaining 25105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.03: 10800 34.03 - 68.06: 367 68.06 - 102.09: 23 102.09 - 136.11: 3 136.11 - 170.14: 2 Dihedral angle restraints: 11195 sinusoidal: 4589 harmonic: 6606 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 129.86 170.14 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 103.71 -163.71 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 164.64 135.36 1 2.00e+01 2.50e-03 4.11e+01 ... (remaining 11192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2445 0.059 - 0.117: 319 0.117 - 0.176: 7 0.176 - 0.235: 0 0.235 - 0.293: 3 Chirality restraints: 2774 Sorted by residual: chirality pdb=" CA HYP I 6 " pdb=" N HYP I 6 " pdb=" C HYP I 6 " pdb=" CB HYP I 6 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA HYP J 6 " pdb=" N HYP J 6 " pdb=" C HYP J 6 " pdb=" CB HYP J 6 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA HYP H 6 " pdb=" N HYP H 6 " pdb=" C HYP H 6 " pdb=" CB HYP H 6 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2771 not shown) Planarity restraints: 3208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F1310 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO F1311 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO F1311 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F1311 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 241 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" CD GLU C 241 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU C 241 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C 241 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 366 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.53e+00 pdb=" N PRO D 367 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " -0.017 5.00e-02 4.00e+02 ... (remaining 3205 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 8 2.03 - 2.75: 2164 2.75 - 3.47: 25053 3.47 - 4.18: 41468 4.18 - 4.90: 76349 Nonbonded interactions: 145042 Sorted by model distance: nonbonded pdb=" N TRP I 1 " pdb=" C ALA I 7 " model vdw 1.317 3.350 nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.321 3.350 nonbonded pdb=" N TRP J 1 " pdb=" C ALA J 7 " model vdw 1.324 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.740 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.757 3.620 ... (remaining 145037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 375 or resid 401 through 402)) selection = (chain 'B' and (resid 6 through 375 or resid 401 through 402)) selection = (chain 'C' and (resid 6 through 375 or resid 401 through 402)) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 984 through 1377) selection = (chain 'F' and (resid 984 through 1036 or resid 1050 through 1377)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 7.460 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 49.950 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.150 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.004 0.164 18539 Z= 0.295 Angle : 0.522 9.227 25110 Z= 0.251 Chirality : 0.040 0.293 2774 Planarity : 0.003 0.035 3208 Dihedral : 16.491 170.142 6939 Min Nonbonded Distance : 1.317 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.20 % Allowed : 20.25 % Favored : 79.55 % 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: 0.18 (0.18), residues: 2228 helix: 0.27 (0.16), residues: 1100 sheet: 0.36 (0.37), residues: 232 loop : 0.09 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 995 HIS 0.004 0.001 HIS F1236 PHE 0.009 0.001 PHE F1004 TYR 0.005 0.001 TYR D 166 ARG 0.008 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1154 MET cc_start: 0.8247 (mmp) cc_final: 0.7752 (mmm) outliers start: 4 outliers final: 1 residues processed: 150 average time/residue: 0.2647 time to fit residues: 65.4198 Evaluate side-chains 146 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 995 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 137 GLN B 225 GLN D 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18539 Z= 0.293 Angle : 0.567 6.714 25110 Z= 0.279 Chirality : 0.043 0.254 2774 Planarity : 0.004 0.034 3208 Dihedral : 8.412 175.518 2554 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.76 % Allowed : 18.35 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2228 helix: 0.61 (0.16), residues: 1101 sheet: 0.33 (0.32), residues: 276 loop : 0.07 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 1 HIS 0.006 0.001 HIS C 87 PHE 0.012 0.001 PHE D 31 TYR 0.010 0.001 TYR F1137 ARG 0.006 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 163 time to evaluate : 2.229 Fit side-chains revert: symmetry clash REVERT: A 325 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6694 (mmt) REVERT: D 153 MET cc_start: 0.7960 (tmm) cc_final: 0.7703 (tpt) REVERT: E 1378 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: I 5 CYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7130 (m) REVERT: J 5 CYS cc_start: 0.6804 (OUTLIER) cc_final: 0.6175 (m) REVERT: F 1161 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.8160 (m-40) outliers start: 54 outliers final: 30 residues processed: 205 average time/residue: 0.2437 time to fit residues: 84.0688 Evaluate side-chains 182 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 147 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1171 VAL Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1286 ILE Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1161 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 203 optimal weight: 0.9990 chunk 220 optimal weight: 20.0000 chunk 181 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 163 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18539 Z= 0.204 Angle : 0.513 6.904 25110 Z= 0.246 Chirality : 0.041 0.202 2774 Planarity : 0.003 0.033 3208 Dihedral : 7.678 145.483 2554 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.61 % Allowed : 19.53 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2228 helix: 0.68 (0.16), residues: 1103 sheet: 0.37 (0.32), residues: 268 loop : 0.12 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F1312 HIS 0.004 0.001 HIS A 87 PHE 0.011 0.001 PHE D 31 TYR 0.015 0.001 TYR A 53 ARG 0.006 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 154 time to evaluate : 2.141 Fit side-chains REVERT: B 87 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.8000 (t70) REVERT: D 153 MET cc_start: 0.8002 (tmm) cc_final: 0.7752 (tpt) REVERT: E 1378 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6812 (mt-10) REVERT: I 5 CYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7129 (m) REVERT: J 5 CYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6072 (m) REVERT: F 1154 MET cc_start: 0.8115 (mmp) cc_final: 0.7850 (mmm) outliers start: 51 outliers final: 27 residues processed: 192 average time/residue: 0.2565 time to fit residues: 81.0922 Evaluate side-chains 173 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1171 VAL Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1286 ILE Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1326 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 136 optimal weight: 0.2980 chunk 204 optimal weight: 20.0000 chunk 216 optimal weight: 0.5980 chunk 106 optimal weight: 0.2980 chunk 193 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18539 Z= 0.184 Angle : 0.505 7.737 25110 Z= 0.240 Chirality : 0.041 0.190 2774 Planarity : 0.003 0.033 3208 Dihedral : 7.189 129.163 2554 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.30 % Allowed : 20.14 % Favored : 77.56 % 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: 0.74 (0.18), residues: 2228 helix: 0.89 (0.16), residues: 1081 sheet: 0.38 (0.32), residues: 268 loop : 0.23 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F1312 HIS 0.005 0.001 HIS C 101 PHE 0.011 0.001 PHE F1341 TYR 0.011 0.001 TYR A 53 ARG 0.002 0.000 ARG E1134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 144 time to evaluate : 2.201 Fit side-chains REVERT: B 87 HIS cc_start: 0.8310 (OUTLIER) cc_final: 0.8000 (t70) REVERT: D 153 MET cc_start: 0.7998 (tmm) cc_final: 0.7763 (tpt) REVERT: E 1378 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6767 (mt-10) REVERT: I 5 CYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7318 (m) REVERT: J 5 CYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6181 (m) outliers start: 45 outliers final: 37 residues processed: 180 average time/residue: 0.2493 time to fit residues: 75.3884 Evaluate side-chains 180 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1015 ASN Chi-restraints excluded: chain E residue 1171 VAL Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1061 PHE Chi-restraints excluded: chain F residue 1326 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 161 optimal weight: 0.0570 chunk 89 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 149 optimal weight: 50.0000 chunk 0 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 115 ASN C 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18539 Z= 0.329 Angle : 0.561 6.583 25110 Z= 0.271 Chirality : 0.043 0.197 2774 Planarity : 0.004 0.034 3208 Dihedral : 7.144 140.561 2554 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.32 % Allowed : 20.19 % Favored : 76.48 % 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: 0.52 (0.18), residues: 2228 helix: 0.75 (0.16), residues: 1080 sheet: 0.20 (0.33), residues: 264 loop : 0.07 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F1312 HIS 0.004 0.001 HIS C 101 PHE 0.013 0.001 PHE E1361 TYR 0.012 0.001 TYR A 53 ARG 0.006 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 148 time to evaluate : 2.203 Fit side-chains REVERT: B 47 MET cc_start: 0.6895 (tpp) cc_final: 0.6676 (tpt) REVERT: B 87 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.8024 (t70) REVERT: D 153 MET cc_start: 0.8064 (tmm) cc_final: 0.7799 (tpt) REVERT: E 1194 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8793 (mm) REVERT: E 1378 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6585 (mt-10) REVERT: I 5 CYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7263 (m) REVERT: J 5 CYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6359 (m) outliers start: 65 outliers final: 49 residues processed: 200 average time/residue: 0.2533 time to fit residues: 83.8121 Evaluate side-chains 194 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 140 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1015 ASN Chi-restraints excluded: chain E residue 1170 LEU Chi-restraints excluded: chain E residue 1171 VAL Chi-restraints excluded: chain E residue 1194 LEU Chi-restraints excluded: chain E residue 1237 ILE Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1286 ILE Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1061 PHE Chi-restraints excluded: chain F residue 1189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 42 optimal weight: 0.0970 chunk 127 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 216 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 100 optimal weight: 0.0040 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18539 Z= 0.146 Angle : 0.498 6.858 25110 Z= 0.237 Chirality : 0.040 0.176 2774 Planarity : 0.003 0.034 3208 Dihedral : 6.767 138.811 2554 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.30 % Allowed : 21.06 % Favored : 76.64 % 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: 0.77 (0.18), residues: 2228 helix: 0.96 (0.17), residues: 1077 sheet: 0.27 (0.32), residues: 268 loop : 0.22 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F1312 HIS 0.003 0.001 HIS C 101 PHE 0.010 0.001 PHE B 31 TYR 0.008 0.001 TYR E1167 ARG 0.002 0.000 ARG E1134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 151 time to evaluate : 2.176 Fit side-chains REVERT: D 153 MET cc_start: 0.7961 (tmm) cc_final: 0.7626 (tpt) REVERT: D 227 MET cc_start: 0.8144 (tpp) cc_final: 0.7743 (tpp) REVERT: E 1378 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6760 (mt-10) REVERT: I 5 CYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7187 (m) REVERT: J 5 CYS cc_start: 0.6910 (p) cc_final: 0.6483 (m) REVERT: F 1154 MET cc_start: 0.7875 (mmp) cc_final: 0.7647 (mmm) outliers start: 45 outliers final: 33 residues processed: 189 average time/residue: 0.2604 time to fit residues: 81.4343 Evaluate side-chains 173 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1015 ASN Chi-restraints excluded: chain E residue 1237 ILE Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1061 PHE Chi-restraints excluded: chain F residue 1189 VAL Chi-restraints excluded: chain F residue 1326 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 40.0000 chunk 24 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 158 optimal weight: 0.4980 chunk 122 optimal weight: 0.9990 chunk 182 optimal weight: 10.0000 chunk 121 optimal weight: 0.5980 chunk 215 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18539 Z= 0.153 Angle : 0.495 7.298 25110 Z= 0.234 Chirality : 0.040 0.173 2774 Planarity : 0.003 0.033 3208 Dihedral : 6.483 133.125 2554 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.30 % Allowed : 21.42 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 2228 helix: 1.07 (0.17), residues: 1077 sheet: 0.29 (0.32), residues: 268 loop : 0.24 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F1312 HIS 0.003 0.001 HIS D 87 PHE 0.009 0.001 PHE D 31 TYR 0.007 0.001 TYR A 53 ARG 0.010 0.000 ARG F1172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 142 time to evaluate : 2.152 Fit side-chains REVERT: B 87 HIS cc_start: 0.8258 (OUTLIER) cc_final: 0.7902 (t70) REVERT: D 153 MET cc_start: 0.7959 (tmm) cc_final: 0.7706 (tpt) REVERT: D 227 MET cc_start: 0.8164 (tpp) cc_final: 0.7771 (tpp) REVERT: E 1378 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6829 (mt-10) REVERT: I 5 CYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7185 (m) REVERT: J 5 CYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6558 (m) outliers start: 45 outliers final: 34 residues processed: 180 average time/residue: 0.2427 time to fit residues: 72.6209 Evaluate side-chains 178 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 140 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1060 LEU Chi-restraints excluded: chain E residue 1237 ILE Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1061 PHE Chi-restraints excluded: chain F residue 1189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 106 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18539 Z= 0.204 Angle : 0.508 6.940 25110 Z= 0.241 Chirality : 0.041 0.178 2774 Planarity : 0.003 0.033 3208 Dihedral : 6.360 127.435 2554 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.86 % Allowed : 21.06 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2228 helix: 1.04 (0.17), residues: 1083 sheet: 0.21 (0.33), residues: 264 loop : 0.09 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F1116 HIS 0.003 0.001 HIS C 101 PHE 0.010 0.001 PHE B 31 TYR 0.008 0.001 TYR A 53 ARG 0.007 0.000 ARG F1172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 142 time to evaluate : 2.188 Fit side-chains revert: symmetry clash REVERT: B 87 HIS cc_start: 0.8282 (OUTLIER) cc_final: 0.7945 (t70) REVERT: D 153 MET cc_start: 0.7992 (tmm) cc_final: 0.7735 (tpt) REVERT: D 227 MET cc_start: 0.8209 (tpp) cc_final: 0.7795 (tpp) REVERT: E 1378 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6736 (mt-10) REVERT: I 5 CYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7277 (m) REVERT: J 5 CYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6621 (m) REVERT: F 1154 MET cc_start: 0.7819 (mmp) cc_final: 0.7524 (mmm) outliers start: 56 outliers final: 43 residues processed: 191 average time/residue: 0.2601 time to fit residues: 82.7930 Evaluate side-chains 186 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 139 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1060 LEU Chi-restraints excluded: chain E residue 1237 ILE Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1041 THR Chi-restraints excluded: chain F residue 1061 PHE Chi-restraints excluded: chain F residue 1189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 4.9990 chunk 206 optimal weight: 50.0000 chunk 188 optimal weight: 0.9990 chunk 201 optimal weight: 4.9990 chunk 121 optimal weight: 0.0010 chunk 87 optimal weight: 4.9990 chunk 157 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN E1383 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18539 Z= 0.170 Angle : 0.500 7.637 25110 Z= 0.237 Chirality : 0.041 0.183 2774 Planarity : 0.003 0.032 3208 Dihedral : 6.227 122.158 2554 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.71 % Allowed : 21.17 % Favored : 76.12 % 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: 0.86 (0.18), residues: 2228 helix: 1.14 (0.17), residues: 1069 sheet: 0.20 (0.32), residues: 268 loop : 0.16 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F1116 HIS 0.013 0.001 HIS E1383 PHE 0.010 0.001 PHE B 31 TYR 0.006 0.001 TYR E1167 ARG 0.004 0.000 ARG F1172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 141 time to evaluate : 2.126 Fit side-chains revert: symmetry clash REVERT: D 153 MET cc_start: 0.7956 (tmm) cc_final: 0.7706 (tpt) REVERT: D 227 MET cc_start: 0.8168 (tpp) cc_final: 0.7772 (tpp) REVERT: E 1378 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6730 (mt-10) REVERT: I 5 CYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7254 (m) REVERT: J 5 CYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6562 (m) REVERT: F 1087 MET cc_start: 0.7910 (tpp) cc_final: 0.7605 (tpp) REVERT: F 1154 MET cc_start: 0.7869 (mmp) cc_final: 0.7601 (mmm) outliers start: 53 outliers final: 43 residues processed: 187 average time/residue: 0.2498 time to fit residues: 78.0919 Evaluate side-chains 184 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 138 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1060 LEU Chi-restraints excluded: chain E residue 1237 ILE Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1041 THR Chi-restraints excluded: chain F residue 1061 PHE Chi-restraints excluded: chain F residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 223 optimal weight: 9.9990 chunk 205 optimal weight: 0.2980 chunk 177 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 137 optimal weight: 0.0060 chunk 108 optimal weight: 5.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 115 ASN E1383 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18539 Z= 0.246 Angle : 0.528 7.726 25110 Z= 0.252 Chirality : 0.042 0.196 2774 Planarity : 0.003 0.032 3208 Dihedral : 6.296 121.463 2554 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.51 % Allowed : 21.42 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2228 helix: 1.02 (0.17), residues: 1075 sheet: 0.22 (0.33), residues: 256 loop : 0.10 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F1116 HIS 0.004 0.001 HIS E1383 PHE 0.010 0.001 PHE B 31 TYR 0.008 0.001 TYR A 53 ARG 0.005 0.000 ARG F1172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 141 time to evaluate : 2.114 Fit side-chains revert: symmetry clash REVERT: B 47 MET cc_start: 0.7300 (tpp) cc_final: 0.7074 (tpt) REVERT: D 153 MET cc_start: 0.7993 (tmm) cc_final: 0.7710 (tpt) REVERT: D 227 MET cc_start: 0.8204 (tpp) cc_final: 0.7828 (tpp) REVERT: E 1378 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6659 (mt-10) REVERT: E 1384 ARG cc_start: 0.7222 (mmp80) cc_final: 0.7013 (tmm-80) REVERT: I 5 CYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7276 (m) REVERT: J 5 CYS cc_start: 0.6941 (OUTLIER) cc_final: 0.6605 (m) REVERT: F 1087 MET cc_start: 0.7941 (tpp) cc_final: 0.7597 (tpp) REVERT: F 1154 MET cc_start: 0.7832 (mmp) cc_final: 0.7587 (mmm) outliers start: 49 outliers final: 44 residues processed: 183 average time/residue: 0.2593 time to fit residues: 78.2118 Evaluate side-chains 188 residues out of total 1956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 141 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 1005 THR Chi-restraints excluded: chain E residue 1060 LEU Chi-restraints excluded: chain E residue 1237 ILE Chi-restraints excluded: chain E residue 1281 CYS Chi-restraints excluded: chain E residue 1378 GLU Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Chi-restraints excluded: chain F residue 995 TRP Chi-restraints excluded: chain F residue 1041 THR Chi-restraints excluded: chain F residue 1061 PHE Chi-restraints excluded: chain F residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 0.0170 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.136840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.095356 restraints weight = 32930.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.098055 restraints weight = 18958.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.099868 restraints weight = 12844.812| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 18539 Z= 0.293 Angle : 0.717 59.099 25110 Z= 0.398 Chirality : 0.046 1.051 2774 Planarity : 0.003 0.047 3208 Dihedral : 6.328 121.462 2554 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.51 % Allowed : 21.57 % Favored : 75.92 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.74 (0.18), residues: 2228 helix: 1.01 (0.17), residues: 1075 sheet: 0.13 (0.33), residues: 260 loop : 0.12 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F1116 HIS 0.003 0.001 HIS C 101 PHE 0.010 0.001 PHE B 31 TYR 0.010 0.001 TYR C 133 ARG 0.004 0.000 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3050.74 seconds wall clock time: 57 minutes 12.72 seconds (3432.72 seconds total)