Starting phenix.real_space_refine on Sat Jul 26 12:41:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7scg_25034/07_2025/7scg_25034.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scg_25034/07_2025/7scg_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/cci-nas-00/data/ceres_data/7scg_25034/07_2025/7scg_25034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scg_25034/07_2025/7scg_25034.map" model { file = "/net/cci-nas-00/data/ceres_data/7scg_25034/07_2025/7scg_25034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scg_25034/07_2025/7scg_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.26, per 1000 atoms: 0.62 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: 2.20 Conformation dependent library (CDL) restraints added in 1.0 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: 1.01 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: 2.69 Time building geometry restraints manager: 2.54 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.390 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.610 ------------------------------------------------------------------------------- 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 8719 Z= 0.224 Angle : 0.610 8.129 11848 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 Details of bonding type rmsd hydrogen bonds : bond 0.17825 ( 398) hydrogen bonds : angle 6.36831 ( 1128) SS BOND : bond 0.00625 ( 3) SS BOND : angle 0.67504 ( 6) covalent geometry : bond 0.00491 ( 8716) covalent geometry : angle 0.60956 (11842) *********************** 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 to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.049 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: 1.3217 time to fit residues: 162.8203 Evaluate side-chains 100 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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: 6.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.097421 restraints weight = 10931.746| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.30 r_work: 0.3125 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 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 8719 Z= 0.133 Angle : 0.582 8.122 11848 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 Details of bonding type rmsd hydrogen bonds : bond 0.04781 ( 398) hydrogen bonds : angle 4.45918 ( 1128) SS BOND : bond 0.00603 ( 3) SS BOND : angle 0.63517 ( 6) covalent geometry : bond 0.00309 ( 8716) covalent geometry : angle 0.58178 (11842) *********************** 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 to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.923 Fit side-chains REVERT: B 23 LYS cc_start: 0.8258 (tppt) cc_final: 0.7700 (tmmt) REVERT: B 247 ASP cc_start: 0.7972 (t0) cc_final: 0.7728 (t0) REVERT: D 243 MET cc_start: 0.7812 (ttp) cc_final: 0.7588 (ttt) REVERT: A 205 ARG cc_start: 0.7909 (pmt170) cc_final: 0.7496 (mmm160) outliers start: 11 outliers final: 3 residues processed: 115 average time/residue: 1.3444 time to fit residues: 163.9743 Evaluate side-chains 108 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 89 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 97 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.142272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095890 restraints weight = 11184.938| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.34 r_work: 0.3103 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8719 Z= 0.148 Angle : 0.574 7.633 11848 Z= 0.297 Chirality : 0.043 0.150 1379 Planarity : 0.004 0.035 1486 Dihedral : 4.748 35.629 1222 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % 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: 0.30 (0.26), residues: 1105 helix: 2.23 (0.28), residues: 371 sheet: -0.28 (0.31), residues: 290 loop : -1.23 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.001 PHE A 189 TYR 0.016 0.001 TYR E 178 ARG 0.005 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.04848 ( 398) hydrogen bonds : angle 4.27857 ( 1128) SS BOND : bond 0.00612 ( 3) SS BOND : angle 0.64557 ( 6) covalent geometry : bond 0.00355 ( 8716) covalent geometry : angle 0.57346 (11842) *********************** 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 127 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.064 Fit side-chains REVERT: B 247 ASP cc_start: 0.7922 (t0) cc_final: 0.7654 (t0) REVERT: D 243 MET cc_start: 0.7824 (ttp) cc_final: 0.7615 (ttt) REVERT: A 205 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7632 (mmm160) outliers start: 19 outliers final: 7 residues processed: 116 average time/residue: 1.3377 time to fit residues: 164.6688 Evaluate side-chains 114 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Chi-restraints excluded: chain A residue 205 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.093849 restraints weight = 10655.349| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.28 r_work: 0.3139 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8719 Z= 0.155 Angle : 0.575 7.834 11848 Z= 0.298 Chirality : 0.043 0.150 1379 Planarity : 0.004 0.035 1486 Dihedral : 4.707 35.336 1222 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.25 % Allowed : 12.84 % 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: 0.42 (0.26), residues: 1105 helix: 2.33 (0.28), residues: 371 sheet: -0.18 (0.31), residues: 290 loop : -1.18 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 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 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 398) hydrogen bonds : angle 4.20012 ( 1128) SS BOND : bond 0.00568 ( 3) SS BOND : angle 0.67228 ( 6) covalent geometry : bond 0.00374 ( 8716) covalent geometry : angle 0.57537 (11842) *********************** 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 to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.000 Fit side-chains REVERT: B 247 ASP cc_start: 0.7879 (t0) cc_final: 0.7594 (t0) REVERT: D 243 MET cc_start: 0.7806 (ttp) cc_final: 0.7588 (ttt) REVERT: A 205 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7651 (mmm160) outliers start: 20 outliers final: 9 residues processed: 117 average time/residue: 1.3661 time to fit residues: 169.4188 Evaluate side-chains 115 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain A residue 205 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 50.0000 chunk 101 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.138414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093954 restraints weight = 10742.108| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.29 r_work: 0.3140 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8719 Z= 0.145 Angle : 0.564 7.549 11848 Z= 0.292 Chirality : 0.042 0.149 1379 Planarity : 0.003 0.035 1486 Dihedral : 4.627 34.610 1222 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.82 % Allowed : 13.18 % 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: 0.53 (0.26), residues: 1105 helix: 2.37 (0.27), residues: 372 sheet: -0.10 (0.30), residues: 290 loop : -1.10 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.001 PHE A 189 TYR 0.015 0.001 TYR E 178 ARG 0.006 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 398) hydrogen bonds : angle 4.12293 ( 1128) SS BOND : bond 0.00527 ( 3) SS BOND : angle 0.71549 ( 6) covalent geometry : bond 0.00349 ( 8716) covalent geometry : angle 0.56440 (11842) *********************** 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 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.915 Fit side-chains REVERT: B 247 ASP cc_start: 0.7894 (t0) cc_final: 0.7599 (t0) REVERT: B 327 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8631 (t) outliers start: 25 outliers final: 14 residues processed: 124 average time/residue: 1.2303 time to fit residues: 162.2943 Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 208 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 266 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 0.0000 chunk 81 optimal weight: 8.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.146392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.100677 restraints weight = 11000.858| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.30 r_work: 0.3181 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8719 Z= 0.101 Angle : 0.508 6.646 11848 Z= 0.266 Chirality : 0.041 0.151 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.334 32.047 1222 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.25 % Allowed : 14.19 % Favored : 83.56 % 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: 0.73 (0.26), residues: 1105 helix: 2.61 (0.28), residues: 369 sheet: 0.10 (0.31), residues: 278 loop : -1.09 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE A 189 TYR 0.015 0.001 TYR E 178 ARG 0.004 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 398) hydrogen bonds : angle 3.95291 ( 1128) SS BOND : bond 0.00435 ( 3) SS BOND : angle 0.70575 ( 6) covalent geometry : bond 0.00222 ( 8716) covalent geometry : angle 0.50775 (11842) *********************** 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 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.942 Fit side-chains REVERT: B 46 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.7846 (mtp-110) REVERT: B 58 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8276 (mt) REVERT: B 247 ASP cc_start: 0.7812 (t0) cc_final: 0.7516 (t0) REVERT: B 327 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8560 (t) REVERT: E 51 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8382 (tp) outliers start: 20 outliers final: 12 residues processed: 128 average time/residue: 1.1980 time to fit residues: 163.3878 Evaluate side-chains 126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 A residue 276 GLU 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 41 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 E 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.139765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.095476 restraints weight = 10649.580| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.28 r_work: 0.3164 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8719 Z= 0.124 Angle : 0.534 7.615 11848 Z= 0.278 Chirality : 0.042 0.151 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.374 31.649 1222 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.70 % Allowed : 14.75 % Favored : 82.55 % 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: 0.82 (0.26), residues: 1105 helix: 2.68 (0.27), residues: 369 sheet: 0.08 (0.31), residues: 288 loop : -0.99 (0.28), residues: 448 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 B 241 TYR 0.014 0.001 TYR E 178 ARG 0.004 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 398) hydrogen bonds : angle 3.96181 ( 1128) SS BOND : bond 0.00528 ( 3) SS BOND : angle 0.60464 ( 6) covalent geometry : bond 0.00292 ( 8716) covalent geometry : angle 0.53393 (11842) *********************** 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 to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.934 Fit side-chains REVERT: B 46 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.7813 (mtp-110) REVERT: B 247 ASP cc_start: 0.7806 (t0) cc_final: 0.7507 (t0) REVERT: B 327 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8605 (t) REVERT: A 309 ASP cc_start: 0.8051 (p0) cc_final: 0.7824 (p0) REVERT: E 51 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8397 (tp) outliers start: 24 outliers final: 16 residues processed: 129 average time/residue: 1.1774 time to fit residues: 162.1042 Evaluate side-chains 129 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 264 MET 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 A residue 276 GLU 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 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.0060 chunk 3 optimal weight: 0.0170 chunk 44 optimal weight: 0.0060 chunk 48 optimal weight: 0.5980 chunk 49 optimal weight: 0.0270 chunk 14 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.0308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.153532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109044 restraints weight = 11170.242| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.31 r_work: 0.3265 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8719 Z= 0.084 Angle : 0.452 5.635 11848 Z= 0.239 Chirality : 0.040 0.151 1379 Planarity : 0.003 0.031 1486 Dihedral : 3.799 23.945 1222 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.46 % Allowed : 16.10 % Favored : 82.43 % 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: 0.99 (0.26), residues: 1105 helix: 2.87 (0.28), residues: 362 sheet: 0.28 (0.32), residues: 264 loop : -0.89 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.000 HIS B 225 PHE 0.010 0.001 PHE A 189 TYR 0.016 0.001 TYR E 178 ARG 0.003 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.02869 ( 398) hydrogen bonds : angle 3.71415 ( 1128) SS BOND : bond 0.00241 ( 3) SS BOND : angle 0.52118 ( 6) covalent geometry : bond 0.00166 ( 8716) covalent geometry : angle 0.45237 (11842) *********************** 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 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.920 Fit side-chains REVERT: B 46 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.7849 (mtp-110) REVERT: B 61 MET cc_start: 0.9038 (ppp) cc_final: 0.8826 (ptm) REVERT: B 95 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8286 (pt) REVERT: B 247 ASP cc_start: 0.7623 (t0) cc_final: 0.7409 (t0) REVERT: B 258 ASP cc_start: 0.7841 (t70) cc_final: 0.7357 (t0) outliers start: 13 outliers final: 5 residues processed: 140 average time/residue: 1.1616 time to fit residues: 173.8882 Evaluate side-chains 122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 266 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.145966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.099809 restraints weight = 11088.854| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.32 r_work: 0.3136 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8719 Z= 0.130 Angle : 0.535 7.791 11848 Z= 0.279 Chirality : 0.042 0.155 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.097 26.625 1222 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.35 % Allowed : 17.45 % Favored : 81.19 % 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: 1.02 (0.26), residues: 1105 helix: 2.87 (0.27), residues: 366 sheet: 0.14 (0.30), residues: 290 loop : -0.82 (0.28), residues: 449 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 0.011 0.001 PHE A 189 TYR 0.012 0.001 TYR E 178 ARG 0.002 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 398) hydrogen bonds : angle 3.85455 ( 1128) SS BOND : bond 0.00472 ( 3) SS BOND : angle 0.63489 ( 6) covalent geometry : bond 0.00310 ( 8716) covalent geometry : angle 0.53446 (11842) *********************** 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 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.011 Fit side-chains REVERT: B 23 LYS cc_start: 0.8199 (tppt) cc_final: 0.7982 (tmtt) REVERT: B 46 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.7930 (mtp-110) REVERT: B 247 ASP cc_start: 0.7889 (t0) cc_final: 0.7544 (t0) REVERT: B 258 ASP cc_start: 0.8258 (t70) cc_final: 0.7647 (t0) REVERT: A 33 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8488 (mt-10) REVERT: A 182 THR cc_start: 0.7326 (p) cc_final: 0.7016 (t) outliers start: 12 outliers final: 8 residues processed: 123 average time/residue: 1.2149 time to fit residues: 159.3763 Evaluate side-chains 123 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.141878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.095129 restraints weight = 10984.453| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.31 r_work: 0.3089 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8719 Z= 0.167 Angle : 0.584 8.227 11848 Z= 0.303 Chirality : 0.043 0.145 1379 Planarity : 0.003 0.034 1486 Dihedral : 4.523 29.873 1222 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.46 % Allowed : 17.34 % Favored : 81.19 % 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: 0.87 (0.26), residues: 1105 helix: 2.69 (0.27), residues: 369 sheet: 0.19 (0.31), residues: 280 loop : -0.96 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR E 178 ARG 0.003 0.000 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.04740 ( 398) hydrogen bonds : angle 4.05967 ( 1128) SS BOND : bond 0.00598 ( 3) SS BOND : angle 0.61401 ( 6) covalent geometry : bond 0.00409 ( 8716) covalent geometry : angle 0.58442 (11842) ********************** 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 123 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.933 Fit side-chains REVERT: B 23 LYS cc_start: 0.8152 (tppt) cc_final: 0.7934 (tmtt) REVERT: B 46 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.7932 (mtp-110) REVERT: B 327 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8660 (t) REVERT: A 182 THR cc_start: 0.7359 (p) cc_final: 0.7013 (t) outliers start: 13 outliers final: 7 residues processed: 118 average time/residue: 1.2195 time to fit residues: 153.2347 Evaluate side-chains 117 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 2 optimal weight: 0.0050 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.099089 restraints weight = 11038.557| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.33 r_work: 0.3146 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8719 Z= 0.100 Angle : 0.503 7.326 11848 Z= 0.265 Chirality : 0.041 0.141 1379 Planarity : 0.003 0.032 1486 Dihedral : 4.126 27.310 1222 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.58 % Allowed : 17.12 % Favored : 81.31 % 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: 0.96 (0.26), residues: 1105 helix: 2.70 (0.27), residues: 372 sheet: 0.17 (0.31), residues: 291 loop : -0.84 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.001 PHE A 189 TYR 0.015 0.001 TYR E 178 ARG 0.002 0.000 ARG E 148 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 398) hydrogen bonds : angle 3.86098 ( 1128) SS BOND : bond 0.00406 ( 3) SS BOND : angle 0.56778 ( 6) covalent geometry : bond 0.00219 ( 8716) covalent geometry : angle 0.50282 (11842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6487.95 seconds wall clock time: 111 minutes 3.02 seconds (6663.02 seconds total)