Starting phenix.real_space_refine on Thu Jul 31 08:45:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ijq_35492/07_2025/8ijq_35492.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijq_35492/07_2025/8ijq_35492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ijq_35492/07_2025/8ijq_35492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijq_35492/07_2025/8ijq_35492.map" model { file = "/net/cci-nas-00/data/ceres_data/8ijq_35492/07_2025/8ijq_35492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijq_35492/07_2025/8ijq_35492.cif" } resolution = 3.45 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= 0.003 sd= 0.086 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 114 5.16 5 C 8994 2.51 5 N 2130 2.21 5 O 2142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13380 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "B" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "C" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "D" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "E" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "F" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'16C': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'16C': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'16C': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'16C': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'16C': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'16C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.93, per 1000 atoms: 0.67 Number of scatterers: 13380 At special positions: 0 Unit cell: (161.7, 122.1, 79.2, 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 114 16.00 O 2142 8.00 N 2130 7.00 C 8994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 293 " distance=2.04 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 293 " distance=2.04 Simple disulfide: pdb=" SG CYS E 261 " - pdb=" SG CYS E 293 " distance=2.04 Simple disulfide: pdb=" SG CYS F 261 " - pdb=" SG CYS F 293 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.7 seconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 0 sheets defined 60.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 151 through 177 removed outlier: 4.325A pdb=" N VAL A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 221 removed outlier: 3.909A pdb=" N GLU A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 250 removed outlier: 3.805A pdb=" N CYS A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 299 through 315 removed outlier: 3.972A pdb=" N VAL A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 341 Processing helix chain 'A' and resid 345 through 370 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'B' and resid 150 through 175 removed outlier: 3.611A pdb=" N LEU B 154 " --> pdb=" O TRP B 150 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 221 removed outlier: 3.637A pdb=" N MET B 203 " --> pdb=" O TRP B 199 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 206 " --> pdb=" O ALA B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 250 removed outlier: 3.587A pdb=" N LEU B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 237 " --> pdb=" O CYS B 233 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 281 Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.921A pdb=" N VAL B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 341 removed outlier: 3.548A pdb=" N ILE B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 368 removed outlier: 3.576A pdb=" N VAL B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.431A pdb=" N SER B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'C' and resid 148 through 177 removed outlier: 3.846A pdb=" N THR C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE C 153 " --> pdb=" O TYR C 149 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 154 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 172 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 177 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 221 removed outlier: 3.736A pdb=" N MET C 203 " --> pdb=" O TRP C 199 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C 204 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 250 removed outlier: 3.645A pdb=" N ARG C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C 237 " --> pdb=" O CYS C 233 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 281 Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.946A pdb=" N VAL C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 305 " --> pdb=" O HIS C 301 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 341 removed outlier: 3.566A pdb=" N ASN C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 338 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 370 removed outlier: 3.706A pdb=" N VAL C 349 " --> pdb=" O TYR C 345 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 355 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 removed outlier: 3.738A pdb=" N GLN C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 370 through 375' Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.691A pdb=" N PHE C 388 " --> pdb=" O MET C 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 175 removed outlier: 3.646A pdb=" N LEU D 154 " --> pdb=" O TRP D 150 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE D 160 " --> pdb=" O CYS D 156 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU D 175 " --> pdb=" O VAL D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 203 through 221 Processing helix chain 'D' and resid 224 through 250 removed outlier: 3.915A pdb=" N LEU D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR D 250 " --> pdb=" O THR D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 removed outlier: 3.895A pdb=" N HIS D 274 " --> pdb=" O TRP D 270 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 315 removed outlier: 3.893A pdb=" N VAL D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 341 removed outlier: 3.561A pdb=" N LEU D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 339 " --> pdb=" O ILE D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 370 removed outlier: 3.726A pdb=" N VAL D 349 " --> pdb=" O TYR D 345 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE D 351 " --> pdb=" O ILE D 347 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 355 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR D 356 " --> pdb=" O ALA D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 375 removed outlier: 3.748A pdb=" N GLN D 374 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 375' Processing helix chain 'D' and resid 385 through 390 Processing helix chain 'E' and resid 148 through 177 removed outlier: 3.957A pdb=" N THR E 152 " --> pdb=" O GLU E 148 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE E 153 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 154 " --> pdb=" O TRP E 150 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE E 160 " --> pdb=" O CYS E 156 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE E 172 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU E 175 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL E 177 " --> pdb=" O VAL E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 221 removed outlier: 3.676A pdb=" N GLY E 208 " --> pdb=" O THR E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 250 removed outlier: 3.925A pdb=" N LEU E 228 " --> pdb=" O HIS E 224 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU E 241 " --> pdb=" O GLY E 237 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR E 250 " --> pdb=" O THR E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 281 removed outlier: 3.993A pdb=" N ARG E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 315 removed outlier: 3.891A pdb=" N VAL E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 341 removed outlier: 3.711A pdb=" N LEU E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 370 removed outlier: 3.781A pdb=" N VAL E 349 " --> pdb=" O TYR E 345 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 390 removed outlier: 3.826A pdb=" N PHE E 388 " --> pdb=" O MET E 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 177 removed outlier: 4.146A pdb=" N ILE F 153 " --> pdb=" O TYR F 149 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 154 " --> pdb=" O TRP F 150 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL F 159 " --> pdb=" O SER F 155 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE F 160 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET F 170 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE F 172 " --> pdb=" O PHE F 168 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL F 177 " --> pdb=" O VAL F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 221 removed outlier: 3.704A pdb=" N MET F 203 " --> pdb=" O TRP F 199 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU F 205 " --> pdb=" O PHE F 201 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE F 210 " --> pdb=" O VAL F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 250 removed outlier: 3.691A pdb=" N THR F 238 " --> pdb=" O SER F 234 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET F 247 " --> pdb=" O ARG F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 281 Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.984A pdb=" N VAL F 303 " --> pdb=" O SER F 299 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU F 305 " --> pdb=" O HIS F 301 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL F 312 " --> pdb=" O LEU F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 341 removed outlier: 3.588A pdb=" N LEU F 339 " --> pdb=" O ILE F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 369 removed outlier: 3.725A pdb=" N VAL F 349 " --> pdb=" O TYR F 345 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE F 355 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR F 356 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 375 removed outlier: 3.707A pdb=" N GLN F 374 " --> pdb=" O ARG F 370 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 370 through 375' Processing helix chain 'F' and resid 384 through 389 628 hydrogen bonds defined for protein. 1884 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: 3.06 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1830 1.29 - 1.42: 4314 1.42 - 1.56: 7535 1.56 - 1.69: 1 1.69 - 1.83: 174 Bond restraints: 13854 Sorted by residual: bond pdb=" C HIS B 344 " pdb=" O HIS B 344 " ideal model delta sigma weight residual 1.234 1.151 0.083 1.20e-02 6.94e+03 4.75e+01 bond pdb=" C HIS A 344 " pdb=" O HIS A 344 " ideal model delta sigma weight residual 1.234 1.152 0.082 1.20e-02 6.94e+03 4.68e+01 bond pdb=" C19 16C E 500 " pdb=" N2 16C E 500 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C19 16C D 500 " pdb=" N2 16C D 500 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C19 16C A 500 " pdb=" N2 16C A 500 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 ... (remaining 13849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 18389 1.84 - 3.69: 349 3.69 - 5.53: 70 5.53 - 7.38: 10 7.38 - 9.22: 4 Bond angle restraints: 18822 Sorted by residual: angle pdb=" N PRO D 255 " pdb=" CD PRO D 255 " pdb=" CG PRO D 255 " ideal model delta sigma weight residual 103.20 94.63 8.57 1.50e+00 4.44e-01 3.27e+01 angle pdb=" CA PRO D 255 " pdb=" N PRO D 255 " pdb=" CD PRO D 255 " ideal model delta sigma weight residual 112.00 104.14 7.86 1.40e+00 5.10e-01 3.15e+01 angle pdb=" N VAL C 290 " pdb=" CA VAL C 290 " pdb=" C VAL C 290 " ideal model delta sigma weight residual 112.12 107.84 4.28 8.40e-01 1.42e+00 2.59e+01 angle pdb=" N VAL E 290 " pdb=" CA VAL E 290 " pdb=" C VAL E 290 " ideal model delta sigma weight residual 111.62 107.81 3.81 7.90e-01 1.60e+00 2.32e+01 angle pdb=" N GLY F 294 " pdb=" CA GLY F 294 " pdb=" C GLY F 294 " ideal model delta sigma weight residual 112.25 117.13 -4.88 1.34e+00 5.57e-01 1.33e+01 ... (remaining 18817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.41: 7368 24.41 - 48.82: 498 48.82 - 73.23: 51 73.23 - 97.65: 6 97.65 - 122.06: 3 Dihedral angle restraints: 7926 sinusoidal: 3258 harmonic: 4668 Sorted by residual: dihedral pdb=" CB CYS E 261 " pdb=" SG CYS E 261 " pdb=" SG CYS E 293 " pdb=" CB CYS E 293 " ideal model delta sinusoidal sigma weight residual -86.00 -16.39 -69.61 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS C 261 " pdb=" SG CYS C 261 " pdb=" SG CYS C 293 " pdb=" CB CYS C 293 " ideal model delta sinusoidal sigma weight residual 93.00 36.80 56.20 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CA CYS F 293 " pdb=" C CYS F 293 " pdb=" N GLY F 294 " pdb=" CA GLY F 294 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 7923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1619 0.046 - 0.092: 357 0.092 - 0.139: 56 0.139 - 0.185: 11 0.185 - 0.231: 9 Chirality restraints: 2052 Sorted by residual: chirality pdb=" C3 16C B 500 " pdb=" C2 16C B 500 " pdb=" C4 16C B 500 " pdb=" O3 16C B 500 " both_signs ideal model delta sigma weight residual False -2.28 -2.51 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3 16C A 500 " pdb=" C2 16C A 500 " pdb=" C4 16C A 500 " pdb=" O3 16C A 500 " both_signs ideal model delta sigma weight residual False -2.28 -2.51 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3 16C E 500 " pdb=" C2 16C E 500 " pdb=" C4 16C E 500 " pdb=" O3 16C E 500 " both_signs ideal model delta sigma weight residual False -2.28 -2.51 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2049 not shown) Planarity restraints: 2262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 343 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.10e+00 pdb=" C GLU A 343 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU A 343 " 0.020 2.00e-02 2.50e+03 pdb=" N HIS A 344 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 343 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C GLU B 343 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU B 343 " 0.014 2.00e-02 2.50e+03 pdb=" N HIS B 344 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 254 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 255 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 255 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 255 " 0.021 5.00e-02 4.00e+02 ... (remaining 2259 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 626 2.73 - 3.27: 13564 3.27 - 3.82: 20600 3.82 - 4.36: 23678 4.36 - 4.90: 41393 Nonbonded interactions: 99861 Sorted by model distance: nonbonded pdb=" OG SER C 268 " pdb=" OE1 GLU C 271 " model vdw 2.191 3.040 nonbonded pdb=" OD1 ASN F 309 " pdb=" OG SER F 327 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR B 372 " pdb=" O VAL B 392 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR F 372 " pdb=" O VAL F 392 " model vdw 2.259 3.040 nonbonded pdb=" OE2 GLU E 148 " pdb=" ND2 ASN E 391 " model vdw 2.270 3.120 ... (remaining 99856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 31.240 Find NCS groups from input model: 0.580 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: 0.010 Load rotamer database and sin/cos tables:3.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 13860 Z= 0.215 Angle : 0.624 9.222 18834 Z= 0.338 Chirality : 0.041 0.231 2052 Planarity : 0.004 0.041 2262 Dihedral : 15.195 122.058 4896 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.67 % Favored : 90.20 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -1.63 (0.21), residues: 1572 helix: -0.04 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.63 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.011 0.001 HIS A 344 PHE 0.018 0.001 PHE E 190 TYR 0.010 0.001 TYR E 213 ARG 0.007 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.27502 ( 628) hydrogen bonds : angle 6.68362 ( 1884) SS BOND : bond 0.00477 ( 6) SS BOND : angle 1.11162 ( 12) covalent geometry : bond 0.00387 (13854) covalent geometry : angle 0.62399 (18822) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 2.102 Fit side-chains REVERT: A 370 ARG cc_start: 0.7525 (ttm110) cc_final: 0.6899 (ttp80) REVERT: B 296 TYR cc_start: 0.8055 (m-80) cc_final: 0.7799 (m-80) REVERT: C 180 MET cc_start: 0.5433 (tpp) cc_final: 0.4384 (tmm) REVERT: D 224 HIS cc_start: 0.7634 (m-70) cc_final: 0.7143 (m170) REVERT: E 148 GLU cc_start: 0.7445 (mp0) cc_final: 0.7226 (mp0) REVERT: E 183 TYR cc_start: 0.5844 (m-80) cc_final: 0.5632 (m-80) REVERT: E 207 CYS cc_start: 0.8891 (m) cc_final: 0.8484 (m) REVERT: E 224 HIS cc_start: 0.6231 (m170) cc_final: 0.5628 (m170) REVERT: E 350 PHE cc_start: 0.7666 (t80) cc_final: 0.7386 (t80) REVERT: F 151 LYS cc_start: 0.7771 (mttp) cc_final: 0.7298 (mmtp) REVERT: F 180 MET cc_start: 0.4442 (tpt) cc_final: 0.3853 (tmm) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2504 time to fit residues: 100.4552 Evaluate side-chains 234 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS E 224 HIS E 301 HIS F 301 HIS F 393 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.194596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133345 restraints weight = 16291.847| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.69 r_work: 0.3318 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13860 Z= 0.213 Angle : 0.650 6.653 18834 Z= 0.348 Chirality : 0.044 0.169 2052 Planarity : 0.004 0.039 2262 Dihedral : 9.815 60.346 1956 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.56 % Favored : 89.31 % Rotamer: Outliers : 1.73 % Allowed : 8.37 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1572 helix: 0.84 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.66 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 150 HIS 0.004 0.001 HIS B 364 PHE 0.025 0.002 PHE E 168 TYR 0.022 0.002 TYR B 296 ARG 0.004 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.08001 ( 628) hydrogen bonds : angle 3.82572 ( 1884) SS BOND : bond 0.00484 ( 6) SS BOND : angle 1.35164 ( 12) covalent geometry : bond 0.00508 (13854) covalent geometry : angle 0.64897 (18822) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 2.259 Fit side-chains revert: symmetry clash REVERT: A 370 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7042 (ttp80) REVERT: B 213 TYR cc_start: 0.8561 (t80) cc_final: 0.7994 (t80) REVERT: B 314 GLU cc_start: 0.8660 (tp30) cc_final: 0.8414 (tp30) REVERT: C 180 MET cc_start: 0.5948 (tpp) cc_final: 0.4514 (tmm) REVERT: C 241 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8684 (mp) REVERT: C 285 MET cc_start: 0.7345 (mmm) cc_final: 0.7144 (mtp) REVERT: D 160 PHE cc_start: 0.6803 (m-80) cc_final: 0.6536 (m-80) REVERT: D 213 TYR cc_start: 0.8873 (t80) cc_final: 0.8658 (t80) REVERT: E 180 MET cc_start: 0.6870 (tpp) cc_final: 0.6534 (ttp) REVERT: E 183 TYR cc_start: 0.5927 (m-80) cc_final: 0.5604 (m-80) REVERT: F 165 PHE cc_start: 0.8709 (t80) cc_final: 0.8507 (t80) REVERT: F 180 MET cc_start: 0.5256 (tpt) cc_final: 0.4185 (tmm) outliers start: 25 outliers final: 21 residues processed: 277 average time/residue: 0.2554 time to fit residues: 104.8912 Evaluate side-chains 263 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 241 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 369 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 15 optimal weight: 0.8980 chunk 87 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 149 optimal weight: 0.0470 chunk 121 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 HIS F 174 HIS F 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.200770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.153846 restraints weight = 16389.210| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 3.68 r_work: 0.3366 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13860 Z= 0.111 Angle : 0.543 7.125 18834 Z= 0.288 Chirality : 0.040 0.168 2052 Planarity : 0.003 0.035 2262 Dihedral : 8.309 59.575 1956 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.81 % Favored : 89.06 % Rotamer: Outliers : 1.31 % Allowed : 12.59 % Favored : 86.10 % 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: -0.17 (0.22), residues: 1572 helix: 1.42 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.63 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 150 HIS 0.004 0.001 HIS F 301 PHE 0.012 0.001 PHE E 168 TYR 0.021 0.001 TYR D 213 ARG 0.007 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.05190 ( 628) hydrogen bonds : angle 3.34254 ( 1884) SS BOND : bond 0.00351 ( 6) SS BOND : angle 1.05436 ( 12) covalent geometry : bond 0.00225 (13854) covalent geometry : angle 0.54222 (18822) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 252 time to evaluate : 2.271 Fit side-chains REVERT: A 170 MET cc_start: 0.8614 (ttm) cc_final: 0.8379 (ttm) REVERT: A 370 ARG cc_start: 0.7343 (ttm110) cc_final: 0.6770 (ttp80) REVERT: B 213 TYR cc_start: 0.8545 (t80) cc_final: 0.7971 (t80) REVERT: B 314 GLU cc_start: 0.8628 (tp30) cc_final: 0.8252 (tp30) REVERT: C 151 LYS cc_start: 0.7979 (mttp) cc_final: 0.7750 (mttm) REVERT: C 285 MET cc_start: 0.7165 (mmm) cc_final: 0.6844 (mtp) REVERT: D 160 PHE cc_start: 0.6959 (m-80) cc_final: 0.6723 (m-80) REVERT: D 203 MET cc_start: 0.7928 (mmt) cc_final: 0.7673 (mpp) REVERT: E 148 GLU cc_start: 0.7969 (mp0) cc_final: 0.7697 (mp0) REVERT: E 180 MET cc_start: 0.7247 (tpp) cc_final: 0.6741 (ttp) REVERT: E 183 TYR cc_start: 0.5852 (m-80) cc_final: 0.5448 (m-80) REVERT: E 203 MET cc_start: 0.8749 (ppp) cc_final: 0.8235 (ppp) REVERT: F 180 MET cc_start: 0.5479 (tpt) cc_final: 0.5145 (tpp) REVERT: F 260 GLN cc_start: 0.7789 (pt0) cc_final: 0.7503 (pm20) outliers start: 19 outliers final: 9 residues processed: 263 average time/residue: 0.3592 time to fit residues: 147.9908 Evaluate side-chains 241 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 232 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 319 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 127 optimal weight: 0.3980 chunk 83 optimal weight: 0.0670 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS B 258 HIS C 331 ASN ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.199767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135813 restraints weight = 16219.790| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.65 r_work: 0.3414 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13860 Z= 0.109 Angle : 0.531 7.761 18834 Z= 0.280 Chirality : 0.039 0.169 2052 Planarity : 0.003 0.035 2262 Dihedral : 8.025 59.827 1956 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.05 % Favored : 89.82 % Rotamer: Outliers : 1.45 % Allowed : 14.66 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1572 helix: 1.56 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -2.58 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 150 HIS 0.003 0.001 HIS A 224 PHE 0.023 0.001 PHE E 190 TYR 0.012 0.001 TYR B 296 ARG 0.004 0.000 ARG F 243 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 628) hydrogen bonds : angle 3.19038 ( 1884) SS BOND : bond 0.00428 ( 6) SS BOND : angle 1.00510 ( 12) covalent geometry : bond 0.00234 (13854) covalent geometry : angle 0.53085 (18822) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.8548 (ttm) cc_final: 0.8308 (ttm) REVERT: A 370 ARG cc_start: 0.7528 (ttm110) cc_final: 0.6831 (ttp80) REVERT: B 213 TYR cc_start: 0.8450 (t80) cc_final: 0.7880 (t80) REVERT: B 314 GLU cc_start: 0.8574 (tp30) cc_final: 0.8365 (tp30) REVERT: C 151 LYS cc_start: 0.7939 (mttp) cc_final: 0.7657 (mttm) REVERT: C 241 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8664 (mp) REVERT: C 285 MET cc_start: 0.7168 (mmm) cc_final: 0.6718 (mtp) REVERT: D 203 MET cc_start: 0.7924 (mmt) cc_final: 0.7576 (mpp) REVERT: D 212 CYS cc_start: 0.8603 (p) cc_final: 0.8322 (p) REVERT: D 223 LYS cc_start: 0.7710 (ptmt) cc_final: 0.7501 (ptmt) REVERT: D 339 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7985 (mp) REVERT: E 203 MET cc_start: 0.8620 (ppp) cc_final: 0.8390 (tmm) REVERT: E 348 ASP cc_start: 0.8011 (m-30) cc_final: 0.7797 (m-30) REVERT: F 180 MET cc_start: 0.5454 (tpt) cc_final: 0.5082 (tpp) REVERT: F 183 TYR cc_start: 0.6224 (m-80) cc_final: 0.6016 (m-80) REVERT: F 214 ILE cc_start: 0.8564 (mm) cc_final: 0.8350 (mt) REVERT: F 381 TRP cc_start: 0.8219 (m100) cc_final: 0.7949 (m100) outliers start: 21 outliers final: 15 residues processed: 259 average time/residue: 0.2513 time to fit residues: 96.6139 Evaluate side-chains 249 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain F residue 162 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 88 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN E 344 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.196360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132845 restraints weight = 16393.317| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.72 r_work: 0.3347 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13860 Z= 0.147 Angle : 0.564 8.384 18834 Z= 0.297 Chirality : 0.041 0.171 2052 Planarity : 0.003 0.034 2262 Dihedral : 8.286 59.609 1956 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.37 % Favored : 89.57 % Rotamer: Outliers : 2.07 % Allowed : 15.98 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.22), residues: 1572 helix: 1.52 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 320 HIS 0.004 0.001 HIS B 344 PHE 0.023 0.001 PHE D 160 TYR 0.025 0.001 TYR D 213 ARG 0.005 0.000 ARG F 243 Details of bonding type rmsd hydrogen bonds : bond 0.05600 ( 628) hydrogen bonds : angle 3.26658 ( 1884) SS BOND : bond 0.00420 ( 6) SS BOND : angle 1.10322 ( 12) covalent geometry : bond 0.00346 (13854) covalent geometry : angle 0.56358 (18822) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.8586 (ttm) cc_final: 0.8358 (ttm) REVERT: A 370 ARG cc_start: 0.7587 (ttm110) cc_final: 0.6870 (ttp80) REVERT: B 213 TYR cc_start: 0.8417 (t80) cc_final: 0.7882 (t80) REVERT: B 314 GLU cc_start: 0.8666 (tp30) cc_final: 0.8460 (tp30) REVERT: C 151 LYS cc_start: 0.7962 (mttp) cc_final: 0.7663 (mttm) REVERT: C 165 PHE cc_start: 0.8452 (t80) cc_final: 0.7910 (t80) REVERT: C 241 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8676 (mp) REVERT: C 285 MET cc_start: 0.7307 (mmm) cc_final: 0.7095 (mtp) REVERT: D 203 MET cc_start: 0.7935 (mmt) cc_final: 0.7634 (mpp) REVERT: D 212 CYS cc_start: 0.8606 (p) cc_final: 0.8400 (p) REVERT: E 183 TYR cc_start: 0.6697 (m-80) cc_final: 0.6090 (m-80) REVERT: E 212 CYS cc_start: 0.8523 (p) cc_final: 0.8318 (p) REVERT: E 213 TYR cc_start: 0.8991 (t80) cc_final: 0.8779 (t80) REVERT: F 203 MET cc_start: 0.7180 (mmt) cc_final: 0.6896 (mmt) REVERT: F 314 GLU cc_start: 0.8153 (tp30) cc_final: 0.7803 (tp30) outliers start: 30 outliers final: 24 residues processed: 269 average time/residue: 0.2338 time to fit residues: 92.8314 Evaluate side-chains 264 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.0010 chunk 54 optimal weight: 4.9990 chunk 134 optimal weight: 0.0570 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** 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 = 0.4256 r_free = 0.4256 target = 0.197209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.135997 restraints weight = 16483.437| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.86 r_work: 0.3329 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13860 Z= 0.129 Angle : 0.551 8.295 18834 Z= 0.290 Chirality : 0.040 0.169 2052 Planarity : 0.003 0.034 2262 Dihedral : 8.290 59.347 1956 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 2.21 % Allowed : 16.11 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1572 helix: 1.57 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.56 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 150 HIS 0.004 0.001 HIS B 344 PHE 0.020 0.001 PHE E 190 TYR 0.014 0.001 TYR B 158 ARG 0.003 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.05177 ( 628) hydrogen bonds : angle 3.23191 ( 1884) SS BOND : bond 0.00408 ( 6) SS BOND : angle 1.34041 ( 12) covalent geometry : bond 0.00296 (13854) covalent geometry : angle 0.55047 (18822) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 1.448 Fit side-chains revert: symmetry clash REVERT: A 370 ARG cc_start: 0.7561 (ttm110) cc_final: 0.6854 (ttp80) REVERT: B 213 TYR cc_start: 0.8455 (t80) cc_final: 0.7925 (t80) REVERT: B 314 GLU cc_start: 0.8693 (tp30) cc_final: 0.8485 (tp30) REVERT: C 151 LYS cc_start: 0.7910 (mttp) cc_final: 0.7606 (mttm) REVERT: C 165 PHE cc_start: 0.8401 (t80) cc_final: 0.7854 (t80) REVERT: C 214 ILE cc_start: 0.8611 (mm) cc_final: 0.8410 (mt) REVERT: C 241 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8693 (mp) REVERT: C 285 MET cc_start: 0.7394 (mmm) cc_final: 0.7076 (mtp) REVERT: D 203 MET cc_start: 0.7916 (mmt) cc_final: 0.7383 (mpp) REVERT: D 212 CYS cc_start: 0.8654 (p) cc_final: 0.8413 (p) REVERT: E 168 PHE cc_start: 0.7921 (t80) cc_final: 0.7466 (t80) REVERT: E 183 TYR cc_start: 0.6764 (m-80) cc_final: 0.6110 (m-80) REVERT: E 212 CYS cc_start: 0.8591 (p) cc_final: 0.8369 (p) REVERT: E 213 TYR cc_start: 0.9049 (t80) cc_final: 0.8803 (t80) REVERT: E 297 MET cc_start: 0.8384 (tpt) cc_final: 0.8102 (tpt) REVERT: E 348 ASP cc_start: 0.8082 (m-30) cc_final: 0.7874 (m-30) REVERT: F 203 MET cc_start: 0.7079 (mmt) cc_final: 0.6763 (mmt) REVERT: F 314 GLU cc_start: 0.8207 (tp30) cc_final: 0.7973 (tp30) outliers start: 32 outliers final: 26 residues processed: 270 average time/residue: 0.2385 time to fit residues: 94.8155 Evaluate side-chains 260 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 111 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 96 optimal weight: 0.0870 chunk 152 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 154 optimal weight: 0.0050 chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** 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 = 0.4264 r_free = 0.4264 target = 0.197998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.149856 restraints weight = 16370.157| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.59 r_work: 0.3316 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13860 Z= 0.116 Angle : 0.544 7.535 18834 Z= 0.285 Chirality : 0.040 0.168 2052 Planarity : 0.003 0.033 2262 Dihedral : 8.273 59.075 1956 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 2.14 % Allowed : 17.01 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1572 helix: 1.65 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -2.52 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 270 HIS 0.003 0.001 HIS B 344 PHE 0.031 0.001 PHE C 168 TYR 0.017 0.001 TYR E 213 ARG 0.004 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04816 ( 628) hydrogen bonds : angle 3.16666 ( 1884) SS BOND : bond 0.00425 ( 6) SS BOND : angle 1.16656 ( 12) covalent geometry : bond 0.00261 (13854) covalent geometry : angle 0.54325 (18822) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 1.474 Fit side-chains revert: symmetry clash REVERT: A 370 ARG cc_start: 0.7572 (ttm110) cc_final: 0.6907 (ttp80) REVERT: B 213 TYR cc_start: 0.8513 (t80) cc_final: 0.7985 (t80) REVERT: C 151 LYS cc_start: 0.7882 (mttp) cc_final: 0.7602 (mttm) REVERT: C 165 PHE cc_start: 0.8395 (t80) cc_final: 0.7927 (t80) REVERT: C 214 ILE cc_start: 0.8660 (mm) cc_final: 0.8440 (mt) REVERT: C 285 MET cc_start: 0.7427 (mmm) cc_final: 0.6980 (mtp) REVERT: D 203 MET cc_start: 0.7921 (mmt) cc_final: 0.7364 (mpp) REVERT: D 212 CYS cc_start: 0.8661 (p) cc_final: 0.8384 (p) REVERT: E 168 PHE cc_start: 0.7945 (t80) cc_final: 0.7571 (t80) REVERT: E 183 TYR cc_start: 0.6804 (m-80) cc_final: 0.6197 (m-80) REVERT: E 212 CYS cc_start: 0.8521 (p) cc_final: 0.8241 (p) REVERT: E 297 MET cc_start: 0.8346 (tpt) cc_final: 0.8007 (tpt) REVERT: F 180 MET cc_start: 0.5878 (tpp) cc_final: 0.4627 (tmm) REVERT: F 203 MET cc_start: 0.7212 (mmt) cc_final: 0.6889 (mmt) outliers start: 31 outliers final: 28 residues processed: 259 average time/residue: 0.2423 time to fit residues: 92.7658 Evaluate side-chains 255 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 139 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 76 optimal weight: 0.0870 chunk 72 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.198642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148899 restraints weight = 16506.072| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 4.25 r_work: 0.3325 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13860 Z= 0.113 Angle : 0.540 8.260 18834 Z= 0.282 Chirality : 0.039 0.168 2052 Planarity : 0.003 0.033 2262 Dihedral : 8.179 59.741 1956 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 2.56 % Allowed : 17.01 % Favored : 80.43 % 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: 0.17 (0.22), residues: 1572 helix: 1.69 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -2.47 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 270 HIS 0.003 0.001 HIS B 344 PHE 0.025 0.001 PHE C 168 TYR 0.012 0.001 TYR B 158 ARG 0.004 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04605 ( 628) hydrogen bonds : angle 3.16604 ( 1884) SS BOND : bond 0.00404 ( 6) SS BOND : angle 1.09729 ( 12) covalent geometry : bond 0.00252 (13854) covalent geometry : angle 0.53904 (18822) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 2.315 Fit side-chains revert: symmetry clash REVERT: B 213 TYR cc_start: 0.8480 (t80) cc_final: 0.7947 (t80) REVERT: C 151 LYS cc_start: 0.7841 (mttp) cc_final: 0.7568 (mttp) REVERT: C 165 PHE cc_start: 0.8384 (t80) cc_final: 0.7921 (t80) REVERT: C 214 ILE cc_start: 0.8604 (mm) cc_final: 0.8370 (mt) REVERT: C 241 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8737 (mp) REVERT: C 285 MET cc_start: 0.7421 (mmm) cc_final: 0.6980 (mtp) REVERT: D 203 MET cc_start: 0.7982 (mmt) cc_final: 0.7406 (mpp) REVERT: D 212 CYS cc_start: 0.8652 (p) cc_final: 0.8439 (p) REVERT: E 168 PHE cc_start: 0.7896 (t80) cc_final: 0.7534 (t80) REVERT: E 183 TYR cc_start: 0.6962 (m-80) cc_final: 0.6291 (m-80) REVERT: E 257 GLN cc_start: 0.6457 (OUTLIER) cc_final: 0.5933 (mp10) REVERT: E 348 ASP cc_start: 0.8158 (m-30) cc_final: 0.7863 (m-30) REVERT: F 180 MET cc_start: 0.6072 (tpp) cc_final: 0.4794 (tmm) REVERT: F 214 ILE cc_start: 0.8609 (mm) cc_final: 0.8403 (mt) outliers start: 37 outliers final: 30 residues processed: 264 average time/residue: 0.2475 time to fit residues: 97.3689 Evaluate side-chains 258 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 GLN Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 332 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 56 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 140 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** 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 = 0.4258 r_free = 0.4258 target = 0.197410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.132816 restraints weight = 16354.830| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.68 r_work: 0.3383 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13860 Z= 0.126 Angle : 0.561 9.631 18834 Z= 0.294 Chirality : 0.040 0.184 2052 Planarity : 0.003 0.034 2262 Dihedral : 8.227 59.020 1956 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 2.42 % Allowed : 17.08 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.22), residues: 1572 helix: 1.66 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -2.47 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 270 HIS 0.003 0.001 HIS B 344 PHE 0.022 0.001 PHE C 168 TYR 0.027 0.001 TYR E 213 ARG 0.005 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 628) hydrogen bonds : angle 3.17600 ( 1884) SS BOND : bond 0.00402 ( 6) SS BOND : angle 1.37834 ( 12) covalent geometry : bond 0.00290 (13854) covalent geometry : angle 0.56016 (18822) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.8529 (ttm) cc_final: 0.8307 (mtp) REVERT: A 370 ARG cc_start: 0.7255 (ttm110) cc_final: 0.6543 (ttp80) REVERT: B 213 TYR cc_start: 0.8335 (t80) cc_final: 0.7844 (t80) REVERT: C 151 LYS cc_start: 0.7880 (mttp) cc_final: 0.7597 (mttp) REVERT: C 165 PHE cc_start: 0.8412 (t80) cc_final: 0.7967 (t80) REVERT: C 214 ILE cc_start: 0.8602 (mm) cc_final: 0.8388 (mt) REVERT: C 241 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8698 (mp) REVERT: C 285 MET cc_start: 0.7424 (mmm) cc_final: 0.7056 (mtp) REVERT: D 203 MET cc_start: 0.7881 (mmt) cc_final: 0.7286 (mpp) REVERT: E 168 PHE cc_start: 0.7933 (t80) cc_final: 0.7563 (t80) REVERT: E 183 TYR cc_start: 0.7097 (m-80) cc_final: 0.6248 (m-80) REVERT: E 348 ASP cc_start: 0.8067 (m-30) cc_final: 0.7537 (m-30) REVERT: F 180 MET cc_start: 0.6035 (tpp) cc_final: 0.4771 (tmm) outliers start: 35 outliers final: 32 residues processed: 255 average time/residue: 0.2552 time to fit residues: 97.0457 Evaluate side-chains 259 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 57 optimal weight: 0.0370 chunk 23 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.195032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129496 restraints weight = 16273.016| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.70 r_work: 0.3347 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13860 Z= 0.121 Angle : 0.568 9.945 18834 Z= 0.297 Chirality : 0.040 0.187 2052 Planarity : 0.003 0.034 2262 Dihedral : 8.228 59.697 1956 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 2.35 % Allowed : 17.08 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1572 helix: 1.67 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 270 HIS 0.003 0.001 HIS A 224 PHE 0.021 0.001 PHE E 337 TYR 0.013 0.001 TYR B 296 ARG 0.005 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 628) hydrogen bonds : angle 3.23607 ( 1884) SS BOND : bond 0.00446 ( 6) SS BOND : angle 1.35681 ( 12) covalent geometry : bond 0.00275 (13854) covalent geometry : angle 0.56679 (18822) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.8548 (ttm) cc_final: 0.8342 (mtp) REVERT: A 370 ARG cc_start: 0.7256 (ttm110) cc_final: 0.6548 (ttp80) REVERT: B 213 TYR cc_start: 0.8289 (t80) cc_final: 0.7801 (t80) REVERT: C 151 LYS cc_start: 0.7814 (mttp) cc_final: 0.7532 (mttp) REVERT: C 209 MET cc_start: 0.8397 (mmp) cc_final: 0.7986 (mmt) REVERT: C 214 ILE cc_start: 0.8506 (mm) cc_final: 0.8286 (mt) REVERT: C 241 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8670 (mp) REVERT: D 203 MET cc_start: 0.7759 (mmt) cc_final: 0.7261 (mpp) REVERT: E 168 PHE cc_start: 0.7870 (t80) cc_final: 0.7528 (t80) REVERT: E 183 TYR cc_start: 0.7016 (m-80) cc_final: 0.6253 (m-80) REVERT: E 297 MET cc_start: 0.8380 (tpt) cc_final: 0.8073 (tpt) REVERT: F 180 MET cc_start: 0.6145 (tpp) cc_final: 0.4839 (tmm) outliers start: 34 outliers final: 31 residues processed: 252 average time/residue: 0.2387 time to fit residues: 89.3101 Evaluate side-chains 258 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 183 TYR Chi-restraints excluded: chain F residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 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 331 ASN ** D 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** 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 = 0.4227 r_free = 0.4227 target = 0.194524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132080 restraints weight = 16274.127| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.90 r_work: 0.3307 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13860 Z= 0.124 Angle : 0.572 12.189 18834 Z= 0.300 Chirality : 0.040 0.194 2052 Planarity : 0.003 0.033 2262 Dihedral : 8.238 58.873 1956 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 2.07 % Allowed : 17.36 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1572 helix: 1.67 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -2.42 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 270 HIS 0.004 0.001 HIS B 344 PHE 0.017 0.001 PHE E 201 TYR 0.014 0.001 TYR B 296 ARG 0.005 0.000 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 628) hydrogen bonds : angle 3.24216 ( 1884) SS BOND : bond 0.00458 ( 6) SS BOND : angle 1.26366 ( 12) covalent geometry : bond 0.00286 (13854) covalent geometry : angle 0.57103 (18822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7314.87 seconds wall clock time: 132 minutes 33.38 seconds (7953.38 seconds total)