Starting phenix.real_space_refine on Mon Mar 25 11:58:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyw_12656/03_2024/7nyw_12656_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyw_12656/03_2024/7nyw_12656.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyw_12656/03_2024/7nyw_12656_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyw_12656/03_2024/7nyw_12656_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyw_12656/03_2024/7nyw_12656_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyw_12656/03_2024/7nyw_12656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyw_12656/03_2024/7nyw_12656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyw_12656/03_2024/7nyw_12656_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyw_12656/03_2024/7nyw_12656_trim_updated.pdb" } resolution = 3.1 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= 0.002 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: 7 Type Number sf(0) Gaussians P 111 5.49 5 Mg 2 5.21 5 S 89 5.16 5 C 15169 2.51 5 N 4484 2.21 5 O 4933 1.98 5 H 23780 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 41": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48568 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 11041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 11041 Classifications: {'peptide': 685} Link IDs: {'PTRANS': 15, 'TRANS': 669} Chain breaks: 1 Chain: "B" Number of atoms: 13847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 13847 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 17, 'TRANS': 840} Chain breaks: 3 Chain: "C" Number of atoms: 5330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 5330 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 327} Chain breaks: 1 Chain: "D" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1469 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3441 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3246 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "G" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1105 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "H" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1105 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "I" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2272 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "J" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2288 Classifications: {'peptide': 135} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "K" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 694 Classifications: {'DNA': 22} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 21} Chain: "L" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 702 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "M" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 961 Classifications: {'DNA': 30} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 29} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 961 Classifications: {'DNA': 30} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 20.11, per 1000 atoms: 0.41 Number of scatterers: 48568 At special positions: 0 Unit cell: (130.822, 162.801, 181.697, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 89 16.00 P 111 15.00 Mg 2 11.99 O 4933 8.00 N 4484 7.00 C 15169 6.00 H 23780 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 41.45 Conformation dependent library (CDL) restraints added in 4.8 seconds 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5306 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 11 sheets defined 59.9% alpha, 6.9% beta 52 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 26.45 Creating SS restraints... Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 132 through 135 No H-bonds generated for 'chain 'A' and resid 132 through 135' Processing helix chain 'A' and resid 150 through 158 Processing helix chain 'A' and resid 171 through 180 Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 226 through 305 removed outlier: 3.882A pdb=" N HIS A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1125 removed outlier: 4.374A pdb=" N ALA A1119 " --> pdb=" O ALA A1115 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 4.100A pdb=" N TYR A1140 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1160 removed outlier: 3.607A pdb=" N SER A1148 " --> pdb=" O GLY A1144 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A1159 " --> pdb=" O GLY A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 3.926A pdb=" N GLU A1175 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1198 removed outlier: 4.092A pdb=" N GLN A1192 " --> pdb=" O ALA A1189 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG A1197 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A1198 " --> pdb=" O ARG A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1262 removed outlier: 3.517A pdb=" N ILE A1212 " --> pdb=" O PRO A1208 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLU A1213 " --> pdb=" O VAL A1209 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A1260 " --> pdb=" O ARG A1256 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY A1261 " --> pdb=" O MET A1257 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1292 removed outlier: 4.145A pdb=" N LEU A1286 " --> pdb=" O SER A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1300 No H-bonds generated for 'chain 'A' and resid 1298 through 1300' Processing helix chain 'A' and resid 1308 through 1318 Processing helix chain 'A' and resid 1330 through 1337 Processing helix chain 'A' and resid 1340 through 1343 Processing helix chain 'A' and resid 1362 through 1364 No H-bonds generated for 'chain 'A' and resid 1362 through 1364' Processing helix chain 'A' and resid 1367 through 1392 removed outlier: 4.675A pdb=" N ARG A1391 " --> pdb=" O GLU A1387 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU A1392 " --> pdb=" O GLU A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1410 No H-bonds generated for 'chain 'A' and resid 1408 through 1410' Processing helix chain 'A' and resid 1413 through 1425 Processing helix chain 'B' and resid 40 through 51 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 132 through 135 No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 150 through 158 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 191 through 206 Processing helix chain 'B' and resid 211 through 214 No H-bonds generated for 'chain 'B' and resid 211 through 214' Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 227 through 305 removed outlier: 3.981A pdb=" N ALA B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP B 273 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 616 removed outlier: 3.726A pdb=" N GLY B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Proline residue: B 602 - end of helix Processing helix chain 'B' and resid 625 through 662 Processing helix chain 'B' and resid 788 through 827 removed outlier: 3.711A pdb=" N LEU B 826 " --> pdb=" O VAL B 822 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER B 827 " --> pdb=" O GLY B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 862 removed outlier: 3.699A pdb=" N GLU B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN B 858 " --> pdb=" O ARG B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1123 Processing helix chain 'B' and resid 1136 through 1140 removed outlier: 3.757A pdb=" N TYR B1140 " --> pdb=" O GLU B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1160 removed outlier: 3.701A pdb=" N LEU B1159 " --> pdb=" O GLY B1155 " (cutoff:3.500A) Processing helix chain 'B' and resid 1166 through 1175 removed outlier: 3.850A pdb=" N GLU B1175 " --> pdb=" O LEU B1171 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1194 Processing helix chain 'B' and resid 1201 through 1203 No H-bonds generated for 'chain 'B' and resid 1201 through 1203' Processing helix chain 'B' and resid 1208 through 1261 removed outlier: 3.657A pdb=" N ILE B1212 " --> pdb=" O PRO B1208 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLU B1213 " --> pdb=" O VAL B1209 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN B1214 " --> pdb=" O ASP B1210 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B1260 " --> pdb=" O ARG B1256 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY B1261 " --> pdb=" O MET B1257 " (cutoff:3.500A) Processing helix chain 'B' and resid 1281 through 1292 removed outlier: 4.059A pdb=" N LEU B1286 " --> pdb=" O SER B1282 " (cutoff:3.500A) Processing helix chain 'B' and resid 1295 through 1301 removed outlier: 3.582A pdb=" N GLN B1298 " --> pdb=" O GLU B1295 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP B1299 " --> pdb=" O GLN B1296 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B1301 " --> pdb=" O GLN B1298 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1318 Processing helix chain 'B' and resid 1330 through 1337 Processing helix chain 'B' and resid 1340 through 1343 Processing helix chain 'B' and resid 1362 through 1364 No H-bonds generated for 'chain 'B' and resid 1362 through 1364' Processing helix chain 'B' and resid 1367 through 1388 Processing helix chain 'B' and resid 1408 through 1410 No H-bonds generated for 'chain 'B' and resid 1408 through 1410' Processing helix chain 'B' and resid 1413 through 1426 Processing helix chain 'C' and resid 11 through 18 Processing helix chain 'C' and resid 122 through 145 Processing helix chain 'C' and resid 149 through 156 Processing helix chain 'C' and resid 159 through 196 removed outlier: 3.532A pdb=" N ASN C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 223 Processing helix chain 'C' and resid 226 through 242 removed outlier: 4.195A pdb=" N MET C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLY C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 287 removed outlier: 4.304A pdb=" N GLN C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER C 258 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 308 through 311 Processing helix chain 'C' and resid 354 through 372 removed outlier: 4.456A pdb=" N VAL C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR C 369 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 388 removed outlier: 3.891A pdb=" N ALA C 387 " --> pdb=" O ARG C 383 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN C 388 " --> pdb=" O ASP C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 406 removed outlier: 4.490A pdb=" N PHE C 395 " --> pdb=" O PRO C 392 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG C 399 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 Processing helix chain 'D' and resid 26 through 41 Processing helix chain 'D' and resid 49 through 63 removed outlier: 3.825A pdb=" N ASP D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 105 through 114 removed outlier: 4.223A pdb=" N TYR D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 8 No H-bonds generated for 'chain 'E' and resid 6 through 8' Processing helix chain 'E' and resid 12 through 18 Processing helix chain 'E' and resid 23 through 31 Processing helix chain 'E' and resid 41 through 49 Processing helix chain 'E' and resid 51 through 61 removed outlier: 3.726A pdb=" N ARG E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR E 61 " --> pdb=" O PHE E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 104 Processing helix chain 'E' and resid 109 through 111 No H-bonds generated for 'chain 'E' and resid 109 through 111' Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 130 through 137 removed outlier: 4.158A pdb=" N PHE E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 165 Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'E' and resid 197 through 207 removed outlier: 3.533A pdb=" N LEU E 202 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 19 Processing helix chain 'F' and resid 23 through 31 Processing helix chain 'F' and resid 41 through 59 removed outlier: 5.641A pdb=" N GLU F 52 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLN F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 102 Processing helix chain 'F' and resid 107 through 110 No H-bonds generated for 'chain 'F' and resid 107 through 110' Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'F' and resid 130 through 137 Processing helix chain 'F' and resid 145 through 165 Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'F' and resid 197 through 205 Processing helix chain 'G' and resid 3 through 15 removed outlier: 3.863A pdb=" N LYS G 8 " --> pdb=" O GLU G 5 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE G 11 " --> pdb=" O LYS G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 31 No H-bonds generated for 'chain 'G' and resid 28 through 31' Processing helix chain 'G' and resid 36 through 49 Processing helix chain 'G' and resid 56 through 61 removed outlier: 3.906A pdb=" N LYS G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 70 Processing helix chain 'H' and resid 3 through 15 removed outlier: 4.298A pdb=" N LYS H 8 " --> pdb=" O GLU H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 50 removed outlier: 3.615A pdb=" N PHE H 50 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'I' and resid 7 through 23 removed outlier: 3.905A pdb=" N GLY I 12 " --> pdb=" O ASN I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 47 Processing helix chain 'I' and resid 51 through 61 removed outlier: 3.930A pdb=" N GLU I 56 " --> pdb=" O VAL I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 85 removed outlier: 4.548A pdb=" N ASN I 68 " --> pdb=" O ASP I 65 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA I 84 " --> pdb=" O HIS I 81 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU I 85 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 111 Processing helix chain 'I' and resid 115 through 133 Processing helix chain 'J' and resid 7 through 23 removed outlier: 4.116A pdb=" N GLY J 12 " --> pdb=" O ASN J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 49 removed outlier: 3.728A pdb=" N GLU J 48 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N SER J 49 " --> pdb=" O ILE J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 61 removed outlier: 3.613A pdb=" N HIS J 61 " --> pdb=" O ILE J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 85 removed outlier: 3.829A pdb=" N PHE J 67 " --> pdb=" O PRO J 64 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN J 68 " --> pdb=" O ASP J 65 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE J 74 " --> pdb=" O LYS J 71 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA J 84 " --> pdb=" O HIS J 81 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU J 85 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 89 No H-bonds generated for 'chain 'J' and resid 87 through 89' Processing helix chain 'J' and resid 98 through 111 Processing helix chain 'J' and resid 115 through 134 Processing sheet with id= A, first strand: chain 'A' and resid 20 through 23 removed outlier: 6.672A pdb=" N ASP A 91 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A 10 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR A 89 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 12 " --> pdb=" O TYR A 87 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR A 87 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS A 115 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1456 through 1465 removed outlier: 6.196A pdb=" N LEU A1430 " --> pdb=" O THR A 30 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU A 32 " --> pdb=" O LEU A1430 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A1432 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1273 through 1279 Processing sheet with id= D, first strand: chain 'B' and resid 20 through 24 removed outlier: 6.916A pdb=" N ASP B 91 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU B 10 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR B 89 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU B 12 " --> pdb=" O TYR B 87 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR B 87 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 1456 through 1463 removed outlier: 6.385A pdb=" N LEU B1430 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU B 32 " --> pdb=" O LEU B1430 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE B1432 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1273 through 1279 Processing sheet with id= G, first strand: chain 'D' and resid 87 through 90 Processing sheet with id= H, first strand: chain 'E' and resid 63 through 67 Processing sheet with id= I, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= J, first strand: chain 'F' and resid 63 through 67 Processing sheet with id= K, first strand: chain 'F' and resid 168 through 170 1278 hydrogen bonds defined for protein. 3513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 228 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 20.01 Time building geometry restraints manager: 42.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 23757 1.03 - 1.23: 109 1.23 - 1.42: 10647 1.42 - 1.62: 14485 1.62 - 1.81: 161 Bond restraints: 49159 Sorted by residual: bond pdb=" NE2 GLN A1407 " pdb="HE22 GLN A1407 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" NE2 GLN A1407 " pdb="HE21 GLN A1407 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" NE2 GLN B1407 " pdb="HE22 GLN B1407 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" NE2 GLN B1407 " pdb="HE21 GLN B1407 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" C34 PNS G 101 " pdb=" N36 PNS G 101 " ideal model delta sigma weight residual 1.452 1.326 0.126 2.00e-02 2.50e+03 3.99e+01 ... (remaining 49154 not shown) Histogram of bond angle deviations from ideal: 45.05 - 63.96: 2 63.96 - 82.86: 3 82.86 - 101.77: 81 101.77 - 120.67: 76982 120.67 - 139.58: 11668 Bond angle restraints: 88736 Sorted by residual: angle pdb=" C MET B 581 " pdb=" N GLU B 582 " pdb=" H GLU B 582 " ideal model delta sigma weight residual 125.01 45.05 79.96 3.00e+00 1.11e-01 7.10e+02 angle pdb=" C GLN B 617 " pdb=" N SER B 618 " pdb=" H SER B 618 " ideal model delta sigma weight residual 123.64 54.44 69.19 3.00e+00 1.11e-01 5.32e+02 angle pdb=" C SER F 144 " pdb=" CA SER F 144 " pdb=" HA SER F 144 " ideal model delta sigma weight residual 109.00 73.68 35.32 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N SER F 144 " pdb=" CA SER F 144 " pdb=" HA SER F 144 " ideal model delta sigma weight residual 110.00 75.86 34.14 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CB SER F 144 " pdb=" CA SER F 144 " pdb=" HA SER F 144 " ideal model delta sigma weight residual 109.00 75.47 33.53 3.00e+00 1.11e-01 1.25e+02 ... (remaining 88731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 19437 17.77 - 35.53: 2048 35.53 - 53.30: 754 53.30 - 71.07: 245 71.07 - 88.83: 38 Dihedral angle restraints: 22522 sinusoidal: 13244 harmonic: 9278 Sorted by residual: dihedral pdb=" CA THR A 63 " pdb=" C THR A 63 " pdb=" N THR A 64 " pdb=" CA THR A 64 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASP J 65 " pdb=" C ASP J 65 " pdb=" N LEU J 66 " pdb=" CA LEU J 66 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" C SER F 144 " pdb=" N SER F 144 " pdb=" CA SER F 144 " pdb=" CB SER F 144 " ideal model delta harmonic sigma weight residual -122.60 -131.71 9.11 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 22519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3587 0.073 - 0.146: 258 0.146 - 0.219: 4 0.219 - 0.293: 2 0.293 - 0.366: 3 Chirality restraints: 3854 Sorted by residual: chirality pdb=" CA SER F 144 " pdb=" N SER F 144 " pdb=" C SER F 144 " pdb=" CB SER F 144 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C2' ATP A1502 " pdb=" C1' ATP A1502 " pdb=" C3' ATP A1502 " pdb=" O2' ATP A1502 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C2' ATP B1502 " pdb=" C1' ATP B1502 " pdb=" C3' ATP B1502 " pdb=" O2' ATP B1502 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 3851 not shown) Planarity restraints: 6941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 581 " 0.077 2.00e-02 2.50e+03 2.48e-01 6.16e+02 pdb=" N GLU B 582 " 0.345 2.00e-02 2.50e+03 pdb=" CA GLU B 582 " -0.082 2.00e-02 2.50e+03 pdb=" H GLU B 582 " -0.339 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 617 " -0.076 2.00e-02 2.50e+03 2.46e-01 6.04e+02 pdb=" N SER B 618 " 0.419 2.00e-02 2.50e+03 pdb=" CA SER B 618 " -0.143 2.00e-02 2.50e+03 pdb=" H SER B 618 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PNS H 101 " -0.054 2.00e-02 2.50e+03 5.75e-02 4.13e+01 pdb=" C39 PNS H 101 " 0.025 2.00e-02 2.50e+03 pdb=" C42 PNS H 101 " -0.070 2.00e-02 2.50e+03 pdb=" N41 PNS H 101 " 0.089 2.00e-02 2.50e+03 pdb=" O40 PNS H 101 " 0.009 2.00e-02 2.50e+03 ... (remaining 6938 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1779 2.16 - 2.77: 92764 2.77 - 3.38: 136550 3.38 - 3.99: 173251 3.99 - 4.60: 272137 Nonbonded interactions: 676481 Sorted by model distance: nonbonded pdb=" OE1 GLU E 52 " pdb=" H GLU E 52 " model vdw 1.549 1.850 nonbonded pdb=" O MET D 47 " pdb=" H TYR D 101 " model vdw 1.573 1.850 nonbonded pdb=" OE1 GLU A1142 " pdb=" H GLU A1142 " model vdw 1.576 1.850 nonbonded pdb=" H SER F 144 " pdb=" HA SER F 144 " model vdw 1.577 1.816 nonbonded pdb=" HG SER B 41 " pdb="MG MG B1501 " model vdw 1.577 1.700 ... (remaining 676476 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 'E' and resid 9 through 206) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 62 through 134)) selection = (chain 'J' and resid 1 through 134) } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 0.660 Extract box with map and model: 9.270 Check model and map are aligned: 0.720 Set scattering table: 0.420 Process input model: 169.190 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.003 0.126 25379 Z= 0.208 Angle : 0.502 6.735 34652 Z= 0.285 Chirality : 0.038 0.366 3854 Planarity : 0.003 0.059 4167 Dihedral : 18.241 88.834 10082 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.17), residues: 2765 helix: 1.89 (0.13), residues: 1665 sheet: 0.12 (0.35), residues: 220 loop : -0.65 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 101 HIS 0.004 0.001 HIS J 22 PHE 0.011 0.001 PHE B 197 TYR 0.017 0.001 TYR A 174 ARG 0.006 0.000 ARG F 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 583 MET cc_start: 0.7608 (ppp) cc_final: 0.7112 (ppp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 1.0708 time to fit residues: 307.1436 Evaluate side-chains 154 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.0980 chunk 216 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 73 optimal weight: 0.0010 chunk 145 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 258 optimal weight: 0.5980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1294 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1134 HIS J 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25379 Z= 0.163 Angle : 0.481 5.873 34652 Z= 0.274 Chirality : 0.036 0.364 3854 Planarity : 0.003 0.059 4167 Dihedral : 17.104 79.692 4375 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.54 % Allowed : 3.71 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.17), residues: 2765 helix: 2.07 (0.13), residues: 1664 sheet: 0.31 (0.35), residues: 220 loop : -0.47 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 274 HIS 0.004 0.001 HIS J 22 PHE 0.012 0.001 PHE C 351 TYR 0.015 0.001 TYR A 174 ARG 0.003 0.000 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 3.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 581 MET cc_start: 0.5305 (tmm) cc_final: 0.4643 (tmm) REVERT: B 632 MET cc_start: 0.5196 (tmm) cc_final: 0.4646 (tmm) outliers start: 13 outliers final: 8 residues processed: 159 average time/residue: 0.9720 time to fit residues: 231.7772 Evaluate side-chains 156 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 3.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1305 ARG Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain J residue 65 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1297 HIS D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25379 Z= 0.358 Angle : 0.521 5.877 34652 Z= 0.298 Chirality : 0.039 0.364 3854 Planarity : 0.004 0.056 4167 Dihedral : 17.130 84.228 4375 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.62 % Allowed : 5.81 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.16), residues: 2765 helix: 1.88 (0.13), residues: 1675 sheet: 0.13 (0.35), residues: 222 loop : -0.61 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 266 HIS 0.003 0.001 HIS C 280 PHE 0.011 0.001 PHE E 23 TYR 0.019 0.001 TYR A 174 ARG 0.003 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 4.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 581 MET cc_start: 0.5373 (tmm) cc_final: 0.4646 (tmm) REVERT: B 632 MET cc_start: 0.5224 (tmm) cc_final: 0.4757 (tmm) outliers start: 15 outliers final: 13 residues processed: 154 average time/residue: 0.9621 time to fit residues: 224.9177 Evaluate side-chains 155 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 4.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 1467 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 65 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 246 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1294 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN I 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25379 Z= 0.302 Angle : 0.497 4.639 34652 Z= 0.285 Chirality : 0.038 0.364 3854 Planarity : 0.003 0.057 4167 Dihedral : 17.078 82.697 4375 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.74 % Allowed : 6.92 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.16), residues: 2765 helix: 1.91 (0.13), residues: 1675 sheet: 0.11 (0.35), residues: 224 loop : -0.58 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 266 HIS 0.004 0.001 HIS A 261 PHE 0.011 0.001 PHE E 23 TYR 0.018 0.001 TYR A 174 ARG 0.006 0.000 ARG G 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 581 MET cc_start: 0.5330 (tmm) cc_final: 0.4788 (tmm) REVERT: B 632 MET cc_start: 0.5524 (tmm) cc_final: 0.4922 (tmm) REVERT: I 1 MET cc_start: 0.7121 (tpp) cc_final: 0.6823 (tpp) outliers start: 18 outliers final: 14 residues processed: 155 average time/residue: 0.9350 time to fit residues: 221.3858 Evaluate side-chains 157 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 1467 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 65 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25379 Z= 0.248 Angle : 0.480 5.002 34652 Z= 0.275 Chirality : 0.037 0.362 3854 Planarity : 0.003 0.057 4167 Dihedral : 17.004 81.110 4375 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.78 % Allowed : 7.74 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.16), residues: 2765 helix: 2.02 (0.13), residues: 1678 sheet: 0.20 (0.35), residues: 224 loop : -0.44 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 266 HIS 0.003 0.001 HIS A 261 PHE 0.011 0.001 PHE E 23 TYR 0.016 0.001 TYR A 174 ARG 0.002 0.000 ARG B1450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 3.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 581 MET cc_start: 0.5218 (tmm) cc_final: 0.4729 (tmm) REVERT: B 632 MET cc_start: 0.5738 (tmm) cc_final: 0.5126 (tmm) REVERT: I 1 MET cc_start: 0.7120 (tpp) cc_final: 0.6878 (tpp) outliers start: 19 outliers final: 15 residues processed: 157 average time/residue: 0.9308 time to fit residues: 221.0066 Evaluate side-chains 160 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 1467 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 97 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 22 optimal weight: 0.0980 chunk 91 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25379 Z= 0.247 Angle : 0.479 7.840 34652 Z= 0.274 Chirality : 0.037 0.363 3854 Planarity : 0.003 0.058 4167 Dihedral : 16.957 82.150 4375 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.70 % Allowed : 8.36 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.16), residues: 2765 helix: 2.09 (0.13), residues: 1678 sheet: 0.22 (0.35), residues: 224 loop : -0.45 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 266 HIS 0.003 0.001 HIS A 261 PHE 0.011 0.001 PHE E 23 TYR 0.017 0.001 TYR A 174 ARG 0.003 0.000 ARG B1450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 4.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 581 MET cc_start: 0.5244 (tmm) cc_final: 0.4876 (tmm) REVERT: B 632 MET cc_start: 0.5907 (tmm) cc_final: 0.5243 (tmm) REVERT: I 1 MET cc_start: 0.7034 (tpp) cc_final: 0.6822 (tpp) outliers start: 17 outliers final: 14 residues processed: 158 average time/residue: 0.9963 time to fit residues: 236.9763 Evaluate side-chains 155 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 1467 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 65 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1294 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 25379 Z= 0.556 Angle : 0.607 6.270 34652 Z= 0.344 Chirality : 0.044 0.366 3854 Planarity : 0.004 0.055 4167 Dihedral : 17.259 85.886 4375 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.68 % Rotamer: Outliers : 1.07 % Allowed : 9.06 % Favored : 89.87 % 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: 0.93 (0.16), residues: 2765 helix: 1.47 (0.13), residues: 1685 sheet: -0.28 (0.35), residues: 225 loop : -0.78 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 266 HIS 0.006 0.001 HIS B1456 PHE 0.016 0.002 PHE A 168 TYR 0.024 0.002 TYR A 174 ARG 0.007 0.001 ARG B1450 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 3.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 581 MET cc_start: 0.5376 (tmm) cc_final: 0.4903 (tmm) REVERT: B 632 MET cc_start: 0.5984 (tmm) cc_final: 0.5176 (tmm) outliers start: 26 outliers final: 23 residues processed: 154 average time/residue: 0.9626 time to fit residues: 223.6574 Evaluate side-chains 159 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 1416 ILE Chi-restraints excluded: chain B residue 1467 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain J residue 8 ASN Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 97 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 249 optimal weight: 0.0000 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1294 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25379 Z= 0.175 Angle : 0.483 8.366 34652 Z= 0.274 Chirality : 0.036 0.363 3854 Planarity : 0.003 0.059 4167 Dihedral : 17.074 77.510 4375 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.86 % Allowed : 9.51 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.17), residues: 2765 helix: 2.00 (0.13), residues: 1682 sheet: 0.09 (0.35), residues: 224 loop : -0.48 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 266 HIS 0.004 0.001 HIS J 22 PHE 0.010 0.001 PHE E 23 TYR 0.017 0.001 TYR A 174 ARG 0.003 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 3.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 632 MET cc_start: 0.5969 (tmm) cc_final: 0.5257 (tmm) outliers start: 21 outliers final: 19 residues processed: 151 average time/residue: 0.9922 time to fit residues: 226.6799 Evaluate side-chains 153 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 4.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 1179 ARG Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 1416 ILE Chi-restraints excluded: chain B residue 1467 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 176 ASN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 97 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 255 optimal weight: 0.5980 chunk 154 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 242 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25379 Z= 0.218 Angle : 0.478 7.498 34652 Z= 0.272 Chirality : 0.036 0.363 3854 Planarity : 0.003 0.058 4167 Dihedral : 16.939 79.901 4375 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.82 % Allowed : 9.47 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.17), residues: 2765 helix: 2.17 (0.13), residues: 1679 sheet: 0.23 (0.35), residues: 224 loop : -0.44 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 266 HIS 0.003 0.001 HIS A 261 PHE 0.012 0.001 PHE E 23 TYR 0.016 0.001 TYR A 174 ARG 0.004 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 632 MET cc_start: 0.5950 (tmm) cc_final: 0.5306 (tmm) outliers start: 20 outliers final: 18 residues processed: 147 average time/residue: 0.8918 time to fit residues: 201.0470 Evaluate side-chains 151 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 1416 ILE Chi-restraints excluded: chain B residue 1467 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 97 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 6.9990 chunk 128 optimal weight: 0.4980 chunk 188 optimal weight: 9.9990 chunk 283 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 240 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1294 GLN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25379 Z= 0.334 Angle : 0.520 11.357 34652 Z= 0.293 Chirality : 0.038 0.365 3854 Planarity : 0.003 0.057 4167 Dihedral : 17.040 83.893 4375 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.91 % Allowed : 9.68 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.16), residues: 2765 helix: 1.98 (0.13), residues: 1681 sheet: 0.03 (0.35), residues: 224 loop : -0.54 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 266 HIS 0.003 0.001 HIS A 261 PHE 0.011 0.001 PHE A 168 TYR 0.018 0.001 TYR A 174 ARG 0.004 0.000 ARG B1450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5530 Ramachandran restraints generated. 2765 Oldfield, 0 Emsley, 2765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 36 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 4.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1240 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8731 (t) REVERT: B 632 MET cc_start: 0.5875 (tmm) cc_final: 0.5143 (tmm) outliers start: 22 outliers final: 20 residues processed: 147 average time/residue: 0.9412 time to fit residues: 211.4150 Evaluate side-chains 153 residues out of total 2428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 3.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 1179 ARG Chi-restraints excluded: chain A residue 1240 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 1416 ILE Chi-restraints excluded: chain B residue 1467 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 137 HIS Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 97 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 0.3980 chunk 208 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.076474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.050519 restraints weight = 238281.549| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.18 r_work: 0.2839 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25379 Z= 0.253 Angle : 0.492 11.300 34652 Z= 0.278 Chirality : 0.037 0.363 3854 Planarity : 0.003 0.058 4167 Dihedral : 17.000 81.763 4375 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.78 % Allowed : 9.93 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.17), residues: 2765 helix: 2.12 (0.13), residues: 1680 sheet: 0.11 (0.35), residues: 224 loop : -0.47 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 266 HIS 0.003 0.001 HIS A 261 PHE 0.012 0.001 PHE E 23 TYR 0.017 0.001 TYR A 174 ARG 0.003 0.000 ARG E 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8924.19 seconds wall clock time: 158 minutes 47.61 seconds (9527.61 seconds total)