Starting phenix.real_space_refine on Thu Feb 15 10:25:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw0_8922/02_2024/6dw0_8922_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw0_8922/02_2024/6dw0_8922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw0_8922/02_2024/6dw0_8922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw0_8922/02_2024/6dw0_8922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw0_8922/02_2024/6dw0_8922_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw0_8922/02_2024/6dw0_8922_updated.pdb" } resolution = 3.8 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= -0.073 sd= 2.932 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 63 5.16 5 C 7643 2.51 5 N 1954 2.21 5 O 2269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11929 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2221 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 11, 'TRANS': 287} Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 159 Chain: "C" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2260 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 12, 'TRANS': 283} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2229 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 12, 'TRANS': 283} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 129 Chain: "E" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2459 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 6, 'ASN:plan1': 1, 'TRP:plan': 3, 'PHE:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2472 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 5, 'ARG:plan': 4, 'TRP:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 110 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {'ABU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.56, per 1000 atoms: 0.55 Number of scatterers: 11929 At special positions: 0 Unit cell: (131.098, 97.35, 92.158, 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 63 16.00 O 2269 8.00 N 1954 7.00 C 7643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " MAN G 6 " - " MAN G 7 " ALPHA1-6 " BMA G 3 " - " MAN G 6 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG F 1 " - " ASN C 110 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN E 149 " " NAG I 1 " - " ASN E 80 " " NAG J 1 " - " ASN B 149 " " NAG K 1 " - " ASN B 80 " Time building additional restraints: 5.00 Conformation dependent library (CDL) restraints added in 2.2 seconds 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2908 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 18 sheets defined 31.6% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 233 through 256 removed outlier: 4.092A pdb=" N ILE D 238 " --> pdb=" O GLY D 234 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN D 239 " --> pdb=" O TYR D 235 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Proline residue: D 243 - end of helix removed outlier: 3.586A pdb=" N LEU D 246 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 248 " --> pdb=" O CYS D 244 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL D 249 " --> pdb=" O THR D 245 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 283 removed outlier: 3.934A pdb=" N THR D 266 " --> pdb=" O VAL D 262 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER D 267 " --> pdb=" O PRO D 263 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR D 278 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER D 280 " --> pdb=" O MET D 276 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 319 removed outlier: 3.548A pdb=" N VAL D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N CYS D 303 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR D 319 " --> pdb=" O GLY D 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.673A pdb=" N LEU C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 87 through 92 removed outlier: 3.649A pdb=" N LYS C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 223 through 243 removed outlier: 4.470A pdb=" N THR C 229 " --> pdb=" O PHE C 225 " (cutoff:3.500A) Proline residue: C 232 - end of helix Processing helix chain 'C' and resid 252 through 273 removed outlier: 3.824A pdb=" N VAL C 256 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE C 257 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR C 260 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET C 265 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 306 removed outlier: 3.915A pdb=" N CYS C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 296 " --> pdb=" O CYS C 292 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C 297 " --> pdb=" O TYR C 293 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA C 299 " --> pdb=" O PHE C 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.808A pdb=" N ARG A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 174 through 177 No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 226 through 239 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 251 through 275 removed outlier: 3.634A pdb=" N THR A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 306 removed outlier: 3.724A pdb=" N VAL A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.650A pdb=" N THR E 15 " --> pdb=" O TYR E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.698A pdb=" N ALA E 88 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 174 removed outlier: 3.669A pdb=" N ALA E 174 " --> pdb=" O GLY E 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 174' Processing helix chain 'E' and resid 218 through 241 Proline residue: E 228 - end of helix removed outlier: 4.405A pdb=" N LEU E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 271 removed outlier: 4.294A pdb=" N LEU E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 258 " --> pdb=" O GLY E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 301 removed outlier: 3.683A pdb=" N LEU E 285 " --> pdb=" O ILE E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 344 removed outlier: 3.766A pdb=" N PHE E 328 " --> pdb=" O SER E 324 " (cutoff:3.500A) Proline residue: E 329 - end of helix Processing helix chain 'B' and resid 11 through 20 removed outlier: 3.528A pdb=" N THR B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 171 through 174 removed outlier: 3.619A pdb=" N ALA B 174 " --> pdb=" O GLY B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 174' Processing helix chain 'B' and resid 218 through 241 removed outlier: 3.556A pdb=" N TYR B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Proline residue: B 228 - end of helix removed outlier: 3.687A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.947A pdb=" N LEU B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 301 removed outlier: 3.762A pdb=" N PHE B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 344 Proline residue: B 329 - end of helix Processing sheet with id= A, first strand: chain 'D' and resid 180 through 182 removed outlier: 6.608A pdb=" N ASP D 75 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE D 62 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 131 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 133 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 202 through 214 removed outlier: 6.652A pdb=" N ASP D 228 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU D 206 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR D 226 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASN D 208 " --> pdb=" O SER D 224 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER D 224 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR D 210 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 222 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL D 212 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR D 220 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 166 through 170 removed outlier: 6.265A pdb=" N THR C 38 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU C 169 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL C 40 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP C 62 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N PHE C 49 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR C 60 " --> pdb=" O PHE C 49 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 82 through 85 removed outlier: 4.121A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 149 through 157 removed outlier: 3.781A pdb=" N GLY C 194 " --> pdb=" O HIS C 217 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS C 219 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU C 192 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 201 through 203 Processing sheet with id= G, first strand: chain 'A' and resid 166 through 170 removed outlier: 6.875A pdb=" N THR A 38 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLU A 169 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL A 40 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A 39 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS A 70 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP A 62 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE A 49 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR A 60 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.804A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 129 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= J, first strand: chain 'A' and resid 149 through 153 removed outlier: 3.567A pdb=" N TYR A 209 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 194 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LYS A 219 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU A 192 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.610A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP E 37 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS E 68 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.980A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS E 192 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG E 213 " --> pdb=" O ASP E 190 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 44 through 47 removed outlier: 6.741A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.772A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.373A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP B 37 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS B 68 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 153 through 155 Processing sheet with id= Q, first strand: chain 'B' and resid 186 through 188 Processing sheet with id= R, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.820A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3599 1.34 - 1.46: 2329 1.46 - 1.58: 6138 1.58 - 1.69: 1 1.69 - 1.81: 109 Bond restraints: 12176 Sorted by residual: bond pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " ideal model delta sigma weight residual 1.524 1.576 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C TYR B 143 " pdb=" N PRO B 144 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.49e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.42e+00 bond pdb=" C5 MAN G 6 " pdb=" O5 MAN G 6 " ideal model delta sigma weight residual 1.418 1.460 -0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.88e+00 ... (remaining 12171 not shown) Histogram of bond angle deviations from ideal: 98.99 - 105.98: 280 105.98 - 112.98: 6833 112.98 - 119.98: 3990 119.98 - 126.98: 5374 126.98 - 133.98: 137 Bond angle restraints: 16614 Sorted by residual: angle pdb=" C MET A 111 " pdb=" N THR A 112 " pdb=" CA THR A 112 " ideal model delta sigma weight residual 121.54 131.44 -9.90 1.91e+00 2.74e-01 2.69e+01 angle pdb=" C ALA D 261 " pdb=" N VAL D 262 " pdb=" CA VAL D 262 " ideal model delta sigma weight residual 120.24 123.33 -3.09 6.30e-01 2.52e+00 2.40e+01 angle pdb=" N VAL A 251 " pdb=" CA VAL A 251 " pdb=" C VAL A 251 " ideal model delta sigma weight residual 108.88 118.87 -9.99 2.16e+00 2.14e-01 2.14e+01 angle pdb=" N GLY A 34 " pdb=" CA GLY A 34 " pdb=" C GLY A 34 " ideal model delta sigma weight residual 115.72 108.83 6.89 1.51e+00 4.39e-01 2.08e+01 angle pdb=" N GLY C 223 " pdb=" CA GLY C 223 " pdb=" C GLY C 223 " ideal model delta sigma weight residual 113.18 122.41 -9.23 2.37e+00 1.78e-01 1.52e+01 ... (remaining 16609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 7180 23.94 - 47.88: 200 47.88 - 71.81: 31 71.81 - 95.75: 39 95.75 - 119.69: 44 Dihedral angle restraints: 7494 sinusoidal: 3000 harmonic: 4494 Sorted by residual: dihedral pdb=" CA THR D 126 " pdb=" C THR D 126 " pdb=" N PRO D 127 " pdb=" CA PRO D 127 " ideal model delta harmonic sigma weight residual -180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " pdb=" SG CYS E 150 " pdb=" CB CYS E 150 " ideal model delta sinusoidal sigma weight residual 93.00 48.69 44.31 1 1.00e+01 1.00e-02 2.73e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 136.97 -43.97 1 1.00e+01 1.00e-02 2.69e+01 ... (remaining 7491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1718 0.070 - 0.141: 297 0.141 - 0.211: 35 0.211 - 0.281: 3 0.281 - 0.351: 5 Chirality restraints: 2058 Sorted by residual: chirality pdb=" CB ILE C 222 " pdb=" CA ILE C 222 " pdb=" CG1 ILE C 222 " pdb=" CG2 ILE C 222 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 110 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 2055 not shown) Planarity restraints: 2052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 227 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO E 228 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 228 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 228 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 142 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C ARG B 142 " -0.036 2.00e-02 2.50e+03 pdb=" O ARG B 142 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR B 143 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 145 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO C 146 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.029 5.00e-02 4.00e+02 ... (remaining 2049 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3290 2.81 - 3.33: 10750 3.33 - 3.85: 19896 3.85 - 4.38: 21772 4.38 - 4.90: 37584 Nonbonded interactions: 93292 Sorted by model distance: nonbonded pdb=" OG SER E 73 " pdb=" O PRO E 120 " model vdw 2.282 2.440 nonbonded pdb=" O GLY C 258 " pdb=" OG1 THR C 261 " model vdw 2.299 2.440 nonbonded pdb=" OG1 THR E 151 " pdb=" OE2 GLU E 153 " model vdw 2.304 2.440 nonbonded pdb=" O GLY E 254 " pdb=" OG1 THR E 257 " model vdw 2.306 2.440 nonbonded pdb=" OG SER C 68 " pdb=" O LEU C 126 " model vdw 2.308 2.440 ... (remaining 93287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 70 or (resid 71 through 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 through 76 or (resid 77 and (na \ me N or name CA or name C or name O or name CB )) or resid 78 through 79 or (res \ id 80 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or \ resid 138 through 227 or (resid 228 and (name N or name CA or name C or name O \ or name CB )) or resid 229 through 233 or (resid 234 through 235 and (name N or \ name CA or name C or name O or name CB )) or resid 236 through 237 or (resid 238 \ and (name N or name CA or name C or name O or name CB )) or resid 239 through 2 \ 40 or (resid 241 through 242 and (name N or name CA or name C or name O or name \ CB )) or resid 243 or (resid 244 through 249 and (name N or name CA or name C or \ name O or name CB )) or resid 250 or (resid 251 and (name N or name CA or name \ C or name O or name CB )) or resid 252 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 307)) selection = (chain 'C' and (resid 12 through 34 or (resid 35 through 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 54 or (resid 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 86 or (res \ id 87 and (name N or name CA or name C or name O or name CB )) or resid 88 throu \ gh 164 or (resid 165 and (name N or name CA or name C or name O or name CB )) or \ resid 166 through 175 or (resid 176 and (name N or name CA or name C or name O \ or name CB )) or resid 177 or (resid 178 and (name N or name CA or name C or nam \ e O or name CB )) or resid 179 through 260 or (resid 261 and (name N or name CA \ or name C or name O or name CB )) or resid 262 through 272 or (resid 273 through \ 274 and (name N or name CA or name C or name O or name CB )) or resid 275 throu \ gh 277 or (resid 278 and (name N or name CA or name C or name O or name CB )) or \ resid 279 through 280 or (resid 281 through 282 and (name N or name CA or name \ C or name O or name CB )) or resid 283 through 285 or (resid 286 and (name N or \ name CA or name C or name O or name CB )) or resid 287 or (resid 288 and (name N \ or name CA or name C or name O or name CB )) or resid 289 through 291 or (resid \ 292 through 295 and (name N or name CA or name C or name O or name CB )) or res \ id 296 or (resid 297 and (name N or name CA or name C or name O or name CB )) or \ resid 298 through 302 or (resid 303 through 304 and (name N or name CA or name \ C or name O or name CB )) or resid 305 through 307)) } ncs_group { reference = (chain 'B' and (resid 10 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 191 or (resid 192 and (name N or n \ ame CA or name C or name O or name CB )) or resid 193 through 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )) or resid 218 through 21 \ 9 or (resid 220 through 221 and (name N or name CA or name C or name O or name C \ B )) or resid 222 through 223 or (resid 224 and (name N or name CA or name C or \ name O or name CB )) or resid 225 through 229 or (resid 230 and (name N or name \ CA or name C or name O or name CB )) or resid 231 through 234 or (resid 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 through 240 or \ (resid 241 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 2 through 243 or (resid 244 and (name N or name CA or name C or name O or name C \ B )) or resid 245 through 270 or (resid 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 276 or (resid 277 and (name N or name \ CA or name C or name O or name CB )) or resid 278 through 290 or (resid 291 and \ (name N or name CA or name C or name O or name CB )) or resid 292 or (resid 293 \ and (name N or name CA or name C or name O or name CB )) or resid 294 through 34 \ 5)) selection = (chain 'E' and (resid 10 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 29 or (resid 30 and (name N or nam \ e CA or name C or name O or name CB )) or resid 31 through 138 or (resid 139 and \ (name N or name CA or name C or name O or name CB )) or resid 140 or (resid 141 \ and (name N or name CA or name C or name O or name CB )) or resid 142 through 2 \ 26 or (resid 227 and (name N or name CA or name C or name O or name CB )) or res \ id 228 through 252 or (resid 253 and (name N or name CA or name C or name O or n \ ame CB )) or resid 254 through 285 or (resid 286 and (name N or name CA or name \ C or name O or name CB )) or resid 287 through 320 or (resid 321 and (name N or \ name CA or name C or name O or name CB )) or resid 322 or (resid 323 and (name N \ or name CA or name C or name O or name CB )) or resid 324 or (resid 325 through \ 329 and (name N or name CA or name C or name O or name CB )) or resid 330 throu \ gh 331 or (resid 332 and (name N or name CA or name C or name O or name CB )) or \ resid 333 through 345)) } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 3.600 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 34.370 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 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 0.055 12176 Z= 0.328 Angle : 0.974 12.802 16614 Z= 0.504 Chirality : 0.055 0.351 2058 Planarity : 0.006 0.058 2046 Dihedral : 16.587 119.691 4571 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.18), residues: 1515 helix: -2.78 (0.16), residues: 455 sheet: -2.19 (0.23), residues: 428 loop : -2.68 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 94 HIS 0.012 0.002 HIS D 122 PHE 0.023 0.002 PHE D 113 TYR 0.026 0.002 TYR E 342 ARG 0.006 0.001 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 788 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 ASN cc_start: 0.9371 (m-40) cc_final: 0.9157 (t0) REVERT: D 36 GLU cc_start: 0.8550 (pm20) cc_final: 0.8292 (pm20) REVERT: D 39 ASP cc_start: 0.9072 (t0) cc_final: 0.8665 (t70) REVERT: D 40 ASN cc_start: 0.8362 (m-40) cc_final: 0.7012 (m-40) REVERT: D 51 THR cc_start: 0.9476 (m) cc_final: 0.8992 (p) REVERT: D 54 HIS cc_start: 0.8977 (m-70) cc_final: 0.8518 (m-70) REVERT: D 57 MET cc_start: 0.9152 (ptp) cc_final: 0.8950 (ptp) REVERT: D 58 TYR cc_start: 0.8678 (t80) cc_final: 0.8284 (t80) REVERT: D 60 ASN cc_start: 0.9258 (t0) cc_final: 0.8807 (m110) REVERT: D 90 ASN cc_start: 0.7174 (t0) cc_final: 0.6471 (p0) REVERT: D 101 ASN cc_start: 0.8345 (m110) cc_final: 0.7703 (t0) REVERT: D 105 LYS cc_start: 0.9133 (mttt) cc_final: 0.8749 (mttp) REVERT: D 107 TRP cc_start: 0.8892 (t60) cc_final: 0.8563 (t60) REVERT: D 110 ASP cc_start: 0.8483 (t70) cc_final: 0.7520 (t70) REVERT: D 112 PHE cc_start: 0.8003 (p90) cc_final: 0.7089 (p90) REVERT: D 122 HIS cc_start: 0.8561 (m-70) cc_final: 0.7594 (m90) REVERT: D 138 ARG cc_start: 0.8926 (ttp-170) cc_final: 0.8095 (ttp80) REVERT: D 144 ARG cc_start: 0.8550 (tmm-80) cc_final: 0.7358 (tmm-80) REVERT: D 161 ASP cc_start: 0.8389 (m-30) cc_final: 0.8159 (m-30) REVERT: D 172 TYR cc_start: 0.7225 (t80) cc_final: 0.6851 (t80) REVERT: D 182 GLN cc_start: 0.8483 (tp40) cc_final: 0.8101 (tp-100) REVERT: D 222 VAL cc_start: 0.9486 (t) cc_final: 0.9067 (m) REVERT: C 13 VAL cc_start: 0.9429 (t) cc_final: 0.9053 (m) REVERT: C 58 GLU cc_start: 0.8104 (pp20) cc_final: 0.7850 (pp20) REVERT: C 113 MET cc_start: 0.8524 (mmm) cc_final: 0.8074 (mmm) REVERT: C 119 ARG cc_start: 0.9221 (mtt180) cc_final: 0.8854 (mtt90) REVERT: C 122 GLU cc_start: 0.8822 (pt0) cc_final: 0.8561 (pt0) REVERT: C 128 TYR cc_start: 0.8145 (t80) cc_final: 0.7888 (t80) REVERT: C 144 ASP cc_start: 0.8315 (t0) cc_final: 0.8052 (t70) REVERT: C 165 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7923 (mp0) REVERT: C 170 TRP cc_start: 0.8579 (m100) cc_final: 0.8065 (m100) REVERT: C 173 GLU cc_start: 0.8355 (mp0) cc_final: 0.8143 (mp0) REVERT: C 191 ASP cc_start: 0.8722 (m-30) cc_final: 0.8457 (m-30) REVERT: C 196 THR cc_start: 0.8396 (m) cc_final: 0.8067 (p) REVERT: C 217 HIS cc_start: 0.9040 (m-70) cc_final: 0.8837 (m90) REVERT: A 20 ARG cc_start: 0.8961 (mtt90) cc_final: 0.8651 (ttm110) REVERT: A 30 ARG cc_start: 0.8161 (ptt90) cc_final: 0.7548 (ptt90) REVERT: A 52 VAL cc_start: 0.8841 (m) cc_final: 0.8540 (p) REVERT: A 54 ASP cc_start: 0.8429 (m-30) cc_final: 0.7813 (m-30) REVERT: A 57 MET cc_start: 0.8998 (ttm) cc_final: 0.8199 (ttm) REVERT: A 89 MET cc_start: 0.8875 (tpp) cc_final: 0.8646 (tpp) REVERT: A 105 LYS cc_start: 0.8631 (tptt) cc_final: 0.8395 (pttp) REVERT: A 109 HIS cc_start: 0.8695 (m-70) cc_final: 0.8369 (m170) REVERT: A 113 MET cc_start: 0.8794 (mmm) cc_final: 0.8348 (mmm) REVERT: A 114 PRO cc_start: 0.9223 (Cg_exo) cc_final: 0.8996 (Cg_endo) REVERT: A 140 MET cc_start: 0.9184 (mpp) cc_final: 0.8408 (mpp) REVERT: A 144 ASP cc_start: 0.8510 (p0) cc_final: 0.8045 (p0) REVERT: A 150 HIS cc_start: 0.8091 (m-70) cc_final: 0.7752 (m90) REVERT: A 245 TRP cc_start: 0.7599 (m100) cc_final: 0.7000 (m100) REVERT: E 21 LYS cc_start: 0.9136 (tmtm) cc_final: 0.8906 (tmtt) REVERT: E 44 VAL cc_start: 0.9583 (t) cc_final: 0.9377 (p) REVERT: E 54 ASN cc_start: 0.9417 (m110) cc_final: 0.9200 (m-40) REVERT: E 55 MET cc_start: 0.9186 (mtt) cc_final: 0.8810 (mtt) REVERT: E 64 GLN cc_start: 0.9082 (tt0) cc_final: 0.8660 (tp40) REVERT: E 69 ASP cc_start: 0.8911 (t0) cc_final: 0.8645 (t0) REVERT: E 81 LEU cc_start: 0.9322 (mt) cc_final: 0.9043 (mt) REVERT: E 90 GLN cc_start: 0.8945 (mt0) cc_final: 0.8409 (mt0) REVERT: E 93 VAL cc_start: 0.9627 (m) cc_final: 0.9093 (m) REVERT: E 101 ASP cc_start: 0.8287 (p0) cc_final: 0.7825 (p0) REVERT: E 126 TYR cc_start: 0.8787 (t80) cc_final: 0.8184 (t80) REVERT: E 167 TYR cc_start: 0.8570 (p90) cc_final: 0.8353 (p90) REVERT: E 169 ASN cc_start: 0.9028 (t0) cc_final: 0.8460 (t0) REVERT: E 175 VAL cc_start: 0.9280 (t) cc_final: 0.9061 (t) REVERT: E 181 ILE cc_start: 0.9252 (mm) cc_final: 0.8970 (mm) REVERT: E 191 TYR cc_start: 0.8987 (p90) cc_final: 0.8466 (p90) REVERT: E 210 LEU cc_start: 0.9321 (tp) cc_final: 0.8678 (tp) REVERT: E 213 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.7710 (ptp-110) REVERT: E 264 ILE cc_start: 0.9287 (mm) cc_final: 0.9038 (mm) REVERT: E 342 TYR cc_start: 0.8231 (m-80) cc_final: 0.7857 (m-80) REVERT: B 13 LYS cc_start: 0.8949 (tttm) cc_final: 0.8517 (ttmt) REVERT: B 17 ASP cc_start: 0.9369 (m-30) cc_final: 0.9020 (m-30) REVERT: B 37 ASP cc_start: 0.8712 (p0) cc_final: 0.8389 (p0) REVERT: B 55 MET cc_start: 0.9091 (mmp) cc_final: 0.8624 (mmm) REVERT: B 63 PHE cc_start: 0.9055 (t80) cc_final: 0.8463 (t80) REVERT: B 65 GLN cc_start: 0.9077 (pt0) cc_final: 0.8697 (pt0) REVERT: B 66 SER cc_start: 0.9553 (p) cc_final: 0.9293 (t) REVERT: B 96 THR cc_start: 0.9609 (m) cc_final: 0.9354 (p) REVERT: B 114 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7814 (mtm180) REVERT: B 125 LEU cc_start: 0.9120 (tp) cc_final: 0.8863 (tp) REVERT: B 133 THR cc_start: 0.8963 (m) cc_final: 0.8583 (p) REVERT: B 147 GLU cc_start: 0.8820 (tt0) cc_final: 0.8446 (tp30) REVERT: B 151 THR cc_start: 0.8347 (p) cc_final: 0.7992 (p) REVERT: B 167 TYR cc_start: 0.8509 (p90) cc_final: 0.8115 (p90) REVERT: B 169 ASN cc_start: 0.8912 (t0) cc_final: 0.8037 (t0) REVERT: B 198 VAL cc_start: 0.9599 (t) cc_final: 0.9302 (m) REVERT: B 209 SER cc_start: 0.9186 (t) cc_final: 0.8878 (t) REVERT: B 213 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7537 (mtm180) REVERT: B 216 ARG cc_start: 0.8903 (ttm-80) cc_final: 0.8589 (mtm180) outliers start: 1 outliers final: 0 residues processed: 788 average time/residue: 0.2578 time to fit residues: 277.8616 Evaluate side-chains 648 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 648 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 0.0030 chunk 116 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 chunk 86 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 HIS D 258 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 ASN A 27 ASN ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12176 Z= 0.193 Angle : 0.758 12.200 16614 Z= 0.365 Chirality : 0.047 0.233 2058 Planarity : 0.005 0.054 2046 Dihedral : 15.523 102.904 2087 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.59 % Allowed : 22.19 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.20), residues: 1515 helix: -1.35 (0.21), residues: 450 sheet: -1.77 (0.24), residues: 419 loop : -2.35 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 168 HIS 0.007 0.001 HIS E 267 PHE 0.030 0.002 PHE B 221 TYR 0.019 0.001 TYR A 59 ARG 0.007 0.001 ARG C 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 684 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 ASN cc_start: 0.9517 (m-40) cc_final: 0.9114 (m110) REVERT: D 36 GLU cc_start: 0.8603 (pm20) cc_final: 0.8402 (pm20) REVERT: D 39 ASP cc_start: 0.9112 (t0) cc_final: 0.8513 (t70) REVERT: D 40 ASN cc_start: 0.8522 (m-40) cc_final: 0.8274 (m-40) REVERT: D 51 THR cc_start: 0.9193 (m) cc_final: 0.8933 (p) REVERT: D 54 HIS cc_start: 0.8991 (m-70) cc_final: 0.8661 (m-70) REVERT: D 82 TRP cc_start: 0.9288 (p90) cc_final: 0.9040 (p90) REVERT: D 90 ASN cc_start: 0.7343 (t0) cc_final: 0.6468 (p0) REVERT: D 101 ASN cc_start: 0.8111 (m110) cc_final: 0.7525 (t0) REVERT: D 107 TRP cc_start: 0.8937 (t60) cc_final: 0.8615 (t60) REVERT: D 110 ASP cc_start: 0.8598 (t70) cc_final: 0.7660 (t70) REVERT: D 112 PHE cc_start: 0.7853 (p90) cc_final: 0.6871 (p90) REVERT: D 122 HIS cc_start: 0.8329 (m90) cc_final: 0.7593 (m90) REVERT: D 138 ARG cc_start: 0.8793 (ttp-170) cc_final: 0.8164 (ttp80) REVERT: D 144 ARG cc_start: 0.8382 (tmm-80) cc_final: 0.7105 (tmm-80) REVERT: D 172 TYR cc_start: 0.7219 (t80) cc_final: 0.6856 (t80) REVERT: D 239 GLN cc_start: 0.8814 (mt0) cc_final: 0.8455 (pt0) REVERT: C 25 TYR cc_start: 0.8585 (t80) cc_final: 0.8161 (t80) REVERT: C 58 GLU cc_start: 0.8207 (pp20) cc_final: 0.7906 (pp20) REVERT: C 67 GLN cc_start: 0.8128 (pt0) cc_final: 0.7878 (pt0) REVERT: C 70 LYS cc_start: 0.7900 (tmtm) cc_final: 0.7666 (tmtm) REVERT: C 97 ASP cc_start: 0.8600 (p0) cc_final: 0.8279 (p0) REVERT: C 113 MET cc_start: 0.8759 (mmm) cc_final: 0.8305 (mmm) REVERT: C 122 GLU cc_start: 0.8835 (pt0) cc_final: 0.8527 (pt0) REVERT: C 144 ASP cc_start: 0.8448 (t0) cc_final: 0.8146 (t70) REVERT: C 220 ARG cc_start: 0.6475 (ttm170) cc_final: 0.5801 (mtm-85) REVERT: C 221 LYS cc_start: 0.8974 (mttm) cc_final: 0.8592 (mptt) REVERT: C 289 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8769 (pp) REVERT: A 86 ASN cc_start: 0.8488 (p0) cc_final: 0.8286 (p0) REVERT: A 105 LYS cc_start: 0.8585 (tptt) cc_final: 0.8258 (pttp) REVERT: A 107 VAL cc_start: 0.7604 (m) cc_final: 0.7396 (p) REVERT: A 113 MET cc_start: 0.8757 (mmm) cc_final: 0.8300 (mmm) REVERT: A 114 PRO cc_start: 0.9157 (Cg_exo) cc_final: 0.8940 (Cg_endo) REVERT: A 128 TYR cc_start: 0.9333 (t80) cc_final: 0.9033 (t80) REVERT: A 130 MET cc_start: 0.8403 (ptp) cc_final: 0.7930 (ptp) REVERT: A 144 ASP cc_start: 0.8341 (p0) cc_final: 0.7815 (p0) REVERT: A 150 HIS cc_start: 0.7795 (m-70) cc_final: 0.7477 (m90) REVERT: A 203 GLN cc_start: 0.7878 (tp40) cc_final: 0.7057 (tp40) REVERT: A 209 TYR cc_start: 0.8155 (m-10) cc_final: 0.7902 (m-10) REVERT: A 216 PHE cc_start: 0.8624 (m-10) cc_final: 0.8407 (m-80) REVERT: A 220 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8372 (ttp80) REVERT: A 241 GLN cc_start: 0.9124 (tp-100) cc_final: 0.8627 (tm-30) REVERT: E 21 LYS cc_start: 0.9096 (tmtm) cc_final: 0.8806 (tmtt) REVERT: E 44 VAL cc_start: 0.9586 (t) cc_final: 0.9383 (p) REVERT: E 64 GLN cc_start: 0.9086 (tt0) cc_final: 0.8628 (tt0) REVERT: E 68 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9030 (mmmm) REVERT: E 69 ASP cc_start: 0.8910 (t0) cc_final: 0.8575 (t0) REVERT: E 74 TYR cc_start: 0.7872 (p90) cc_final: 0.7587 (p90) REVERT: E 81 LEU cc_start: 0.9087 (mt) cc_final: 0.8689 (mt) REVERT: E 112 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8734 (ttmm) REVERT: E 129 ARG cc_start: 0.8093 (ttt-90) cc_final: 0.7294 (ttt90) REVERT: E 169 ASN cc_start: 0.8989 (t0) cc_final: 0.8618 (t0) REVERT: E 172 GLU cc_start: 0.8117 (tp30) cc_final: 0.7885 (tp30) REVERT: E 191 TYR cc_start: 0.8852 (p90) cc_final: 0.8549 (p90) REVERT: E 299 TYR cc_start: 0.7465 (t80) cc_final: 0.7248 (t80) REVERT: E 342 TYR cc_start: 0.8080 (m-80) cc_final: 0.7840 (m-80) REVERT: B 17 ASP cc_start: 0.9417 (m-30) cc_final: 0.9192 (m-30) REVERT: B 37 ASP cc_start: 0.8727 (p0) cc_final: 0.8526 (p0) REVERT: B 55 MET cc_start: 0.9217 (mmp) cc_final: 0.8986 (tpp) REVERT: B 61 MET cc_start: 0.8200 (ppp) cc_final: 0.7584 (ppp) REVERT: B 63 PHE cc_start: 0.8990 (t80) cc_final: 0.8712 (t80) REVERT: B 69 ASP cc_start: 0.8832 (p0) cc_final: 0.8429 (t70) REVERT: B 89 ASP cc_start: 0.8755 (m-30) cc_final: 0.8538 (m-30) REVERT: B 133 THR cc_start: 0.8765 (m) cc_final: 0.8500 (p) REVERT: B 147 GLU cc_start: 0.8826 (tt0) cc_final: 0.8473 (tp30) REVERT: B 148 GLN cc_start: 0.7962 (mm110) cc_final: 0.7498 (mm110) REVERT: B 151 THR cc_start: 0.8323 (p) cc_final: 0.7955 (p) REVERT: B 153 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8675 (mm-30) REVERT: B 169 ASN cc_start: 0.8713 (t0) cc_final: 0.8508 (t0) REVERT: B 192 LYS cc_start: 0.8572 (mmmt) cc_final: 0.7826 (mmmm) REVERT: B 213 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7577 (mtm180) REVERT: B 216 ARG cc_start: 0.8787 (ttm-80) cc_final: 0.8390 (mtm180) REVERT: B 217 ASN cc_start: 0.7684 (p0) cc_final: 0.7453 (p0) REVERT: B 247 SER cc_start: 0.8880 (p) cc_final: 0.8632 (t) outliers start: 56 outliers final: 34 residues processed: 697 average time/residue: 0.2409 time to fit residues: 234.8294 Evaluate side-chains 688 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 653 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain B residue 11 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 275 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 0.0020 chunk 146 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN D 80 GLN A 109 HIS ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12176 Z= 0.242 Angle : 0.752 9.320 16614 Z= 0.364 Chirality : 0.046 0.218 2058 Planarity : 0.005 0.052 2046 Dihedral : 11.887 87.941 2087 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.57 % Allowed : 25.63 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.20), residues: 1515 helix: -0.60 (0.23), residues: 451 sheet: -1.36 (0.25), residues: 414 loop : -2.11 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 168 HIS 0.005 0.001 HIS E 267 PHE 0.018 0.002 PHE B 221 TYR 0.024 0.002 TYR E 126 ARG 0.006 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 653 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.9060 (t0) cc_final: 0.8616 (t70) REVERT: D 51 THR cc_start: 0.9316 (m) cc_final: 0.9052 (p) REVERT: D 54 HIS cc_start: 0.8983 (m-70) cc_final: 0.8699 (m-70) REVERT: D 90 ASN cc_start: 0.7276 (t0) cc_final: 0.6500 (p0) REVERT: D 101 ASN cc_start: 0.7789 (m110) cc_final: 0.7561 (t0) REVERT: D 110 ASP cc_start: 0.8780 (t70) cc_final: 0.7954 (t70) REVERT: D 112 PHE cc_start: 0.7957 (p90) cc_final: 0.7076 (p90) REVERT: D 172 TYR cc_start: 0.7290 (t80) cc_final: 0.6856 (t80) REVERT: D 207 ARG cc_start: 0.8717 (ptt90) cc_final: 0.8272 (ptt90) REVERT: D 214 LYS cc_start: 0.9193 (ttpt) cc_final: 0.8558 (tppt) REVERT: D 222 VAL cc_start: 0.9396 (t) cc_final: 0.8966 (m) REVERT: D 223 MET cc_start: 0.8657 (mmm) cc_final: 0.8100 (mmm) REVERT: C 25 TYR cc_start: 0.8620 (t80) cc_final: 0.7916 (t80) REVERT: C 58 GLU cc_start: 0.8294 (pp20) cc_final: 0.7886 (pp20) REVERT: C 67 GLN cc_start: 0.8294 (pt0) cc_final: 0.7710 (pt0) REVERT: C 70 LYS cc_start: 0.7881 (tmtm) cc_final: 0.7544 (tmtm) REVERT: C 92 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8931 (mmmm) REVERT: C 97 ASP cc_start: 0.8507 (p0) cc_final: 0.8119 (p0) REVERT: C 122 GLU cc_start: 0.8820 (pt0) cc_final: 0.8440 (pt0) REVERT: C 195 GLN cc_start: 0.9154 (pm20) cc_final: 0.8897 (pm20) REVERT: A 16 ARG cc_start: 0.8524 (ptt180) cc_final: 0.8138 (mpp80) REVERT: A 47 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9021 (p) REVERT: A 57 MET cc_start: 0.8305 (tpp) cc_final: 0.7990 (tpp) REVERT: A 101 HIS cc_start: 0.8877 (m-70) cc_final: 0.8613 (m-70) REVERT: A 105 LYS cc_start: 0.8630 (tptt) cc_final: 0.8246 (pttp) REVERT: A 107 VAL cc_start: 0.7630 (m) cc_final: 0.7259 (p) REVERT: A 113 MET cc_start: 0.8755 (mmm) cc_final: 0.8374 (mmm) REVERT: A 114 PRO cc_start: 0.9114 (Cg_exo) cc_final: 0.8905 (Cg_endo) REVERT: A 130 MET cc_start: 0.8500 (ptp) cc_final: 0.8085 (ptp) REVERT: A 137 GLU cc_start: 0.8800 (pp20) cc_final: 0.8500 (tm-30) REVERT: A 144 ASP cc_start: 0.8275 (p0) cc_final: 0.7736 (p0) REVERT: A 150 HIS cc_start: 0.7252 (m-70) cc_final: 0.6971 (m90) REVERT: A 168 TYR cc_start: 0.8917 (m-10) cc_final: 0.8709 (m-80) REVERT: A 209 TYR cc_start: 0.8225 (m-10) cc_final: 0.8010 (m-10) REVERT: A 213 THR cc_start: 0.8085 (m) cc_final: 0.7301 (p) REVERT: A 215 HIS cc_start: 0.8072 (m-70) cc_final: 0.7523 (m90) REVERT: A 241 GLN cc_start: 0.9139 (tp-100) cc_final: 0.8640 (tm-30) REVERT: E 13 LYS cc_start: 0.9693 (ttmt) cc_final: 0.9484 (ttmt) REVERT: E 21 LYS cc_start: 0.9099 (tmtm) cc_final: 0.8676 (pptt) REVERT: E 30 ASP cc_start: 0.8952 (t0) cc_final: 0.8626 (t0) REVERT: E 64 GLN cc_start: 0.9083 (tt0) cc_final: 0.8691 (tt0) REVERT: E 68 LYS cc_start: 0.9305 (mmmm) cc_final: 0.8887 (mmmm) REVERT: E 69 ASP cc_start: 0.8958 (t0) cc_final: 0.8509 (t70) REVERT: E 81 LEU cc_start: 0.9074 (mt) cc_final: 0.8644 (mt) REVERT: E 112 LYS cc_start: 0.9109 (ttmm) cc_final: 0.8762 (ttmm) REVERT: E 121 ASP cc_start: 0.9123 (p0) cc_final: 0.8867 (p0) REVERT: E 133 THR cc_start: 0.9081 (m) cc_final: 0.8685 (p) REVERT: E 169 ASN cc_start: 0.9077 (t0) cc_final: 0.8638 (t0) REVERT: E 172 GLU cc_start: 0.8007 (tp30) cc_final: 0.7594 (tp30) REVERT: E 191 TYR cc_start: 0.8836 (p90) cc_final: 0.8389 (p90) REVERT: E 213 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.7615 (ptp-110) REVERT: E 342 TYR cc_start: 0.8117 (m-80) cc_final: 0.7880 (m-80) REVERT: B 17 ASP cc_start: 0.9500 (m-30) cc_final: 0.9228 (m-30) REVERT: B 37 ASP cc_start: 0.8933 (p0) cc_final: 0.8730 (p0) REVERT: B 61 MET cc_start: 0.8342 (ppp) cc_final: 0.7478 (ppp) REVERT: B 63 PHE cc_start: 0.9032 (t80) cc_final: 0.8664 (t80) REVERT: B 89 ASP cc_start: 0.8875 (m-30) cc_final: 0.8407 (m-30) REVERT: B 90 GLN cc_start: 0.8782 (mm110) cc_final: 0.8539 (mm-40) REVERT: B 112 LYS cc_start: 0.8800 (mtpt) cc_final: 0.8311 (ttmt) REVERT: B 133 THR cc_start: 0.8900 (m) cc_final: 0.8590 (p) REVERT: B 136 CYS cc_start: 0.5219 (t) cc_final: 0.4715 (t) REVERT: B 147 GLU cc_start: 0.8899 (tt0) cc_final: 0.8481 (tp30) REVERT: B 148 GLN cc_start: 0.8023 (mm110) cc_final: 0.7450 (mm110) REVERT: B 150 CYS cc_start: 0.7795 (m) cc_final: 0.7331 (m) REVERT: B 151 THR cc_start: 0.8333 (p) cc_final: 0.7952 (p) REVERT: B 153 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8610 (mm-30) REVERT: B 213 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7520 (mtm180) REVERT: B 216 ARG cc_start: 0.8867 (ttm-80) cc_final: 0.8452 (mtm180) REVERT: B 247 SER cc_start: 0.8927 (p) cc_final: 0.8695 (t) REVERT: B 275 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7690 (mp) REVERT: B 342 TYR cc_start: 0.8067 (t80) cc_final: 0.7733 (t80) outliers start: 68 outliers final: 53 residues processed: 671 average time/residue: 0.2418 time to fit residues: 227.9806 Evaluate side-chains 696 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 641 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 146 ASP Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 80 GLN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12176 Z= 0.270 Angle : 0.767 11.719 16614 Z= 0.371 Chirality : 0.046 0.235 2058 Planarity : 0.005 0.049 2046 Dihedral : 9.705 82.195 2087 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 7.29 % Allowed : 24.98 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.21), residues: 1515 helix: -0.18 (0.23), residues: 455 sheet: -1.22 (0.25), residues: 401 loop : -2.03 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 168 HIS 0.006 0.001 HIS C 150 PHE 0.035 0.002 PHE B 221 TYR 0.026 0.002 TYR E 126 ARG 0.015 0.001 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 651 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.9074 (t0) cc_final: 0.8762 (t70) REVERT: D 54 HIS cc_start: 0.8983 (m-70) cc_final: 0.8690 (m-70) REVERT: D 90 ASN cc_start: 0.7325 (t0) cc_final: 0.6504 (p0) REVERT: D 101 ASN cc_start: 0.7834 (m110) cc_final: 0.7574 (t0) REVERT: D 105 LYS cc_start: 0.8900 (mptt) cc_final: 0.8187 (mptt) REVERT: D 110 ASP cc_start: 0.8853 (t70) cc_final: 0.8126 (t70) REVERT: D 112 PHE cc_start: 0.8024 (p90) cc_final: 0.6973 (p90) REVERT: D 138 ARG cc_start: 0.8722 (ttp-170) cc_final: 0.7983 (ttp80) REVERT: D 172 TYR cc_start: 0.7368 (t80) cc_final: 0.6916 (t80) REVERT: D 207 ARG cc_start: 0.8901 (ptt90) cc_final: 0.8511 (ptt90) REVERT: D 214 LYS cc_start: 0.9288 (ttpt) cc_final: 0.8688 (tppt) REVERT: D 219 ASP cc_start: 0.9238 (t0) cc_final: 0.8910 (t70) REVERT: D 222 VAL cc_start: 0.9417 (t) cc_final: 0.8966 (m) REVERT: D 223 MET cc_start: 0.8685 (mmm) cc_final: 0.7986 (mmm) REVERT: C 25 TYR cc_start: 0.8710 (t80) cc_final: 0.8028 (t80) REVERT: C 58 GLU cc_start: 0.8376 (pp20) cc_final: 0.7956 (pp20) REVERT: C 65 PHE cc_start: 0.8646 (t80) cc_final: 0.7713 (t80) REVERT: C 67 GLN cc_start: 0.8411 (pt0) cc_final: 0.7697 (pt0) REVERT: C 97 ASP cc_start: 0.8410 (p0) cc_final: 0.8110 (p0) REVERT: C 106 SER cc_start: 0.9097 (m) cc_final: 0.8846 (p) REVERT: C 186 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7748 (mmp80) REVERT: A 16 ARG cc_start: 0.8551 (ptt180) cc_final: 0.8348 (ptp90) REVERT: A 44 ILE cc_start: 0.8540 (pp) cc_final: 0.8240 (pp) REVERT: A 77 LYS cc_start: 0.9164 (mppt) cc_final: 0.8962 (mmmt) REVERT: A 105 LYS cc_start: 0.8674 (tptt) cc_final: 0.8213 (pttp) REVERT: A 107 VAL cc_start: 0.7625 (m) cc_final: 0.7389 (p) REVERT: A 113 MET cc_start: 0.8795 (mmm) cc_final: 0.8565 (mmm) REVERT: A 114 PRO cc_start: 0.9143 (Cg_exo) cc_final: 0.8936 (Cg_endo) REVERT: A 128 TYR cc_start: 0.9268 (t80) cc_final: 0.8998 (t80) REVERT: A 130 MET cc_start: 0.8448 (ptp) cc_final: 0.8027 (ptp) REVERT: A 144 ASP cc_start: 0.8179 (p0) cc_final: 0.7638 (p0) REVERT: A 150 HIS cc_start: 0.7272 (m-70) cc_final: 0.6859 (m90) REVERT: A 168 TYR cc_start: 0.8940 (m-10) cc_final: 0.8460 (m-80) REVERT: A 209 TYR cc_start: 0.8235 (m-10) cc_final: 0.7968 (m-10) REVERT: A 215 HIS cc_start: 0.8184 (m-70) cc_final: 0.7972 (m90) REVERT: A 221 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8419 (mmmm) REVERT: A 245 TRP cc_start: 0.7721 (m100) cc_final: 0.7096 (m100) REVERT: A 287 TRP cc_start: 0.8739 (m100) cc_final: 0.8201 (m-10) REVERT: E 13 LYS cc_start: 0.9578 (ttmt) cc_final: 0.9304 (ttmt) REVERT: E 17 ASP cc_start: 0.9353 (m-30) cc_final: 0.9100 (m-30) REVERT: E 21 LYS cc_start: 0.9142 (tmtm) cc_final: 0.8732 (pptt) REVERT: E 30 ASP cc_start: 0.8929 (t0) cc_final: 0.8595 (t0) REVERT: E 64 GLN cc_start: 0.8995 (tt0) cc_final: 0.8602 (tt0) REVERT: E 68 LYS cc_start: 0.9340 (mmmm) cc_final: 0.8929 (mmmm) REVERT: E 69 ASP cc_start: 0.9021 (t0) cc_final: 0.8674 (t70) REVERT: E 97 TYR cc_start: 0.8705 (p90) cc_final: 0.8498 (p90) REVERT: E 112 LYS cc_start: 0.9054 (ttmm) cc_final: 0.8688 (ttmm) REVERT: E 121 ASP cc_start: 0.9271 (p0) cc_final: 0.9014 (p0) REVERT: E 129 ARG cc_start: 0.8174 (ttt-90) cc_final: 0.7236 (ttp80) REVERT: E 133 THR cc_start: 0.9024 (m) cc_final: 0.8661 (p) REVERT: E 172 GLU cc_start: 0.7992 (tp30) cc_final: 0.7626 (tp30) REVERT: E 191 TYR cc_start: 0.8852 (p90) cc_final: 0.8364 (p90) REVERT: E 213 ARG cc_start: 0.8515 (mtm-85) cc_final: 0.7626 (ptp-110) REVERT: E 342 TYR cc_start: 0.8153 (m-80) cc_final: 0.7917 (m-80) REVERT: B 17 ASP cc_start: 0.9492 (m-30) cc_final: 0.9239 (m-30) REVERT: B 37 ASP cc_start: 0.9059 (p0) cc_final: 0.8856 (p0) REVERT: B 41 ARG cc_start: 0.8718 (mtt90) cc_final: 0.8123 (mtt-85) REVERT: B 61 MET cc_start: 0.8446 (ppp) cc_final: 0.7528 (ppp) REVERT: B 63 PHE cc_start: 0.9046 (t80) cc_final: 0.8590 (t80) REVERT: B 89 ASP cc_start: 0.8817 (m-30) cc_final: 0.8447 (m-30) REVERT: B 112 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8473 (ttpp) REVERT: B 129 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7207 (ttt-90) REVERT: B 133 THR cc_start: 0.8936 (m) cc_final: 0.8608 (p) REVERT: B 142 ARG cc_start: 0.8425 (mtp180) cc_final: 0.7845 (mtm180) REVERT: B 145 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8867 (tm) REVERT: B 147 GLU cc_start: 0.8936 (tt0) cc_final: 0.8470 (tp30) REVERT: B 148 GLN cc_start: 0.7971 (mm110) cc_final: 0.7430 (mm110) REVERT: B 151 THR cc_start: 0.8325 (p) cc_final: 0.7100 (p) REVERT: B 153 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8160 (mp0) REVERT: B 213 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7460 (mtm180) REVERT: B 216 ARG cc_start: 0.9228 (ttm-80) cc_final: 0.8056 (ttp-170) REVERT: B 218 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8413 (mp) REVERT: B 247 SER cc_start: 0.8962 (p) cc_final: 0.8721 (t) outliers start: 89 outliers final: 72 residues processed: 677 average time/residue: 0.2464 time to fit residues: 235.5768 Evaluate side-chains 699 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 625 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 331 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 chunk 99 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN B 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12176 Z= 0.301 Angle : 0.769 10.147 16614 Z= 0.375 Chirality : 0.046 0.241 2058 Planarity : 0.005 0.050 2046 Dihedral : 8.713 77.028 2087 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 8.27 % Allowed : 26.29 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.21), residues: 1515 helix: 0.02 (0.24), residues: 455 sheet: -1.19 (0.25), residues: 410 loop : -1.96 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 168 HIS 0.008 0.002 HIS C 150 PHE 0.018 0.002 PHE B 221 TYR 0.024 0.002 TYR E 126 ARG 0.008 0.001 ARG C 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 637 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.9051 (t0) cc_final: 0.8434 (t70) REVERT: D 40 ASN cc_start: 0.8990 (p0) cc_final: 0.8160 (m-40) REVERT: D 54 HIS cc_start: 0.8987 (m-70) cc_final: 0.8577 (m-70) REVERT: D 88 LYS cc_start: 0.9174 (mttt) cc_final: 0.8942 (mtmm) REVERT: D 90 ASN cc_start: 0.7337 (t0) cc_final: 0.6458 (p0) REVERT: D 110 ASP cc_start: 0.8868 (t70) cc_final: 0.8123 (t70) REVERT: D 112 PHE cc_start: 0.8308 (p90) cc_final: 0.7284 (p90) REVERT: D 138 ARG cc_start: 0.8699 (ttp-170) cc_final: 0.7923 (ttp80) REVERT: D 157 ASN cc_start: 0.8096 (m-40) cc_final: 0.7721 (m-40) REVERT: D 160 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7661 (ppp) REVERT: D 172 TYR cc_start: 0.7562 (t80) cc_final: 0.7111 (t80) REVERT: D 207 ARG cc_start: 0.8920 (ptt90) cc_final: 0.8180 (ptt90) REVERT: D 214 LYS cc_start: 0.9288 (ttpt) cc_final: 0.8709 (tppt) REVERT: D 222 VAL cc_start: 0.9395 (t) cc_final: 0.8924 (m) REVERT: D 223 MET cc_start: 0.8695 (mmm) cc_final: 0.8106 (mmm) REVERT: C 25 TYR cc_start: 0.8712 (t80) cc_final: 0.8095 (t80) REVERT: C 55 HIS cc_start: 0.8497 (t-90) cc_final: 0.8175 (m-70) REVERT: C 58 GLU cc_start: 0.8473 (pp20) cc_final: 0.8095 (pp20) REVERT: C 65 PHE cc_start: 0.8714 (t80) cc_final: 0.7774 (t80) REVERT: C 67 GLN cc_start: 0.8563 (pt0) cc_final: 0.7698 (pt0) REVERT: C 97 ASP cc_start: 0.8443 (p0) cc_final: 0.8112 (p0) REVERT: C 172 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7793 (mtp85) REVERT: C 186 ARG cc_start: 0.8308 (mmm160) cc_final: 0.7861 (mmm160) REVERT: A 16 ARG cc_start: 0.8576 (ptt180) cc_final: 0.8305 (ptt-90) REVERT: A 44 ILE cc_start: 0.8603 (pp) cc_final: 0.8337 (pp) REVERT: A 105 LYS cc_start: 0.8759 (tptt) cc_final: 0.8310 (pttp) REVERT: A 107 VAL cc_start: 0.7704 (m) cc_final: 0.7377 (p) REVERT: A 109 HIS cc_start: 0.8683 (m-70) cc_final: 0.8373 (m90) REVERT: A 113 MET cc_start: 0.8813 (mmm) cc_final: 0.8603 (mmm) REVERT: A 130 MET cc_start: 0.8446 (ptp) cc_final: 0.8058 (ptp) REVERT: A 144 ASP cc_start: 0.7596 (p0) cc_final: 0.6990 (p0) REVERT: A 150 HIS cc_start: 0.7114 (m-70) cc_final: 0.6753 (m90) REVERT: A 209 TYR cc_start: 0.8292 (m-10) cc_final: 0.7950 (m-10) REVERT: A 215 HIS cc_start: 0.8181 (m-70) cc_final: 0.7916 (m90) REVERT: A 287 TRP cc_start: 0.8738 (m100) cc_final: 0.8157 (m-10) REVERT: E 13 LYS cc_start: 0.9553 (ttmt) cc_final: 0.9242 (ttmt) REVERT: E 17 ASP cc_start: 0.9347 (m-30) cc_final: 0.9076 (m-30) REVERT: E 20 LEU cc_start: 0.9290 (mm) cc_final: 0.8815 (mm) REVERT: E 21 LYS cc_start: 0.9173 (tmtm) cc_final: 0.8758 (pptt) REVERT: E 30 ASP cc_start: 0.8855 (t0) cc_final: 0.8537 (t0) REVERT: E 41 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7632 (ttm170) REVERT: E 68 LYS cc_start: 0.9354 (mmmm) cc_final: 0.9082 (mmmm) REVERT: E 69 ASP cc_start: 0.8915 (t0) cc_final: 0.8388 (t70) REVERT: E 90 GLN cc_start: 0.8797 (mt0) cc_final: 0.8067 (tt0) REVERT: E 129 ARG cc_start: 0.8133 (ttt-90) cc_final: 0.7151 (ttp80) REVERT: E 133 THR cc_start: 0.9108 (m) cc_final: 0.8777 (p) REVERT: E 213 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.7628 (ptp-110) REVERT: E 342 TYR cc_start: 0.8164 (m-80) cc_final: 0.7922 (m-80) REVERT: B 17 ASP cc_start: 0.9490 (m-30) cc_final: 0.9227 (m-30) REVERT: B 37 ASP cc_start: 0.9078 (p0) cc_final: 0.8845 (p0) REVERT: B 41 ARG cc_start: 0.8720 (mtt90) cc_final: 0.7924 (mtt-85) REVERT: B 61 MET cc_start: 0.8458 (ppp) cc_final: 0.7445 (ppp) REVERT: B 63 PHE cc_start: 0.9134 (t80) cc_final: 0.8664 (t80) REVERT: B 89 ASP cc_start: 0.8849 (m-30) cc_final: 0.8520 (m-30) REVERT: B 112 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8432 (ttpp) REVERT: B 129 ARG cc_start: 0.8397 (ttp80) cc_final: 0.7233 (ttt-90) REVERT: B 133 THR cc_start: 0.9008 (m) cc_final: 0.8719 (p) REVERT: B 147 GLU cc_start: 0.9042 (tt0) cc_final: 0.8508 (tp30) REVERT: B 148 GLN cc_start: 0.7874 (mm110) cc_final: 0.7422 (mm110) REVERT: B 151 THR cc_start: 0.8328 (p) cc_final: 0.7214 (p) REVERT: B 153 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8065 (mp0) REVERT: B 169 ASN cc_start: 0.8728 (t0) cc_final: 0.7452 (t0) REVERT: B 213 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7484 (mtm180) REVERT: B 216 ARG cc_start: 0.9290 (ttm-80) cc_final: 0.7992 (ttp-170) REVERT: B 218 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8350 (mp) outliers start: 101 outliers final: 90 residues processed: 663 average time/residue: 0.2373 time to fit residues: 221.0761 Evaluate side-chains 713 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 620 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 331 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN E 64 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 217 ASN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12176 Z= 0.232 Angle : 0.778 12.227 16614 Z= 0.371 Chirality : 0.046 0.251 2058 Planarity : 0.004 0.047 2046 Dihedral : 8.069 72.143 2087 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 7.86 % Allowed : 28.58 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.22), residues: 1515 helix: 0.27 (0.24), residues: 454 sheet: -1.10 (0.25), residues: 415 loop : -1.83 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 168 HIS 0.009 0.001 HIS C 150 PHE 0.033 0.002 PHE B 221 TYR 0.037 0.002 TYR C 293 ARG 0.007 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 625 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.8881 (t0) cc_final: 0.8529 (t70) REVERT: D 54 HIS cc_start: 0.8972 (m-70) cc_final: 0.8604 (m-70) REVERT: D 88 LYS cc_start: 0.9157 (mttt) cc_final: 0.8915 (mtmm) REVERT: D 90 ASN cc_start: 0.7150 (t0) cc_final: 0.6345 (p0) REVERT: D 110 ASP cc_start: 0.8716 (t70) cc_final: 0.7935 (t70) REVERT: D 112 PHE cc_start: 0.8546 (p90) cc_final: 0.7712 (p90) REVERT: D 138 ARG cc_start: 0.8761 (ttp-170) cc_final: 0.8036 (ttp80) REVERT: D 172 TYR cc_start: 0.7570 (t80) cc_final: 0.6848 (t80) REVERT: D 182 GLN cc_start: 0.8230 (tp-100) cc_final: 0.7731 (tp-100) REVERT: D 207 ARG cc_start: 0.8963 (ptt90) cc_final: 0.8060 (ptt90) REVERT: D 214 LYS cc_start: 0.9318 (ttpt) cc_final: 0.8730 (tppt) REVERT: D 219 ASP cc_start: 0.9097 (t0) cc_final: 0.8844 (t0) REVERT: D 222 VAL cc_start: 0.9437 (t) cc_final: 0.8977 (m) REVERT: D 223 MET cc_start: 0.8711 (mmm) cc_final: 0.8061 (mmm) REVERT: C 25 TYR cc_start: 0.8694 (t80) cc_final: 0.8060 (t80) REVERT: C 55 HIS cc_start: 0.8717 (t-90) cc_final: 0.8482 (m-70) REVERT: C 58 GLU cc_start: 0.8515 (pp20) cc_final: 0.8126 (pp20) REVERT: C 65 PHE cc_start: 0.8734 (t80) cc_final: 0.7815 (t80) REVERT: C 67 GLN cc_start: 0.8480 (pt0) cc_final: 0.7732 (pt0) REVERT: C 97 ASP cc_start: 0.8470 (p0) cc_final: 0.8207 (p0) REVERT: C 165 GLU cc_start: 0.8957 (mm-30) cc_final: 0.7801 (mp0) REVERT: C 172 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7706 (mtp85) REVERT: C 186 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7234 (mmm160) REVERT: A 16 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8306 (ptt-90) REVERT: A 105 LYS cc_start: 0.8791 (tptt) cc_final: 0.8465 (pttp) REVERT: A 107 VAL cc_start: 0.7671 (m) cc_final: 0.7347 (p) REVERT: A 109 HIS cc_start: 0.8626 (m-70) cc_final: 0.8308 (m90) REVERT: A 113 MET cc_start: 0.8792 (mmm) cc_final: 0.8504 (mmm) REVERT: A 144 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.6878 (p0) REVERT: A 150 HIS cc_start: 0.6796 (m-70) cc_final: 0.6486 (m90) REVERT: A 215 HIS cc_start: 0.8193 (m-70) cc_final: 0.7883 (m90) REVERT: A 245 TRP cc_start: 0.7656 (m100) cc_final: 0.7010 (m100) REVERT: A 287 TRP cc_start: 0.8729 (m100) cc_final: 0.8121 (m-10) REVERT: E 13 LYS cc_start: 0.9422 (ttmt) cc_final: 0.9052 (ttmt) REVERT: E 17 ASP cc_start: 0.9323 (m-30) cc_final: 0.9060 (m-30) REVERT: E 20 LEU cc_start: 0.9335 (mm) cc_final: 0.8865 (mm) REVERT: E 21 LYS cc_start: 0.9168 (tmtm) cc_final: 0.8764 (pptt) REVERT: E 30 ASP cc_start: 0.8840 (t0) cc_final: 0.8502 (t0) REVERT: E 68 LYS cc_start: 0.9367 (mmmm) cc_final: 0.9075 (mmmm) REVERT: E 69 ASP cc_start: 0.8934 (t0) cc_final: 0.8531 (t70) REVERT: E 90 GLN cc_start: 0.8778 (mt0) cc_final: 0.8045 (tt0) REVERT: E 133 THR cc_start: 0.9136 (m) cc_final: 0.8840 (p) REVERT: E 194 VAL cc_start: 0.8734 (t) cc_final: 0.8497 (p) REVERT: E 213 ARG cc_start: 0.8510 (mtm-85) cc_final: 0.7655 (ptp-110) REVERT: E 342 TYR cc_start: 0.8032 (m-80) cc_final: 0.7773 (m-80) REVERT: B 17 ASP cc_start: 0.9475 (m-30) cc_final: 0.9220 (m-30) REVERT: B 41 ARG cc_start: 0.8658 (mtt90) cc_final: 0.7953 (mtt90) REVERT: B 61 MET cc_start: 0.8453 (ppp) cc_final: 0.7348 (ppp) REVERT: B 63 PHE cc_start: 0.9109 (t80) cc_final: 0.8570 (t80) REVERT: B 89 ASP cc_start: 0.8950 (m-30) cc_final: 0.8589 (m-30) REVERT: B 112 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8508 (ttpp) REVERT: B 129 ARG cc_start: 0.8349 (ttp80) cc_final: 0.7116 (ttt-90) REVERT: B 133 THR cc_start: 0.8988 (m) cc_final: 0.8654 (p) REVERT: B 142 ARG cc_start: 0.8631 (mtm180) cc_final: 0.8285 (mtm180) REVERT: B 146 ASP cc_start: 0.8872 (m-30) cc_final: 0.8651 (m-30) REVERT: B 147 GLU cc_start: 0.9056 (tt0) cc_final: 0.8531 (tp30) REVERT: B 151 THR cc_start: 0.8253 (p) cc_final: 0.7108 (p) REVERT: B 153 GLU cc_start: 0.8932 (mm-30) cc_final: 0.7990 (mp0) REVERT: B 169 ASN cc_start: 0.8746 (t0) cc_final: 0.7726 (t0) REVERT: B 213 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7420 (mtm180) REVERT: B 216 ARG cc_start: 0.9313 (ttm-80) cc_final: 0.8218 (ttp-170) outliers start: 96 outliers final: 82 residues processed: 647 average time/residue: 0.2414 time to fit residues: 221.9318 Evaluate side-chains 699 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 614 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 172 ARG Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 331 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 0.7980 chunk 16 optimal weight: 0.0040 chunk 82 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 overall best weight: 0.9754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 ASN E 64 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN B 64 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12176 Z= 0.209 Angle : 0.796 10.979 16614 Z= 0.375 Chirality : 0.046 0.255 2058 Planarity : 0.004 0.051 2046 Dihedral : 7.539 67.624 2087 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 6.96 % Allowed : 31.04 % Favored : 62.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.22), residues: 1515 helix: 0.20 (0.24), residues: 467 sheet: -0.94 (0.26), residues: 392 loop : -1.83 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 168 HIS 0.009 0.001 HIS C 150 PHE 0.015 0.001 PHE B 221 TYR 0.060 0.002 TYR C 293 ARG 0.007 0.001 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 624 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.8892 (t0) cc_final: 0.8548 (t70) REVERT: D 54 HIS cc_start: 0.8967 (m-70) cc_final: 0.8611 (m-70) REVERT: D 88 LYS cc_start: 0.9152 (mttt) cc_final: 0.8907 (mtmm) REVERT: D 90 ASN cc_start: 0.7166 (t0) cc_final: 0.6358 (p0) REVERT: D 110 ASP cc_start: 0.8705 (t70) cc_final: 0.8032 (t70) REVERT: D 112 PHE cc_start: 0.8614 (p90) cc_final: 0.7726 (p90) REVERT: D 138 ARG cc_start: 0.8816 (ttp-170) cc_final: 0.8116 (ttp80) REVERT: D 172 TYR cc_start: 0.7675 (t80) cc_final: 0.7018 (t80) REVERT: D 182 GLN cc_start: 0.8260 (tp-100) cc_final: 0.7810 (tp-100) REVERT: D 207 ARG cc_start: 0.8985 (ptt90) cc_final: 0.8055 (ptt90) REVERT: D 214 LYS cc_start: 0.9319 (ttpt) cc_final: 0.8759 (tppt) REVERT: D 219 ASP cc_start: 0.9099 (t0) cc_final: 0.8861 (t0) REVERT: D 222 VAL cc_start: 0.9435 (t) cc_final: 0.8956 (m) REVERT: D 223 MET cc_start: 0.8713 (mmm) cc_final: 0.8033 (mmm) REVERT: C 25 TYR cc_start: 0.8618 (t80) cc_final: 0.7907 (t80) REVERT: C 30 ARG cc_start: 0.9342 (ptt90) cc_final: 0.9042 (ptt90) REVERT: C 55 HIS cc_start: 0.8729 (t-90) cc_final: 0.8492 (m-70) REVERT: C 58 GLU cc_start: 0.8557 (pp20) cc_final: 0.8181 (pp20) REVERT: C 65 PHE cc_start: 0.8659 (t80) cc_final: 0.7836 (t80) REVERT: C 67 GLN cc_start: 0.8369 (pt0) cc_final: 0.7832 (pt0) REVERT: C 70 LYS cc_start: 0.7926 (tmtm) cc_final: 0.7691 (tmtm) REVERT: C 106 SER cc_start: 0.9110 (m) cc_final: 0.8827 (p) REVERT: C 165 GLU cc_start: 0.8936 (mm-30) cc_final: 0.7756 (mp0) REVERT: C 285 MET cc_start: 0.7152 (mtt) cc_final: 0.6938 (mpt) REVERT: A 16 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8343 (ptt-90) REVERT: A 44 ILE cc_start: 0.8703 (pp) cc_final: 0.8477 (pp) REVERT: A 105 LYS cc_start: 0.8792 (tptt) cc_final: 0.8457 (pttp) REVERT: A 107 VAL cc_start: 0.7718 (m) cc_final: 0.7423 (p) REVERT: A 109 HIS cc_start: 0.8597 (m-70) cc_final: 0.8294 (m90) REVERT: A 113 MET cc_start: 0.8771 (mmm) cc_final: 0.8483 (mmm) REVERT: A 144 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6786 (p0) REVERT: A 150 HIS cc_start: 0.6757 (m-70) cc_final: 0.6465 (m90) REVERT: A 209 TYR cc_start: 0.8028 (m-10) cc_final: 0.7747 (m-10) REVERT: A 215 HIS cc_start: 0.8070 (m-70) cc_final: 0.7732 (m90) REVERT: A 221 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8396 (mmmm) REVERT: A 287 TRP cc_start: 0.8773 (m100) cc_final: 0.8175 (m-10) REVERT: E 13 LYS cc_start: 0.9386 (ttmt) cc_final: 0.9032 (ttmt) REVERT: E 17 ASP cc_start: 0.9338 (m-30) cc_final: 0.9068 (m-30) REVERT: E 20 LEU cc_start: 0.9377 (mm) cc_final: 0.8907 (mm) REVERT: E 21 LYS cc_start: 0.9162 (tmtm) cc_final: 0.8767 (pptt) REVERT: E 30 ASP cc_start: 0.8842 (t0) cc_final: 0.8485 (t0) REVERT: E 68 LYS cc_start: 0.9380 (mmmm) cc_final: 0.9081 (mmmm) REVERT: E 69 ASP cc_start: 0.8909 (t0) cc_final: 0.8494 (t70) REVERT: E 90 GLN cc_start: 0.8682 (mt0) cc_final: 0.7965 (tt0) REVERT: E 133 THR cc_start: 0.9123 (m) cc_final: 0.8830 (p) REVERT: E 167 TYR cc_start: 0.8585 (p90) cc_final: 0.8233 (p90) REVERT: E 196 LYS cc_start: 0.8106 (ptpp) cc_final: 0.7732 (ptpp) REVERT: E 213 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.7635 (ptp-110) REVERT: E 342 TYR cc_start: 0.8073 (m-80) cc_final: 0.7803 (m-80) REVERT: B 17 ASP cc_start: 0.9399 (m-30) cc_final: 0.9085 (m-30) REVERT: B 18 ARG cc_start: 0.9366 (ptm-80) cc_final: 0.8994 (ttp-110) REVERT: B 41 ARG cc_start: 0.8707 (mtt90) cc_final: 0.7982 (mtt-85) REVERT: B 61 MET cc_start: 0.8511 (ppp) cc_final: 0.7315 (ppp) REVERT: B 63 PHE cc_start: 0.9107 (t80) cc_final: 0.8614 (t80) REVERT: B 89 ASP cc_start: 0.8964 (m-30) cc_final: 0.8604 (m-30) REVERT: B 112 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8507 (ttpp) REVERT: B 133 THR cc_start: 0.8980 (m) cc_final: 0.8652 (p) REVERT: B 142 ARG cc_start: 0.8569 (mtm180) cc_final: 0.8251 (mtm180) REVERT: B 146 ASP cc_start: 0.8853 (m-30) cc_final: 0.8649 (m-30) REVERT: B 147 GLU cc_start: 0.9078 (tt0) cc_final: 0.8088 (tp30) REVERT: B 151 THR cc_start: 0.8199 (p) cc_final: 0.7126 (p) REVERT: B 153 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8173 (mp0) REVERT: B 169 ASN cc_start: 0.8779 (t0) cc_final: 0.7549 (t0) REVERT: B 213 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.5994 (mmm-85) REVERT: B 216 ARG cc_start: 0.9287 (ttm-80) cc_final: 0.7968 (ttp-170) outliers start: 85 outliers final: 72 residues processed: 649 average time/residue: 0.2406 time to fit residues: 221.8357 Evaluate side-chains 686 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 612 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 91 optimal weight: 0.0170 chunk 97 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12176 Z= 0.200 Angle : 0.817 12.233 16614 Z= 0.380 Chirality : 0.046 0.253 2058 Planarity : 0.004 0.049 2046 Dihedral : 7.084 62.794 2087 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 6.31 % Allowed : 32.27 % Favored : 61.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1515 helix: 0.32 (0.24), residues: 467 sheet: -0.87 (0.26), residues: 396 loop : -1.70 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B 168 HIS 0.009 0.001 HIS C 150 PHE 0.034 0.001 PHE B 221 TYR 0.029 0.002 TYR A 128 ARG 0.007 0.001 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 629 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.8900 (t0) cc_final: 0.8577 (t70) REVERT: D 54 HIS cc_start: 0.8969 (m-70) cc_final: 0.8689 (m-70) REVERT: D 88 LYS cc_start: 0.9144 (mttt) cc_final: 0.8902 (mtmm) REVERT: D 90 ASN cc_start: 0.7170 (t0) cc_final: 0.6380 (p0) REVERT: D 110 ASP cc_start: 0.8721 (t70) cc_final: 0.8089 (t70) REVERT: D 112 PHE cc_start: 0.8621 (p90) cc_final: 0.7730 (p90) REVERT: D 138 ARG cc_start: 0.8844 (ttp-170) cc_final: 0.8193 (ttp80) REVERT: D 172 TYR cc_start: 0.7649 (t80) cc_final: 0.7033 (t80) REVERT: D 207 ARG cc_start: 0.9069 (ptt90) cc_final: 0.8434 (ptt90) REVERT: D 214 LYS cc_start: 0.9313 (ttpt) cc_final: 0.8787 (tppt) REVERT: D 219 ASP cc_start: 0.9071 (t0) cc_final: 0.8832 (t0) REVERT: D 222 VAL cc_start: 0.9427 (t) cc_final: 0.8950 (m) REVERT: D 223 MET cc_start: 0.8666 (mmm) cc_final: 0.7921 (mmm) REVERT: C 25 TYR cc_start: 0.8616 (t80) cc_final: 0.7954 (t80) REVERT: C 55 HIS cc_start: 0.8738 (t-90) cc_final: 0.8517 (m-70) REVERT: C 58 GLU cc_start: 0.8549 (pp20) cc_final: 0.8175 (pp20) REVERT: C 65 PHE cc_start: 0.8623 (t80) cc_final: 0.7833 (t80) REVERT: C 67 GLN cc_start: 0.8179 (pt0) cc_final: 0.7830 (pt0) REVERT: C 70 LYS cc_start: 0.7973 (tmtm) cc_final: 0.7700 (tmtm) REVERT: C 118 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8652 (mp) REVERT: C 186 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7789 (mmm160) REVERT: C 189 GLN cc_start: 0.8798 (pm20) cc_final: 0.8511 (pm20) REVERT: A 16 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8344 (ptt-90) REVERT: A 105 LYS cc_start: 0.8711 (tptt) cc_final: 0.8368 (pttp) REVERT: A 107 VAL cc_start: 0.7649 (m) cc_final: 0.7353 (p) REVERT: A 109 HIS cc_start: 0.8566 (m-70) cc_final: 0.8299 (m90) REVERT: A 113 MET cc_start: 0.8728 (mmm) cc_final: 0.8451 (mmm) REVERT: A 144 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6872 (p0) REVERT: A 150 HIS cc_start: 0.6896 (m-70) cc_final: 0.6643 (m90) REVERT: A 209 TYR cc_start: 0.7957 (m-10) cc_final: 0.7622 (m-10) REVERT: A 215 HIS cc_start: 0.7934 (m-70) cc_final: 0.7602 (m90) REVERT: A 220 ARG cc_start: 0.8783 (tpp80) cc_final: 0.7843 (ttm-80) REVERT: A 221 LYS cc_start: 0.8729 (mmmm) cc_final: 0.8487 (mmmm) REVERT: A 241 GLN cc_start: 0.9083 (tp-100) cc_final: 0.7844 (tp-100) REVERT: A 245 TRP cc_start: 0.7652 (m100) cc_final: 0.6474 (m100) REVERT: A 287 TRP cc_start: 0.8743 (m100) cc_final: 0.8117 (m-10) REVERT: E 13 LYS cc_start: 0.9381 (ttmt) cc_final: 0.9015 (ttmt) REVERT: E 17 ASP cc_start: 0.9339 (m-30) cc_final: 0.9066 (m-30) REVERT: E 20 LEU cc_start: 0.9373 (mm) cc_final: 0.8900 (mm) REVERT: E 21 LYS cc_start: 0.9124 (tmtm) cc_final: 0.8718 (pptt) REVERT: E 30 ASP cc_start: 0.8862 (t0) cc_final: 0.8493 (t0) REVERT: E 68 LYS cc_start: 0.9387 (mmmm) cc_final: 0.9086 (mmmm) REVERT: E 69 ASP cc_start: 0.8873 (t0) cc_final: 0.8435 (t70) REVERT: E 90 GLN cc_start: 0.8739 (mt0) cc_final: 0.8110 (tt0) REVERT: E 133 THR cc_start: 0.9104 (m) cc_final: 0.8813 (p) REVERT: E 167 TYR cc_start: 0.8573 (p90) cc_final: 0.8298 (p90) REVERT: E 213 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.7643 (ptp-110) REVERT: E 216 ARG cc_start: 0.8658 (ttp-170) cc_final: 0.8163 (ttp-170) REVERT: E 299 TYR cc_start: 0.7490 (t80) cc_final: 0.7173 (t80) REVERT: E 342 TYR cc_start: 0.8074 (m-80) cc_final: 0.7799 (m-80) REVERT: B 17 ASP cc_start: 0.9459 (m-30) cc_final: 0.9171 (m-30) REVERT: B 18 ARG cc_start: 0.9344 (ptm-80) cc_final: 0.8969 (ttp-110) REVERT: B 41 ARG cc_start: 0.8801 (mtt90) cc_final: 0.8003 (mtt-85) REVERT: B 61 MET cc_start: 0.8524 (ppp) cc_final: 0.7359 (ppp) REVERT: B 63 PHE cc_start: 0.9086 (t80) cc_final: 0.8615 (t80) REVERT: B 89 ASP cc_start: 0.8994 (m-30) cc_final: 0.8645 (m-30) REVERT: B 112 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8515 (ttpp) REVERT: B 126 TYR cc_start: 0.8366 (t80) cc_final: 0.8040 (t80) REVERT: B 133 THR cc_start: 0.8961 (m) cc_final: 0.8636 (p) REVERT: B 142 ARG cc_start: 0.8460 (mtm180) cc_final: 0.8164 (mtm180) REVERT: B 147 GLU cc_start: 0.9086 (tt0) cc_final: 0.7997 (tp30) REVERT: B 153 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8256 (mp0) REVERT: B 169 ASN cc_start: 0.8785 (t0) cc_final: 0.7641 (t0) REVERT: B 205 TYR cc_start: 0.8706 (m-80) cc_final: 0.8455 (m-80) REVERT: B 213 ARG cc_start: 0.7146 (mtm-85) cc_final: 0.5916 (mmm-85) REVERT: B 216 ARG cc_start: 0.9252 (ttm-80) cc_final: 0.8128 (ttp-170) REVERT: B 291 PHE cc_start: 0.8760 (m-80) cc_final: 0.8535 (m-80) REVERT: B 342 TYR cc_start: 0.7881 (t80) cc_final: 0.7679 (t80) outliers start: 77 outliers final: 67 residues processed: 654 average time/residue: 0.2455 time to fit residues: 226.8995 Evaluate side-chains 700 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 630 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 16 ARG Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 0.5980 chunk 137 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 126 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN B 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12176 Z= 0.204 Angle : 0.819 13.039 16614 Z= 0.382 Chirality : 0.046 0.247 2058 Planarity : 0.004 0.052 2046 Dihedral : 6.668 57.322 2087 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 6.14 % Allowed : 32.51 % Favored : 61.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1515 helix: 0.42 (0.24), residues: 461 sheet: -0.84 (0.26), residues: 397 loop : -1.67 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP B 168 HIS 0.007 0.001 HIS C 150 PHE 0.023 0.001 PHE B 221 TYR 0.032 0.002 TYR B 220 ARG 0.005 0.001 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 635 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.8882 (t0) cc_final: 0.8578 (t70) REVERT: D 54 HIS cc_start: 0.8969 (m-70) cc_final: 0.8677 (m-70) REVERT: D 88 LYS cc_start: 0.9131 (mttt) cc_final: 0.8883 (mtmm) REVERT: D 90 ASN cc_start: 0.7068 (t0) cc_final: 0.6278 (p0) REVERT: D 110 ASP cc_start: 0.8760 (t70) cc_final: 0.8157 (t70) REVERT: D 112 PHE cc_start: 0.8634 (p90) cc_final: 0.7758 (p90) REVERT: D 138 ARG cc_start: 0.8849 (ttp-170) cc_final: 0.8217 (ttp80) REVERT: D 172 TYR cc_start: 0.7570 (t80) cc_final: 0.7128 (t80) REVERT: D 207 ARG cc_start: 0.9066 (ptt90) cc_final: 0.8425 (ptt90) REVERT: D 214 LYS cc_start: 0.9266 (ttpt) cc_final: 0.8747 (tppt) REVERT: D 219 ASP cc_start: 0.9093 (t0) cc_final: 0.8874 (t0) REVERT: D 222 VAL cc_start: 0.9422 (t) cc_final: 0.9184 (m) REVERT: D 223 MET cc_start: 0.8597 (mmm) cc_final: 0.8270 (mmp) REVERT: C 25 TYR cc_start: 0.8640 (t80) cc_final: 0.7957 (t80) REVERT: C 30 ARG cc_start: 0.9376 (ptt90) cc_final: 0.8596 (ppt90) REVERT: C 55 HIS cc_start: 0.8748 (t-90) cc_final: 0.8524 (m-70) REVERT: C 58 GLU cc_start: 0.8534 (pp20) cc_final: 0.8090 (pp20) REVERT: C 65 PHE cc_start: 0.8561 (t80) cc_final: 0.7869 (t80) REVERT: C 70 LYS cc_start: 0.7997 (tmtm) cc_final: 0.7751 (tmtm) REVERT: C 102 ASN cc_start: 0.8587 (p0) cc_final: 0.6903 (t0) REVERT: C 118 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8672 (mp) REVERT: C 165 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8273 (mm-30) REVERT: C 186 ARG cc_start: 0.8252 (mmm160) cc_final: 0.7729 (mmm160) REVERT: C 189 GLN cc_start: 0.8719 (pm20) cc_final: 0.8433 (pm20) REVERT: A 102 ASN cc_start: 0.7618 (t0) cc_final: 0.7228 (t0) REVERT: A 105 LYS cc_start: 0.8719 (tptt) cc_final: 0.8315 (pttp) REVERT: A 107 VAL cc_start: 0.7634 (m) cc_final: 0.7318 (p) REVERT: A 109 HIS cc_start: 0.8607 (m-70) cc_final: 0.8366 (m90) REVERT: A 113 MET cc_start: 0.8692 (mmm) cc_final: 0.8410 (mmm) REVERT: A 144 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6725 (p0) REVERT: A 150 HIS cc_start: 0.6831 (m-70) cc_final: 0.6581 (m90) REVERT: A 209 TYR cc_start: 0.7864 (m-10) cc_final: 0.7458 (m-10) REVERT: A 215 HIS cc_start: 0.7910 (m-70) cc_final: 0.7562 (m90) REVERT: A 220 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8027 (ttm-80) REVERT: A 241 GLN cc_start: 0.9073 (tp-100) cc_final: 0.7838 (tp-100) REVERT: A 245 TRP cc_start: 0.7648 (m100) cc_final: 0.6452 (m100) REVERT: A 287 TRP cc_start: 0.8746 (m100) cc_final: 0.8112 (m-10) REVERT: E 13 LYS cc_start: 0.9377 (ttmt) cc_final: 0.9014 (ttmt) REVERT: E 17 ASP cc_start: 0.9275 (m-30) cc_final: 0.8970 (m-30) REVERT: E 20 LEU cc_start: 0.9372 (mm) cc_final: 0.8860 (mm) REVERT: E 21 LYS cc_start: 0.9135 (tmtm) cc_final: 0.8740 (pptt) REVERT: E 30 ASP cc_start: 0.8899 (t0) cc_final: 0.8539 (t0) REVERT: E 68 LYS cc_start: 0.9390 (mmmm) cc_final: 0.9088 (mmmm) REVERT: E 69 ASP cc_start: 0.8861 (t0) cc_final: 0.8434 (t70) REVERT: E 90 GLN cc_start: 0.8742 (mt0) cc_final: 0.8006 (tt0) REVERT: E 133 THR cc_start: 0.9133 (m) cc_final: 0.8804 (p) REVERT: E 167 TYR cc_start: 0.8562 (p90) cc_final: 0.8271 (p90) REVERT: E 213 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.7639 (ptp-110) REVERT: E 216 ARG cc_start: 0.8722 (ttp-170) cc_final: 0.8249 (ttp-170) REVERT: E 299 TYR cc_start: 0.7595 (t80) cc_final: 0.7330 (t80) REVERT: E 342 TYR cc_start: 0.8068 (m-80) cc_final: 0.7760 (m-80) REVERT: B 17 ASP cc_start: 0.9454 (m-30) cc_final: 0.9167 (m-30) REVERT: B 18 ARG cc_start: 0.9357 (ptm-80) cc_final: 0.8986 (ttp-110) REVERT: B 41 ARG cc_start: 0.8769 (mtt90) cc_final: 0.8096 (mtt90) REVERT: B 61 MET cc_start: 0.8532 (ppp) cc_final: 0.7462 (ppp) REVERT: B 63 PHE cc_start: 0.9068 (t80) cc_final: 0.8590 (t80) REVERT: B 71 ARG cc_start: 0.8955 (ttp80) cc_final: 0.8695 (ttp80) REVERT: B 89 ASP cc_start: 0.9009 (m-30) cc_final: 0.8659 (m-30) REVERT: B 112 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8502 (ttpp) REVERT: B 126 TYR cc_start: 0.8408 (t80) cc_final: 0.8096 (t80) REVERT: B 130 ILE cc_start: 0.8214 (pp) cc_final: 0.7602 (mm) REVERT: B 133 THR cc_start: 0.8936 (m) cc_final: 0.8611 (p) REVERT: B 142 ARG cc_start: 0.8457 (mtm180) cc_final: 0.8144 (mtm180) REVERT: B 147 GLU cc_start: 0.9011 (tt0) cc_final: 0.8306 (tp30) REVERT: B 153 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8089 (mp0) REVERT: B 169 ASN cc_start: 0.8728 (t0) cc_final: 0.7675 (t0) REVERT: B 205 TYR cc_start: 0.8901 (m-80) cc_final: 0.8467 (m-80) REVERT: B 216 ARG cc_start: 0.9231 (ttm-80) cc_final: 0.8064 (ttp-170) REVERT: B 241 TRP cc_start: 0.8927 (m100) cc_final: 0.8292 (t-100) outliers start: 75 outliers final: 67 residues processed: 659 average time/residue: 0.2375 time to fit residues: 219.3990 Evaluate side-chains 699 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 630 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 0.0470 chunk 86 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN B 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12176 Z= 0.220 Angle : 0.835 13.492 16614 Z= 0.390 Chirality : 0.046 0.236 2058 Planarity : 0.004 0.051 2046 Dihedral : 6.368 50.941 2087 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.49 % Allowed : 33.42 % Favored : 61.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1515 helix: 0.47 (0.24), residues: 461 sheet: -0.79 (0.26), residues: 394 loop : -1.69 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 168 HIS 0.007 0.001 HIS C 150 PHE 0.036 0.002 PHE B 221 TYR 0.024 0.002 TYR E 126 ARG 0.007 0.001 ARG D 132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 631 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 ASP cc_start: 0.8886 (t0) cc_final: 0.8593 (t70) REVERT: D 54 HIS cc_start: 0.8969 (m-70) cc_final: 0.8735 (m90) REVERT: D 88 LYS cc_start: 0.9134 (mttt) cc_final: 0.8885 (mtmm) REVERT: D 90 ASN cc_start: 0.6985 (t0) cc_final: 0.6315 (p0) REVERT: D 110 ASP cc_start: 0.8785 (t70) cc_final: 0.8198 (t70) REVERT: D 112 PHE cc_start: 0.8619 (p90) cc_final: 0.7651 (p90) REVERT: D 138 ARG cc_start: 0.8836 (ttp-170) cc_final: 0.8164 (ttp80) REVERT: D 139 VAL cc_start: 0.9656 (t) cc_final: 0.9391 (p) REVERT: D 172 TYR cc_start: 0.7580 (t80) cc_final: 0.7153 (t80) REVERT: D 207 ARG cc_start: 0.9060 (ptt90) cc_final: 0.8406 (ptt90) REVERT: D 214 LYS cc_start: 0.9261 (ttpt) cc_final: 0.8755 (tppt) REVERT: D 222 VAL cc_start: 0.9425 (t) cc_final: 0.9185 (m) REVERT: D 223 MET cc_start: 0.8648 (mmm) cc_final: 0.8326 (mmp) REVERT: C 25 TYR cc_start: 0.8650 (t80) cc_final: 0.7963 (t80) REVERT: C 30 ARG cc_start: 0.9394 (ptt90) cc_final: 0.8612 (ppt90) REVERT: C 55 HIS cc_start: 0.8748 (t-90) cc_final: 0.8514 (m-70) REVERT: C 58 GLU cc_start: 0.8550 (pp20) cc_final: 0.8110 (pp20) REVERT: C 70 LYS cc_start: 0.7989 (tmtm) cc_final: 0.7743 (tmtm) REVERT: C 111 MET cc_start: 0.8488 (mmm) cc_final: 0.7876 (mmm) REVERT: C 118 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8774 (mp) REVERT: C 135 ARG cc_start: 0.8027 (ptp-170) cc_final: 0.7625 (ptp-110) REVERT: C 165 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8260 (mm-30) REVERT: C 186 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7819 (mmm160) REVERT: C 189 GLN cc_start: 0.8713 (pm20) cc_final: 0.8414 (pm20) REVERT: A 23 ASP cc_start: 0.9197 (t0) cc_final: 0.8765 (m-30) REVERT: A 102 ASN cc_start: 0.7684 (t0) cc_final: 0.7233 (t0) REVERT: A 105 LYS cc_start: 0.8647 (tptt) cc_final: 0.8245 (pttm) REVERT: A 107 VAL cc_start: 0.7685 (m) cc_final: 0.7389 (p) REVERT: A 109 HIS cc_start: 0.8633 (m-70) cc_final: 0.8385 (m90) REVERT: A 113 MET cc_start: 0.8718 (mmm) cc_final: 0.8453 (mmm) REVERT: A 144 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6864 (p0) REVERT: A 150 HIS cc_start: 0.6862 (m-70) cc_final: 0.6627 (m90) REVERT: A 209 TYR cc_start: 0.7878 (m-10) cc_final: 0.7503 (m-10) REVERT: A 215 HIS cc_start: 0.7690 (m-70) cc_final: 0.7352 (m90) REVERT: A 220 ARG cc_start: 0.8735 (tpp80) cc_final: 0.7633 (ttm-80) REVERT: A 221 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7437 (mmtp) REVERT: A 241 GLN cc_start: 0.9065 (tp-100) cc_final: 0.7848 (tp-100) REVERT: A 245 TRP cc_start: 0.7622 (m100) cc_final: 0.6448 (m100) REVERT: A 287 TRP cc_start: 0.8759 (m100) cc_final: 0.8113 (m-10) REVERT: E 13 LYS cc_start: 0.9379 (ttmt) cc_final: 0.9011 (ttmt) REVERT: E 17 ASP cc_start: 0.9269 (m-30) cc_final: 0.8939 (m-30) REVERT: E 20 LEU cc_start: 0.9315 (mm) cc_final: 0.8829 (mm) REVERT: E 21 LYS cc_start: 0.9111 (tmtm) cc_final: 0.8735 (pptt) REVERT: E 30 ASP cc_start: 0.8849 (t0) cc_final: 0.8492 (t0) REVERT: E 68 LYS cc_start: 0.9398 (mmmm) cc_final: 0.9087 (mmmm) REVERT: E 69 ASP cc_start: 0.8836 (t0) cc_final: 0.8421 (t70) REVERT: E 90 GLN cc_start: 0.8828 (mt0) cc_final: 0.8185 (tt0) REVERT: E 133 THR cc_start: 0.9075 (m) cc_final: 0.8728 (p) REVERT: E 167 TYR cc_start: 0.8529 (p90) cc_final: 0.8212 (p90) REVERT: E 213 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.7671 (ptp-110) REVERT: E 216 ARG cc_start: 0.8733 (ttp-170) cc_final: 0.8266 (ttp-170) REVERT: E 299 TYR cc_start: 0.7604 (t80) cc_final: 0.7341 (t80) REVERT: E 342 TYR cc_start: 0.8075 (m-80) cc_final: 0.7807 (m-80) REVERT: B 17 ASP cc_start: 0.9414 (m-30) cc_final: 0.9137 (m-30) REVERT: B 18 ARG cc_start: 0.9355 (ptm-80) cc_final: 0.9000 (ttp-110) REVERT: B 41 ARG cc_start: 0.8796 (mtt90) cc_final: 0.7919 (mtt-85) REVERT: B 61 MET cc_start: 0.8534 (ppp) cc_final: 0.7375 (ppp) REVERT: B 63 PHE cc_start: 0.9068 (t80) cc_final: 0.8617 (t80) REVERT: B 71 ARG cc_start: 0.8944 (ttp80) cc_final: 0.8696 (ttp80) REVERT: B 89 ASP cc_start: 0.9033 (m-30) cc_final: 0.8671 (m-30) REVERT: B 90 GLN cc_start: 0.8946 (mm110) cc_final: 0.8734 (mm110) REVERT: B 126 TYR cc_start: 0.8450 (t80) cc_final: 0.8106 (t80) REVERT: B 133 THR cc_start: 0.8842 (m) cc_final: 0.8469 (p) REVERT: B 142 ARG cc_start: 0.8447 (mtm180) cc_final: 0.8155 (mtm180) REVERT: B 147 GLU cc_start: 0.9005 (tt0) cc_final: 0.8265 (tp30) REVERT: B 153 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8069 (mp0) REVERT: B 169 ASN cc_start: 0.8706 (t0) cc_final: 0.7325 (t0) REVERT: B 205 TYR cc_start: 0.8761 (m-80) cc_final: 0.8383 (m-80) REVERT: B 215 LYS cc_start: 0.8620 (tmtt) cc_final: 0.8314 (tptp) REVERT: B 216 ARG cc_start: 0.9210 (ttm-80) cc_final: 0.8024 (ttp-170) REVERT: B 241 TRP cc_start: 0.8909 (m100) cc_final: 0.8303 (t-100) outliers start: 67 outliers final: 64 residues processed: 652 average time/residue: 0.2424 time to fit residues: 220.4666 Evaluate side-chains 694 residues out of total 1382 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 628 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 121 optimal weight: 0.0000 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.0370 chunk 103 optimal weight: 3.9990 overall best weight: 0.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.155566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115627 restraints weight = 22430.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120220 restraints weight = 12402.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123331 restraints weight = 8202.079| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12176 Z= 0.203 Angle : 0.844 13.892 16614 Z= 0.393 Chirality : 0.046 0.225 2058 Planarity : 0.004 0.053 2046 Dihedral : 6.096 46.540 2087 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.91 % Allowed : 34.40 % Favored : 60.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.22), residues: 1515 helix: 0.44 (0.24), residues: 461 sheet: -0.95 (0.25), residues: 406 loop : -1.57 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP B 168 HIS 0.006 0.001 HIS E 267 PHE 0.035 0.002 PHE B 221 TYR 0.024 0.002 TYR E 126 ARG 0.007 0.001 ARG D 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4077.30 seconds wall clock time: 73 minutes 49.19 seconds (4429.19 seconds total)