Starting phenix.real_space_refine on Tue Sep 24 17:57:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scg_25034/09_2024/7scg_25034.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scg_25034/09_2024/7scg_25034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scg_25034/09_2024/7scg_25034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scg_25034/09_2024/7scg_25034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scg_25034/09_2024/7scg_25034.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scg_25034/09_2024/7scg_25034.cif" } resolution = 3.0 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= 1.000 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5460 2.51 5 N 1454 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8539 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2158 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 272} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1675 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {'8RI': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 5.37, per 1000 atoms: 0.63 Number of scatterers: 8539 At special positions: 0 Unit cell: (103.244, 122.332, 111.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1561 8.00 N 1454 7.00 C 5460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 37.2% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'B' and resid 9 through 24 Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 67 through 97 removed outlier: 4.002A pdb=" N VAL D 94 " --> pdb=" O MET D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 131 removed outlier: 3.691A pdb=" N GLN D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 171 removed outlier: 3.845A pdb=" N CYS D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE D 142 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 153 " --> pdb=" O TYR D 149 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.734A pdb=" N PHE D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 205 removed outlier: 3.621A pdb=" N TRP D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 224 through 241 Processing helix chain 'D' and resid 241 through 259 removed outlier: 3.653A pdb=" N VAL D 245 " --> pdb=" O PHE D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 261 No H-bonds generated for 'chain 'D' and resid 260 through 261' Processing helix chain 'D' and resid 262 through 266 removed outlier: 3.855A pdb=" N SER D 266 " --> pdb=" O ARG D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 304 Proline residue: D 295 - end of helix Processing helix chain 'D' and resid 311 through 337 removed outlier: 3.517A pdb=" N THR D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA D 323 " --> pdb=" O HIS D 319 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) Proline residue: D 333 - end of helix Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.937A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.773A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.492A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.533A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.958A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.196A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.733A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.755A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.635A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.659A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.097A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.692A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.850A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.548A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.763A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 206 through 210 removed outlier: 3.724A pdb=" N THR D 218 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS D 209 " --> pdb=" O ASP D 216 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP D 216 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.913A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.502A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.502A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.379A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 142 through 147 removed outlier: 3.618A pdb=" N PHE E 200 " --> pdb=" O CYS E 147 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1128 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: 2.48 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1351 1.31 - 1.44: 2431 1.44 - 1.56: 4842 1.56 - 1.69: 1 1.69 - 1.81: 91 Bond restraints: 8716 Sorted by residual: bond pdb=" C01 8RI D 401 " pdb=" N01 8RI D 401 " ideal model delta sigma weight residual 1.341 1.469 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C03 8RI D 401 " pdb=" C04 8RI D 401 " ideal model delta sigma weight residual 1.464 1.568 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C01 8RI D 401 " pdb=" C02 8RI D 401 " ideal model delta sigma weight residual 1.485 1.547 -0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" C22 8RI D 401 " pdb=" O02 8RI D 401 " ideal model delta sigma weight residual 1.350 1.400 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" N SER B 74 " pdb=" CA SER B 74 " ideal model delta sigma weight residual 1.455 1.485 -0.031 1.32e-02 5.74e+03 5.42e+00 ... (remaining 8711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 11562 1.63 - 3.25: 224 3.25 - 4.88: 43 4.88 - 6.50: 9 6.50 - 8.13: 4 Bond angle restraints: 11842 Sorted by residual: angle pdb=" C ASN D 150 " pdb=" CA ASN D 150 " pdb=" CB ASN D 150 " ideal model delta sigma weight residual 110.37 117.34 -6.97 1.78e+00 3.16e-01 1.53e+01 angle pdb=" N THR B 164 " pdb=" CA THR B 164 " pdb=" CB THR B 164 " ideal model delta sigma weight residual 114.17 109.91 4.26 1.14e+00 7.69e-01 1.39e+01 angle pdb=" N ASN D 150 " pdb=" CA ASN D 150 " pdb=" C ASN D 150 " ideal model delta sigma weight residual 113.02 109.14 3.88 1.20e+00 6.94e-01 1.05e+01 angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.20 109.72 3.48 1.21e+00 6.83e-01 8.27e+00 angle pdb=" C THR B 29 " pdb=" N LEU B 30 " pdb=" CA LEU B 30 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.12e+00 ... (remaining 11837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 4684 17.70 - 35.40: 394 35.40 - 53.11: 52 53.11 - 70.81: 5 70.81 - 88.51: 4 Dihedral angle restraints: 5139 sinusoidal: 1883 harmonic: 3256 Sorted by residual: dihedral pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual 93.00 -179.48 -87.52 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CA LEU B 95 " pdb=" C LEU B 95 " pdb=" N ARG B 96 " pdb=" CA ARG B 96 " ideal model delta harmonic sigma weight residual 180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1078 0.049 - 0.098: 239 0.098 - 0.147: 59 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 1379 Sorted by residual: chirality pdb=" CA ASN D 150 " pdb=" N ASN D 150 " pdb=" C ASN D 150 " pdb=" CB ASN D 150 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA MET D 151 " pdb=" N MET D 151 " pdb=" C MET D 151 " pdb=" CB MET D 151 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 1376 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D 149 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C TYR D 149 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR D 149 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN D 150 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 164 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C THR B 164 " -0.030 2.00e-02 2.50e+03 pdb=" O THR B 164 " 0.011 2.00e-02 2.50e+03 pdb=" N THR B 165 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 200 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO D 201 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 201 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 201 " 0.022 5.00e-02 4.00e+02 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2214 2.80 - 3.32: 7517 3.32 - 3.85: 12922 3.85 - 4.37: 15157 4.37 - 4.90: 28551 Nonbonded interactions: 66361 Sorted by model distance: nonbonded pdb=" O SER E 52 " pdb=" NH1 ARG E 72 " model vdw 2.274 3.120 nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.280 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.286 3.040 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.295 3.040 nonbonded pdb=" OG1 THR D 101 " pdb=" OD1 ASN D 104 " model vdw 2.304 3.040 ... (remaining 66356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.270 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.710 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 8716 Z= 0.322 Angle : 0.610 8.129 11842 Z= 0.340 Chirality : 0.043 0.245 1379 Planarity : 0.004 0.038 1486 Dihedral : 12.870 88.509 3028 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1105 helix: 1.82 (0.28), residues: 371 sheet: -0.93 (0.31), residues: 294 loop : -1.41 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE B 151 TYR 0.011 0.002 TYR E 50 ARG 0.005 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.926 Fit side-chains REVERT: B 247 ASP cc_start: 0.7577 (t0) cc_final: 0.7377 (t0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 1.3259 time to fit residues: 163.2247 Evaluate side-chains 100 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.0050 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 40.0000 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8716 Z= 0.204 Angle : 0.582 8.122 11842 Z= 0.301 Chirality : 0.043 0.148 1379 Planarity : 0.004 0.034 1486 Dihedral : 4.829 35.782 1222 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.24 % Allowed : 8.22 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1105 helix: 2.09 (0.28), residues: 371 sheet: -0.51 (0.30), residues: 296 loop : -1.29 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 188 PHE 0.012 0.001 PHE A 189 TYR 0.019 0.001 TYR E 178 ARG 0.003 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 0.966 Fit side-chains REVERT: B 23 LYS cc_start: 0.8372 (tppt) cc_final: 0.8022 (tmmt) outliers start: 11 outliers final: 3 residues processed: 115 average time/residue: 1.3028 time to fit residues: 158.9690 Evaluate side-chains 107 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 17 GLN B 75 GLN D 86 ASN D 109 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8716 Z= 0.186 Angle : 0.539 7.047 11842 Z= 0.281 Chirality : 0.042 0.149 1379 Planarity : 0.003 0.034 1486 Dihedral : 4.573 34.181 1222 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.14 % Allowed : 10.47 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.37 (0.26), residues: 1105 helix: 2.30 (0.28), residues: 371 sheet: -0.26 (0.31), residues: 290 loop : -1.19 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.016 0.001 TYR E 178 ARG 0.004 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 0.869 Fit side-chains REVERT: B 44 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8239 (mt0) outliers start: 19 outliers final: 7 residues processed: 119 average time/residue: 1.2795 time to fit residues: 161.9855 Evaluate side-chains 116 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8716 Z= 0.202 Angle : 0.542 7.062 11842 Z= 0.282 Chirality : 0.042 0.150 1379 Planarity : 0.003 0.034 1486 Dihedral : 4.522 33.870 1222 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.14 % Allowed : 12.95 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1105 helix: 2.39 (0.28), residues: 372 sheet: -0.14 (0.31), residues: 290 loop : -1.11 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 189 TYR 0.015 0.001 TYR E 178 ARG 0.005 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.120 Fit side-chains REVERT: B 44 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8206 (mt0) outliers start: 19 outliers final: 10 residues processed: 119 average time/residue: 1.2889 time to fit residues: 163.1554 Evaluate side-chains 119 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0870 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 0.0170 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8716 Z= 0.209 Angle : 0.547 7.144 11842 Z= 0.283 Chirality : 0.042 0.150 1379 Planarity : 0.003 0.034 1486 Dihedral : 4.489 33.615 1222 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.14 % Allowed : 13.74 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.65 (0.26), residues: 1105 helix: 2.59 (0.27), residues: 366 sheet: -0.00 (0.31), residues: 278 loop : -1.09 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.014 0.001 TYR E 178 ARG 0.005 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.995 Fit side-chains REVERT: B 44 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8191 (mt0) outliers start: 19 outliers final: 12 residues processed: 124 average time/residue: 1.2289 time to fit residues: 162.4302 Evaluate side-chains 121 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 0.0870 chunk 106 optimal weight: 0.0670 chunk 88 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 HIS A 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8716 Z= 0.159 Angle : 0.510 6.330 11842 Z= 0.267 Chirality : 0.041 0.152 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.297 31.654 1222 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.36 % Allowed : 13.63 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1105 helix: 2.67 (0.28), residues: 369 sheet: 0.11 (0.31), residues: 278 loop : -1.07 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE A 189 TYR 0.014 0.001 TYR E 178 ARG 0.004 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.987 Fit side-chains REVERT: B 44 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8125 (mt0) REVERT: B 262 MET cc_start: 0.8712 (tpp) cc_final: 0.8498 (ttm) REVERT: B 327 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8515 (t) REVERT: E 51 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8139 (tp) outliers start: 21 outliers final: 12 residues processed: 131 average time/residue: 1.3823 time to fit residues: 193.8050 Evaluate side-chains 130 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8716 Z= 0.170 Angle : 0.517 7.313 11842 Z= 0.270 Chirality : 0.041 0.151 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.246 30.402 1222 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.36 % Allowed : 14.19 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1105 helix: 2.75 (0.27), residues: 369 sheet: 0.09 (0.31), residues: 288 loop : -0.95 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE B 241 TYR 0.014 0.001 TYR E 178 ARG 0.004 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.894 Fit side-chains REVERT: B 44 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8106 (mt0) REVERT: B 247 ASP cc_start: 0.7179 (t0) cc_final: 0.6976 (t0) REVERT: B 262 MET cc_start: 0.8692 (tpp) cc_final: 0.8480 (ttm) REVERT: B 327 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8516 (t) REVERT: E 51 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8160 (tp) outliers start: 21 outliers final: 13 residues processed: 130 average time/residue: 1.1867 time to fit residues: 164.7391 Evaluate side-chains 128 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 50.0000 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8716 Z= 0.209 Angle : 0.541 7.600 11842 Z= 0.281 Chirality : 0.042 0.152 1379 Planarity : 0.003 0.034 1486 Dihedral : 4.357 30.568 1222 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.82 % Allowed : 14.53 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1105 helix: 2.73 (0.27), residues: 369 sheet: 0.06 (0.31), residues: 290 loop : -0.95 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.001 PHE A 189 TYR 0.013 0.001 TYR E 178 ARG 0.004 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 0.924 Fit side-chains REVERT: B 44 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: B 247 ASP cc_start: 0.7227 (t0) cc_final: 0.6992 (t0) REVERT: B 327 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8533 (t) REVERT: A 33 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: E 51 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8186 (tp) outliers start: 25 outliers final: 15 residues processed: 129 average time/residue: 1.1433 time to fit residues: 157.5653 Evaluate side-chains 131 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8716 Z= 0.177 Angle : 0.522 7.159 11842 Z= 0.272 Chirality : 0.041 0.152 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.258 29.573 1222 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.59 % Allowed : 15.09 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1105 helix: 2.79 (0.27), residues: 369 sheet: 0.10 (0.31), residues: 285 loop : -0.98 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.014 0.001 TYR E 178 ARG 0.004 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 0.967 Fit side-chains REVERT: B 44 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8120 (mt0) REVERT: B 327 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8520 (t) REVERT: A 33 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: E 51 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8159 (tp) outliers start: 23 outliers final: 15 residues processed: 131 average time/residue: 1.1851 time to fit residues: 165.9522 Evaluate side-chains 134 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8716 Z= 0.169 Angle : 0.519 7.042 11842 Z= 0.270 Chirality : 0.041 0.152 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.195 28.437 1222 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.48 % Allowed : 15.43 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.95 (0.26), residues: 1105 helix: 2.81 (0.27), residues: 369 sheet: 0.09 (0.30), residues: 307 loop : -0.92 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.014 0.001 TYR E 178 ARG 0.004 0.000 ARG E 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 0.916 Fit side-chains REVERT: B 44 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: A 33 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: E 51 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8153 (tp) outliers start: 22 outliers final: 15 residues processed: 132 average time/residue: 1.1675 time to fit residues: 164.6279 Evaluate side-chains 130 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097212 restraints weight = 10540.915| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.24 r_work: 0.3183 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8716 Z= 0.161 Angle : 0.514 6.902 11842 Z= 0.269 Chirality : 0.041 0.152 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.132 27.268 1222 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.48 % Allowed : 15.32 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.98 (0.26), residues: 1105 helix: 2.82 (0.27), residues: 369 sheet: 0.15 (0.30), residues: 300 loop : -0.91 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.014 0.001 TYR E 178 ARG 0.003 0.000 ARG E 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3292.27 seconds wall clock time: 58 minutes 27.00 seconds (3507.00 seconds total)