Starting phenix.real_space_refine on Sun Nov 17 08:40:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijq_35492/11_2024/8ijq_35492.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijq_35492/11_2024/8ijq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijq_35492/11_2024/8ijq_35492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijq_35492/11_2024/8ijq_35492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijq_35492/11_2024/8ijq_35492.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijq_35492/11_2024/8ijq_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.60, per 1000 atoms: 0.64 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: 3.55 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: 1.06 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: 3.95 Time building geometry restraints manager: 4.06 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: 0.00 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: 2.370 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.590 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.560 ------------------------------------------------------------------------------- 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 13854 Z= 0.245 Angle : 0.624 9.222 18822 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 *********************** 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 : 1.936 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: 0.2517 time to fit residues: 100.8040 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 : 1.481 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 13854 Z= 0.330 Angle : 0.649 6.653 18822 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 *********************** 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 : 1.416 Fit side-chains revert: symmetry clash REVERT: A 370 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7026 (ttp80) REVERT: B 213 TYR cc_start: 0.8056 (t80) cc_final: 0.7630 (t80) REVERT: B 314 GLU cc_start: 0.8251 (tp30) cc_final: 0.8007 (tp30) REVERT: C 180 MET cc_start: 0.5532 (tpp) cc_final: 0.4372 (tmm) REVERT: D 160 PHE cc_start: 0.6647 (m-80) cc_final: 0.6433 (m-80) REVERT: F 180 MET cc_start: 0.4925 (tpt) cc_final: 0.4094 (tmm) outliers start: 25 outliers final: 21 residues processed: 277 average time/residue: 0.2417 time to fit residues: 99.0839 Evaluate side-chains 260 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 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 78 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 HIS ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 HIS F 393 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13854 Z= 0.185 Angle : 0.559 7.342 18822 Z= 0.297 Chirality : 0.040 0.168 2052 Planarity : 0.003 0.035 2262 Dihedral : 8.595 59.596 1956 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.69 % Favored : 89.19 % Rotamer: Outliers : 1.94 % Allowed : 12.03 % Favored : 86.03 % 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: -0.27 (0.22), residues: 1572 helix: 1.33 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.66 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 150 HIS 0.004 0.001 HIS F 301 PHE 0.012 0.001 PHE E 168 TYR 0.014 0.001 TYR B 158 ARG 0.007 0.000 ARG D 225 *********************** 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 281 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 1.462 Fit side-chains REVERT: A 170 MET cc_start: 0.8321 (ttm) cc_final: 0.8110 (ttm) REVERT: A 370 ARG cc_start: 0.7437 (ttm110) cc_final: 0.6867 (ttp80) REVERT: B 213 TYR cc_start: 0.8010 (t80) cc_final: 0.7591 (t80) REVERT: B 314 GLU cc_start: 0.8214 (tp30) cc_final: 0.8001 (tp30) REVERT: C 151 LYS cc_start: 0.8144 (mttp) cc_final: 0.7940 (mttm) REVERT: C 241 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8364 (mp) REVERT: D 203 MET cc_start: 0.7485 (mmt) cc_final: 0.7276 (mpp) REVERT: D 247 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8314 (ttp) REVERT: E 148 GLU cc_start: 0.7975 (mp0) cc_final: 0.7393 (mp0) REVERT: E 203 MET cc_start: 0.8268 (ppp) cc_final: 0.7626 (ppp) REVERT: E 314 GLU cc_start: 0.7946 (pp20) cc_final: 0.7686 (pp20) REVERT: E 391 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.7129 (t0) REVERT: F 180 MET cc_start: 0.5038 (tpt) cc_final: 0.4770 (tpp) outliers start: 28 outliers final: 16 residues processed: 273 average time/residue: 0.2393 time to fit residues: 96.9513 Evaluate side-chains 258 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU 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 C residue 155 SER 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 D residue 155 SER 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 E residue 155 SER Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 391 ASN 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 140 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 134 optimal weight: 0.0570 chunk 40 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13854 Z= 0.170 Angle : 0.548 8.049 18822 Z= 0.290 Chirality : 0.040 0.169 2052 Planarity : 0.003 0.035 2262 Dihedral : 8.436 59.824 1956 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.31 % Favored : 89.57 % Rotamer: Outliers : 1.87 % Allowed : 14.52 % Favored : 83.61 % 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: -0.11 (0.22), residues: 1572 helix: 1.47 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.61 (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 D 291 PHE 0.029 0.001 PHE D 160 TYR 0.013 0.001 TYR B 296 ARG 0.004 0.000 ARG D 225 *********************** 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 278 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 1.396 Fit side-chains REVERT: A 370 ARG cc_start: 0.7540 (ttm110) cc_final: 0.6837 (ttp80) REVERT: B 213 TYR cc_start: 0.7980 (t80) cc_final: 0.7552 (t80) REVERT: B 314 GLU cc_start: 0.8201 (tp30) cc_final: 0.7995 (tp30) REVERT: B 384 MET cc_start: 0.7843 (mtm) cc_final: 0.7629 (mtp) REVERT: C 151 LYS cc_start: 0.8109 (mttp) cc_final: 0.7823 (mttm) REVERT: C 241 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8377 (mp) REVERT: D 156 CYS cc_start: 0.7981 (t) cc_final: 0.7478 (t) REVERT: D 160 PHE cc_start: 0.6881 (m-80) cc_final: 0.6516 (m-80) REVERT: D 203 MET cc_start: 0.7535 (mmt) cc_final: 0.7151 (mpp) REVERT: E 148 GLU cc_start: 0.7963 (mp0) cc_final: 0.7545 (mp0) REVERT: E 203 MET cc_start: 0.8167 (ppp) cc_final: 0.7947 (tmm) REVERT: F 180 MET cc_start: 0.5050 (tpt) cc_final: 0.4695 (tpp) outliers start: 27 outliers final: 21 residues processed: 270 average time/residue: 0.2467 time to fit residues: 97.7782 Evaluate side-chains 261 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 1.518 ------------------------------------------------------------------------------- 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 253 SER 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 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 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 338 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 332 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13854 Z= 0.214 Angle : 0.566 7.945 18822 Z= 0.298 Chirality : 0.041 0.171 2052 Planarity : 0.003 0.035 2262 Dihedral : 8.514 59.582 1956 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.56 % Favored : 89.38 % Rotamer: Outliers : 2.56 % Allowed : 15.35 % Favored : 82.09 % 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: -0.09 (0.22), residues: 1572 helix: 1.48 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.60 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 270 HIS 0.004 0.001 HIS B 344 PHE 0.016 0.001 PHE D 160 TYR 0.016 0.001 TYR B 296 ARG 0.003 0.000 ARG D 225 *********************** 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 281 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 1.511 Fit side-chains revert: symmetry clash REVERT: A 370 ARG cc_start: 0.7597 (ttm110) cc_final: 0.6905 (ttp80) REVERT: B 213 TYR cc_start: 0.7904 (t80) cc_final: 0.7503 (t80) REVERT: C 151 LYS cc_start: 0.8100 (mttp) cc_final: 0.7825 (mttm) REVERT: C 241 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8355 (mp) REVERT: D 203 MET cc_start: 0.7586 (mmt) cc_final: 0.7272 (mpp) REVERT: E 205 GLU cc_start: 0.8481 (pm20) cc_final: 0.8265 (pm20) REVERT: E 314 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8135 (tm-30) REVERT: E 348 ASP cc_start: 0.7622 (m-30) cc_final: 0.7378 (m-30) outliers start: 37 outliers final: 29 residues processed: 272 average time/residue: 0.2419 time to fit residues: 96.6110 Evaluate side-chains 268 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 1.697 ------------------------------------------------------------------------------- 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 218 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 0.0020 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 ASN ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13854 Z= 0.169 Angle : 0.548 7.615 18822 Z= 0.288 Chirality : 0.040 0.169 2052 Planarity : 0.003 0.034 2262 Dihedral : 8.347 59.221 1956 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 1.94 % Allowed : 16.60 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1572 helix: 1.59 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -2.55 (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 0.021 0.001 PHE E 190 TYR 0.012 0.001 TYR B 158 ARG 0.004 0.000 ARG D 225 *********************** 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 273 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: A 370 ARG cc_start: 0.7554 (ttm110) cc_final: 0.7059 (ttp80) REVERT: B 213 TYR cc_start: 0.7893 (t80) cc_final: 0.7522 (t80) REVERT: B 314 GLU cc_start: 0.8190 (tp30) cc_final: 0.7963 (tp30) REVERT: C 151 LYS cc_start: 0.8040 (mttp) cc_final: 0.7752 (mttm) REVERT: C 214 ILE cc_start: 0.8644 (mm) cc_final: 0.8438 (mt) REVERT: C 241 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8345 (mp) REVERT: C 285 MET cc_start: 0.7042 (mmm) cc_final: 0.6823 (mtp) REVERT: D 203 MET cc_start: 0.7556 (mmt) cc_final: 0.7257 (mpp) REVERT: E 168 PHE cc_start: 0.7848 (t80) cc_final: 0.7459 (t80) REVERT: E 180 MET cc_start: 0.6214 (ttp) cc_final: 0.5663 (ttp) REVERT: E 201 PHE cc_start: 0.7974 (t80) cc_final: 0.7767 (t80) REVERT: E 314 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8115 (tm-30) REVERT: E 348 ASP cc_start: 0.7541 (m-30) cc_final: 0.7275 (m-30) REVERT: F 203 MET cc_start: 0.6976 (mmt) cc_final: 0.6701 (mmt) REVERT: F 381 TRP cc_start: 0.7801 (m100) cc_final: 0.7536 (m100) outliers start: 28 outliers final: 24 residues processed: 266 average time/residue: 0.2484 time to fit residues: 97.2998 Evaluate side-chains 262 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 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 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 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 145 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 0.0970 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 91 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS C 331 ASN ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13854 Z= 0.163 Angle : 0.547 7.852 18822 Z= 0.286 Chirality : 0.040 0.168 2052 Planarity : 0.003 0.034 2262 Dihedral : 8.255 59.648 1956 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 2.21 % Allowed : 17.01 % Favored : 80.77 % 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: 0.10 (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 0.008 0.001 TRP B 270 HIS 0.003 0.001 HIS A 224 PHE 0.020 0.001 PHE E 190 TYR 0.012 0.001 TYR B 158 ARG 0.004 0.000 ARG D 225 *********************** 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 268 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.8392 (ttm) cc_final: 0.8178 (mtp) REVERT: B 213 TYR cc_start: 0.7857 (t80) cc_final: 0.7465 (t80) REVERT: B 314 GLU cc_start: 0.8272 (tp30) cc_final: 0.8056 (tp30) REVERT: C 151 LYS cc_start: 0.8014 (mttp) cc_final: 0.7715 (mttm) REVERT: C 214 ILE cc_start: 0.8621 (mm) cc_final: 0.8395 (mt) REVERT: D 203 MET cc_start: 0.7541 (mmt) cc_final: 0.7047 (mpp) REVERT: E 168 PHE cc_start: 0.7860 (t80) cc_final: 0.7588 (t80) REVERT: E 314 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8144 (tm-30) REVERT: F 180 MET cc_start: 0.5181 (tpp) cc_final: 0.4353 (tmm) outliers start: 32 outliers final: 27 residues processed: 260 average time/residue: 0.2437 time to fit residues: 92.8965 Evaluate side-chains 254 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 258 HIS 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 171 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 392 VAL 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 182 THR Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 249 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 HIS C 331 ASN ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13854 Z= 0.205 Angle : 0.565 8.559 18822 Z= 0.295 Chirality : 0.040 0.171 2052 Planarity : 0.003 0.034 2262 Dihedral : 8.291 59.701 1956 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 2.49 % Allowed : 16.80 % Favored : 80.71 % 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: 1.59 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.53 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 270 HIS 0.005 0.001 HIS A 258 PHE 0.017 0.001 PHE C 248 TYR 0.020 0.001 TYR C 158 ARG 0.004 0.000 ARG D 225 *********************** 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: 36 poor density : 235 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.8417 (ttm) cc_final: 0.8192 (mtp) REVERT: A 370 ARG cc_start: 0.7422 (ttm110) cc_final: 0.6734 (ttp80) REVERT: B 213 TYR cc_start: 0.7847 (t80) cc_final: 0.7445 (t80) REVERT: C 151 LYS cc_start: 0.8020 (mttp) cc_final: 0.7722 (mttp) REVERT: C 214 ILE cc_start: 0.8652 (mm) cc_final: 0.8451 (mt) REVERT: D 203 MET cc_start: 0.7573 (mmt) cc_final: 0.7028 (mpp) REVERT: E 168 PHE cc_start: 0.7872 (t80) cc_final: 0.7538 (t80) REVERT: E 257 GLN cc_start: 0.6143 (OUTLIER) cc_final: 0.5761 (mp10) REVERT: E 314 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8201 (tm-30) outliers start: 36 outliers final: 31 residues processed: 263 average time/residue: 0.2440 time to fit residues: 94.3720 Evaluate side-chains 261 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 258 HIS Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 218 VAL 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 C residue 395 THR 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 182 THR Chi-restraints excluded: chain E residue 205 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 HIS C 331 ASN ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13854 Z= 0.220 Angle : 0.575 11.217 18822 Z= 0.301 Chirality : 0.041 0.165 2052 Planarity : 0.003 0.034 2262 Dihedral : 8.380 59.432 1956 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 2.49 % Allowed : 16.25 % Favored : 81.26 % 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: 0.03 (0.22), residues: 1572 helix: 1.57 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.54 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 270 HIS 0.004 0.001 HIS E 258 PHE 0.017 0.001 PHE E 190 TYR 0.018 0.001 TYR D 213 ARG 0.009 0.000 ARG D 225 *********************** 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 266 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 170 MET cc_start: 0.8415 (ttm) cc_final: 0.8176 (mtp) REVERT: A 370 ARG cc_start: 0.7486 (ttm110) cc_final: 0.6808 (ttp80) REVERT: B 213 TYR cc_start: 0.7876 (t80) cc_final: 0.7511 (t80) REVERT: C 151 LYS cc_start: 0.8018 (mttp) cc_final: 0.7703 (mttp) REVERT: D 203 MET cc_start: 0.7565 (mmt) cc_final: 0.7029 (mpp) REVERT: E 168 PHE cc_start: 0.7876 (t80) cc_final: 0.7534 (t80) REVERT: E 297 MET cc_start: 0.8155 (tpt) cc_final: 0.7862 (tpt) REVERT: E 314 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8138 (tm-30) REVERT: F 180 MET cc_start: 0.5471 (tpp) cc_final: 0.4622 (tmm) outliers start: 36 outliers final: 33 residues processed: 257 average time/residue: 0.2395 time to fit residues: 90.7704 Evaluate side-chains 261 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 228 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 171 VAL Chi-restraints excluded: chain C residue 218 VAL 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 C residue 395 THR 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 182 THR Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 249 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 181 GLN ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN ** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13854 Z= 0.247 Angle : 0.605 9.624 18822 Z= 0.316 Chirality : 0.041 0.183 2052 Planarity : 0.004 0.036 2262 Dihedral : 8.569 59.527 1956 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 2.42 % Allowed : 16.60 % Favored : 80.98 % 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: -0.06 (0.22), residues: 1572 helix: 1.48 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.53 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 270 HIS 0.004 0.001 HIS B 344 PHE 0.020 0.001 PHE C 248 TYR 0.019 0.001 TYR B 296 ARG 0.008 0.000 ARG D 225 ********************** 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 271 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.8363 (ttm) cc_final: 0.8139 (mtp) REVERT: A 370 ARG cc_start: 0.7513 (ttm110) cc_final: 0.6793 (ttp80) REVERT: B 213 TYR cc_start: 0.7885 (t80) cc_final: 0.7513 (t80) REVERT: C 151 LYS cc_start: 0.8004 (mttp) cc_final: 0.7696 (mttp) REVERT: D 203 MET cc_start: 0.7501 (mmt) cc_final: 0.6947 (mpp) REVERT: E 168 PHE cc_start: 0.7961 (t80) cc_final: 0.7618 (t80) REVERT: E 314 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8156 (tm-30) REVERT: F 180 MET cc_start: 0.5753 (tpp) cc_final: 0.4707 (tmm) outliers start: 35 outliers final: 34 residues processed: 263 average time/residue: 0.2462 time to fit residues: 95.1172 Evaluate side-chains 265 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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 171 VAL Chi-restraints excluded: chain C residue 218 VAL 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 C residue 395 THR 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 181 GLN Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 249 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 127 optimal weight: 0.0070 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN ** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.195240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132469 restraints weight = 16196.687| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.92 r_work: 0.3327 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 13854 Z= 0.283 Angle : 0.860 59.098 18822 Z= 0.478 Chirality : 0.045 0.846 2052 Planarity : 0.004 0.035 2262 Dihedral : 8.570 59.528 1956 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 2.49 % Allowed : 16.39 % Favored : 81.12 % Cbeta Deviations : 0.07 % 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: -0.05 (0.22), residues: 1572 helix: 1.49 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.53 (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 364 PHE 0.016 0.001 PHE E 190 TYR 0.017 0.001 TYR B 296 ARG 0.015 0.000 ARG D 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2896.40 seconds wall clock time: 53 minutes 36.14 seconds (3216.14 seconds total)