Starting phenix.real_space_refine on Thu Mar 5 04:58:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6njp_9391/03_2026/6njp_9391.cif Found real_map, /net/cci-nas-00/data/ceres_data/6njp_9391/03_2026/6njp_9391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6njp_9391/03_2026/6njp_9391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6njp_9391/03_2026/6njp_9391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6njp_9391/03_2026/6njp_9391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6njp_9391/03_2026/6njp_9391.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.010 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: 8 Type Number sf(0) Gaussians Al 4 5.89 5 P 8 5.49 5 Mg 4 5.21 5 S 80 5.16 5 C 12408 2.51 5 N 3389 2.21 5 O 3702 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19607 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "B" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3160 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "D" Number of atoms: 3169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3169 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 391} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3164 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 390} Chain: "F" Number of atoms: 3106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3106 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 383} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N GLU A 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A 140 " occ=0.50 residue: pdb=" N PRO A 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO A 141 " occ=0.75 residue: pdb=" N PRO A 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO A 142 " occ=0.50 residue: pdb=" N GLN A 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN A 148 " occ=0.75 residue: pdb=" N GLU B 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU B 140 " occ=0.50 residue: pdb=" N PRO B 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO B 141 " occ=0.75 residue: pdb=" N PRO B 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO B 142 " occ=0.50 residue: pdb=" N GLN B 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN B 148 " occ=0.75 residue: pdb=" N GLU C 140 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU C 140 " occ=0.50 residue: pdb=" N PRO C 141 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO C 141 " occ=0.75 residue: pdb=" N PRO C 142 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO C 142 " occ=0.50 residue: pdb=" N GLN C 148 " occ=0.75 ... (7 atoms not shown) pdb=" NE2 GLN C 148 " occ=0.75 ... (remaining 12 not shown) Time building chain proxies: 4.88, per 1000 atoms: 0.25 Number of scatterers: 19607 At special positions: 0 Unit cell: (123.42, 118.32, 121.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 80 16.00 P 8 15.00 Al 4 13.00 Mg 4 11.99 F 12 9.00 O 3702 8.00 N 3389 7.00 C 12408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 845.8 milliseconds 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 24 sheets defined 41.3% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 236 through 257 removed outlier: 4.754A pdb=" N ALA A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 removed outlier: 3.511A pdb=" N TYR A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 304 removed outlier: 3.997A pdb=" N PHE A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 373 through 398 removed outlier: 3.544A pdb=" N ALA A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.519A pdb=" N LYS A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.890A pdb=" N ALA A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 removed outlier: 4.037A pdb=" N LEU B 110 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 111 " --> pdb=" O ASP B 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 107 through 111' Processing helix chain 'B' and resid 158 through 164 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 209 through 217 removed outlier: 4.197A pdb=" N GLU B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 238 through 257 removed outlier: 5.398A pdb=" N ALA B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE B 245 " --> pdb=" O MET B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 282 removed outlier: 3.969A pdb=" N TYR B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 305 removed outlier: 4.067A pdb=" N PHE B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.049A pdb=" N VAL B 372 " --> pdb=" O MET B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 399 removed outlier: 3.762A pdb=" N VAL B 393 " --> pdb=" O THR B 389 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU B 395 " --> pdb=" O LYS B 391 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 424 removed outlier: 5.332A pdb=" N LYS B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 removed outlier: 3.516A pdb=" N ALA B 446 " --> pdb=" O PHE B 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.829A pdb=" N LEU C 110 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU C 111 " --> pdb=" O ASP C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 107 through 111' Processing helix chain 'C' and resid 143 through 147 removed outlier: 3.894A pdb=" N ARG C 147 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 182 through 192 removed outlier: 3.973A pdb=" N ASN C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 218 removed outlier: 3.817A pdb=" N GLU C 213 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 218 " --> pdb=" O PHE C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'C' and resid 243 through 256 Processing helix chain 'C' and resid 267 through 282 removed outlier: 4.126A pdb=" N TYR C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.982A pdb=" N PHE C 296 " --> pdb=" O PRO C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 347 through 352 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'C' and resid 373 through 400 removed outlier: 4.969A pdb=" N LEU C 395 " --> pdb=" O LYS C 391 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 416 removed outlier: 3.678A pdb=" N ASP C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 412 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 425 Processing helix chain 'C' and resid 433 through 446 removed outlier: 3.823A pdb=" N ALA C 446 " --> pdb=" O PHE C 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 210 through 217 Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 236 through 257 removed outlier: 5.436A pdb=" N ALA D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N PHE D 245 " --> pdb=" O MET D 241 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 282 removed outlier: 4.150A pdb=" N TYR D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 304 removed outlier: 3.930A pdb=" N PHE D 296 " --> pdb=" O PRO D 292 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'D' and resid 329 through 339 Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 373 through 394 Processing helix chain 'D' and resid 395 through 397 No H-bonds generated for 'chain 'D' and resid 395 through 397' Processing helix chain 'D' and resid 407 through 416 removed outlier: 3.745A pdb=" N LYS D 412 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN D 416 " --> pdb=" O LYS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 425 removed outlier: 3.934A pdb=" N ASN D 422 " --> pdb=" O LYS D 418 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE D 423 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.507A pdb=" N ALA D 446 " --> pdb=" O PHE D 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 164 Processing helix chain 'E' and resid 182 through 193 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 210 through 216 Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 236 through 257 removed outlier: 5.264A pdb=" N ALA E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N PHE E 245 " --> pdb=" O MET E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 281 removed outlier: 4.020A pdb=" N TYR E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 303 removed outlier: 4.135A pdb=" N PHE E 296 " --> pdb=" O PRO E 292 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 346 through 351 removed outlier: 3.649A pdb=" N ALA E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 394 removed outlier: 4.123A pdb=" N ASN E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 399 Processing helix chain 'E' and resid 407 through 416 removed outlier: 3.559A pdb=" N LYS E 415 " --> pdb=" O ASP E 411 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN E 416 " --> pdb=" O LYS E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 424 Processing helix chain 'E' and resid 433 through 446 Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.907A pdb=" N LEU F 110 " --> pdb=" O GLY F 107 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU F 111 " --> pdb=" O ASP F 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 107 through 111' Processing helix chain 'F' and resid 143 through 147 removed outlier: 3.692A pdb=" N LEU F 146 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG F 147 " --> pdb=" O PRO F 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 143 through 147' Processing helix chain 'F' and resid 158 through 165 removed outlier: 3.760A pdb=" N ASP F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 192 removed outlier: 3.834A pdb=" N LEU F 186 " --> pdb=" O GLY F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 219 through 224 Processing helix chain 'F' and resid 236 through 256 removed outlier: 4.890A pdb=" N ALA F 244 " --> pdb=" O ARG F 240 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE F 245 " --> pdb=" O MET F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 283 Processing helix chain 'F' and resid 292 through 305 removed outlier: 3.963A pdb=" N PHE F 296 " --> pdb=" O PRO F 292 " (cutoff:3.500A) Proline residue: F 300 - end of helix removed outlier: 4.179A pdb=" N ARG F 305 " --> pdb=" O LYS F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 337 Processing helix chain 'F' and resid 346 through 351 Processing helix chain 'F' and resid 359 through 363 removed outlier: 3.621A pdb=" N LEU F 362 " --> pdb=" O ASP F 359 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER F 363 " --> pdb=" O ILE F 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 359 through 363' Processing helix chain 'F' and resid 373 through 389 Processing helix chain 'F' and resid 390 through 399 removed outlier: 4.132A pdb=" N LEU F 395 " --> pdb=" O LYS F 391 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU F 396 " --> pdb=" O ASN F 392 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE F 399 " --> pdb=" O LEU F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 416 removed outlier: 3.845A pdb=" N ALA F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE F 414 " --> pdb=" O ALA F 410 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS F 415 " --> pdb=" O ASP F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 424 Processing helix chain 'F' and resid 433 through 443 removed outlier: 3.668A pdb=" N ILE F 438 " --> pdb=" O TYR F 434 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU F 439 " --> pdb=" O GLU F 435 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 26 removed outlier: 3.534A pdb=" N ILE G 5 " --> pdb=" O MET G 1 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU G 6 " --> pdb=" O LEU G 2 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 114 removed outlier: 3.741A pdb=" N ASP G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER G 97 " --> pdb=" O SER G 93 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG G 100 " --> pdb=" O ASP G 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 removed outlier: 3.875A pdb=" N LYS A 37 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 47 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE A 79 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 71 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG A 66 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.628A pdb=" N ILE A 199 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL A 229 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 201 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 198 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N MET A 264 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 200 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP A 266 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A 202 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 261 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE A 317 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 263 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N THR A 319 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N MET A 265 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N LEU A 321 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.636A pdb=" N LYS B 37 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS B 47 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU B 81 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL B 70 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG B 66 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 114 through 115 removed outlier: 5.711A pdb=" N ILE B 115 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N THR B 232 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 205 " --> pdb=" O THR B 231 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 115 removed outlier: 5.711A pdb=" N ILE B 115 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N THR B 232 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 205 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE B 343 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY B 174 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 153 through 154 removed outlier: 4.464A pdb=" N CYS B 167 " --> pdb=" O PHE B 154 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 41 removed outlier: 3.792A pdb=" N LYS C 37 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS C 47 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE C 79 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG C 66 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 36 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 106 Processing sheet with id=AB2, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.919A pdb=" N ARG C 113 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 228 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE C 199 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL C 229 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 201 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 198 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N MET C 264 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL C 200 " --> pdb=" O MET C 264 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL C 261 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE C 317 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 263 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR C 319 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N MET C 265 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N LEU C 321 " --> pdb=" O MET C 265 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE C 173 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL C 320 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE C 175 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY C 174 " --> pdb=" O ILE C 343 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 153 through 154 removed outlier: 4.402A pdb=" N CYS C 167 " --> pdb=" O PHE C 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 36 through 40 removed outlier: 5.730A pdb=" N ILE D 38 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG D 49 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 72 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU D 81 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL D 70 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE D 58 " --> pdb=" O GLN D 98 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN D 93 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY D 36 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 103 through 106 Processing sheet with id=AB6, first strand: chain 'D' and resid 114 through 115 removed outlier: 6.534A pdb=" N ILE D 198 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N MET D 264 " --> pdb=" O ILE D 198 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL D 200 " --> pdb=" O MET D 264 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASP D 266 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA D 202 " --> pdb=" O ASP D 266 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE D 173 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL D 320 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE D 175 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY D 341 " --> pdb=" O ARG D 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 153 through 154 removed outlier: 4.221A pdb=" N CYS D 167 " --> pdb=" O PHE D 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 37 through 41 removed outlier: 3.905A pdb=" N LYS E 37 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS E 47 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE E 79 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS E 60 " --> pdb=" O TYR E 97 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR E 97 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 37 through 41 removed outlier: 3.905A pdb=" N LYS E 37 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS E 47 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE E 79 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE E 73 " --> pdb=" O ILE F 41 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS F 37 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS F 47 " --> pdb=" O ILE F 39 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLU F 77 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE F 73 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE F 79 " --> pdb=" O ILE F 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 103 through 106 Processing sheet with id=AC2, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.739A pdb=" N ARG E 113 " --> pdb=" O CYS E 226 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE E 199 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL E 229 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 201 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR E 231 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU E 203 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL E 261 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE E 317 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU E 263 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR E 319 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET E 265 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU E 321 " --> pdb=" O MET E 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 113 through 115 removed outlier: 3.739A pdb=" N ARG E 113 " --> pdb=" O CYS E 226 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE E 199 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL E 229 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU E 201 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR E 231 " --> pdb=" O LEU E 201 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU E 203 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL E 261 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE E 317 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU E 263 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR E 319 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET E 265 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU E 321 " --> pdb=" O MET E 265 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE E 173 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL E 320 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE E 175 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ILE E 343 " --> pdb=" O ARG E 172 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLY E 174 " --> pdb=" O ILE E 343 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 153 through 154 removed outlier: 4.570A pdb=" N CYS E 167 " --> pdb=" O PHE E 154 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 103 through 104 Processing sheet with id=AC6, first strand: chain 'F' and resid 114 through 115 removed outlier: 5.850A pdb=" N ILE F 115 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N THR F 232 " --> pdb=" O ILE F 115 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU F 201 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE F 204 " --> pdb=" O ASP F 266 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL F 261 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE F 317 " --> pdb=" O VAL F 261 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU F 263 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR F 319 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET F 265 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N LEU F 321 " --> pdb=" O MET F 265 " (cutoff:3.500A) 809 hydrogen bonds defined for protein. 2328 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: 3.38 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4177 1.33 - 1.45: 3979 1.45 - 1.57: 11595 1.57 - 1.69: 20 1.69 - 1.81: 134 Bond restraints: 19905 Sorted by residual: bond pdb=" F1 AF3 C 602 " pdb="AL AF3 C 602 " ideal model delta sigma weight residual 1.637 1.734 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" F1 AF3 E 602 " pdb="AL AF3 E 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" F1 AF3 B 602 " pdb="AL AF3 B 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" F1 AF3 D 602 " pdb="AL AF3 D 602 " ideal model delta sigma weight residual 1.637 1.733 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C ALA A 139 " pdb=" N GLU A 140 " ideal model delta sigma weight residual 1.329 1.272 0.057 1.35e-02 5.49e+03 1.77e+01 ... (remaining 19900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 26069 2.84 - 5.68: 758 5.68 - 8.52: 75 8.52 - 11.36: 29 11.36 - 14.19: 7 Bond angle restraints: 26938 Sorted by residual: angle pdb=" C ASP E 74 " pdb=" N GLU E 75 " pdb=" CA GLU E 75 " ideal model delta sigma weight residual 121.54 133.04 -11.50 1.91e+00 2.74e-01 3.63e+01 angle pdb=" C SER B 313 " pdb=" N ILE B 314 " pdb=" CA ILE B 314 " ideal model delta sigma weight residual 123.19 117.56 5.63 1.24e+00 6.50e-01 2.06e+01 angle pdb=" N VAL A 327 " pdb=" CA VAL A 327 " pdb=" C VAL A 327 " ideal model delta sigma weight residual 113.16 106.42 6.74 1.49e+00 4.50e-01 2.05e+01 angle pdb=" C TYR F 97 " pdb=" N GLN F 98 " pdb=" CA GLN F 98 " ideal model delta sigma weight residual 122.61 129.48 -6.87 1.56e+00 4.11e-01 1.94e+01 angle pdb=" C ASP C 74 " pdb=" N GLU C 75 " pdb=" CA GLU C 75 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 ... (remaining 26933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.15: 11964 30.15 - 60.30: 192 60.30 - 90.45: 16 90.45 - 120.60: 0 120.60 - 150.75: 4 Dihedral angle restraints: 12176 sinusoidal: 4949 harmonic: 7227 Sorted by residual: dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 90.75 -150.75 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 89.03 -149.03 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C5' ADP C 600 " pdb=" O5' ADP C 600 " pdb=" PA ADP C 600 " pdb=" O2A ADP C 600 " ideal model delta sinusoidal sigma weight residual -60.00 87.67 -147.67 1 2.00e+01 2.50e-03 4.43e+01 ... (remaining 12173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2736 0.097 - 0.193: 349 0.193 - 0.290: 29 0.290 - 0.386: 3 0.386 - 0.483: 2 Chirality restraints: 3119 Sorted by residual: chirality pdb=" CB ILE F 314 " pdb=" CA ILE F 314 " pdb=" CG1 ILE F 314 " pdb=" CG2 ILE F 314 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" CB ILE F 204 " pdb=" CA ILE F 204 " pdb=" CG1 ILE F 204 " pdb=" CG2 ILE F 204 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB ILE A 317 " pdb=" CA ILE A 317 " pdb=" CG1 ILE A 317 " pdb=" CG2 ILE A 317 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 3116 not shown) Planarity restraints: 3473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 131 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO C 132 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 329 " -0.044 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO D 330 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 330 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 330 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 83 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C PHE F 83 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE F 83 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU F 84 " -0.015 2.00e-02 2.50e+03 ... (remaining 3470 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.00: 5 2.00 - 2.73: 1287 2.73 - 3.45: 26664 3.45 - 4.18: 45810 4.18 - 4.90: 84379 Nonbonded interactions: 158145 Sorted by model distance: nonbonded pdb=" O ILE B 161 " pdb=" O LEU B 165 " model vdw 1.276 3.040 nonbonded pdb=" OG SER B 184 " pdb="MG MG B 601 " model vdw 1.814 2.170 nonbonded pdb=" OG SER C 184 " pdb="MG MG C 601 " model vdw 1.842 2.170 nonbonded pdb=" OG SER D 184 " pdb="MG MG D 601 " model vdw 1.954 2.170 nonbonded pdb=" OG SER E 184 " pdb="MG MG E 601 " model vdw 1.983 2.170 ... (remaining 158140 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' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = (chain 'B' and (resid 35 through 322 or resid 330 through 446)) selection = (chain 'C' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = (chain 'D' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) selection = (chain 'E' and ((resid 35 and (name N or name CA or name C or name O or name CB \ )) or resid 36 through 322 or resid 330 through 446)) 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=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.390 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.009 0.097 19907 Z= 0.363 Angle : 1.171 14.194 26938 Z= 0.622 Chirality : 0.066 0.483 3119 Planarity : 0.008 0.069 3473 Dihedral : 11.572 150.745 7536 Min Nonbonded Distance : 1.276 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.67 % Allowed : 5.67 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.04 (0.13), residues: 2512 helix: -3.08 (0.12), residues: 937 sheet: -1.90 (0.23), residues: 431 loop : -2.53 (0.15), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 305 TYR 0.021 0.003 TYR A 90 PHE 0.039 0.004 PHE D 83 TRP 0.014 0.002 TRP B 94 HIS 0.010 0.002 HIS D 342 Details of bonding type rmsd covalent geometry : bond 0.00871 (19905) covalent geometry : angle 1.17099 (26938) hydrogen bonds : bond 0.17295 ( 775) hydrogen bonds : angle 7.47498 ( 2328) Misc. bond : bond 0.04778 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 353 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 TYR cc_start: 0.6704 (m-80) cc_final: 0.6289 (m-80) REVERT: A 97 TYR cc_start: 0.7059 (t80) cc_final: 0.6726 (t80) REVERT: A 241 MET cc_start: 0.8515 (ttp) cc_final: 0.8238 (ttt) REVERT: A 311 LYS cc_start: 0.8945 (tttp) cc_final: 0.8554 (ttpt) REVERT: A 378 ARG cc_start: 0.7334 (ppp-140) cc_final: 0.7122 (ttm-80) REVERT: A 392 ASN cc_start: 0.7652 (t0) cc_final: 0.7429 (t0) REVERT: B 66 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7815 (mtm180) REVERT: B 80 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8493 (pp) REVERT: B 401 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6984 (tm-30) REVERT: B 407 ASP cc_start: 0.6656 (t70) cc_final: 0.6229 (t70) REVERT: C 35 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5851 (mp0) REVERT: C 54 ARG cc_start: 0.7953 (mmt90) cc_final: 0.7682 (mmm-85) REVERT: C 74 ASP cc_start: 0.7667 (t70) cc_final: 0.7458 (t0) REVERT: C 116 ASP cc_start: 0.7687 (t0) cc_final: 0.7469 (t0) REVERT: C 151 ASP cc_start: 0.8015 (p0) cc_final: 0.7784 (p0) REVERT: C 260 ASN cc_start: 0.8156 (m-40) cc_final: 0.7288 (t0) REVERT: C 378 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7623 (mtm110) REVERT: D 66 ARG cc_start: 0.6885 (mtm180) cc_final: 0.6525 (mtm180) REVERT: D 85 HIS cc_start: 0.8222 (p90) cc_final: 0.7428 (m-70) REVERT: D 348 GLU cc_start: 0.8122 (pp20) cc_final: 0.7812 (pm20) REVERT: E 47 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8122 (ttmt) REVERT: E 415 LYS cc_start: 0.8672 (ttpm) cc_final: 0.8419 (ttmm) REVERT: F 54 ARG cc_start: 0.7021 (mtp-110) cc_final: 0.6790 (mtt180) REVERT: F 77 GLU cc_start: 0.6243 (mp0) cc_final: 0.5924 (mp0) REVERT: F 368 MET cc_start: 0.6861 (mtm) cc_final: 0.6624 (mtp) REVERT: F 422 ASN cc_start: 0.7717 (p0) cc_final: 0.7444 (p0) outliers start: 14 outliers final: 4 residues processed: 365 average time/residue: 0.1772 time to fit residues: 93.3552 Evaluate side-chains 234 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain F residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 247 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN C 98 GLN D 416 ASN D 421 GLN E 376 HIS F 98 GLN G 26 GLN G 106 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.135971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110876 restraints weight = 26441.221| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.43 r_work: 0.3092 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19907 Z= 0.114 Angle : 0.649 11.807 26938 Z= 0.320 Chirality : 0.045 0.168 3119 Planarity : 0.005 0.055 3473 Dihedral : 7.566 136.509 2811 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.57 % Allowed : 9.25 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.15), residues: 2512 helix: -1.26 (0.16), residues: 971 sheet: -1.55 (0.24), residues: 423 loop : -2.21 (0.16), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 105 TYR 0.018 0.001 TYR A 390 PHE 0.027 0.001 PHE D 58 TRP 0.005 0.001 TRP C 94 HIS 0.005 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00254 (19905) covalent geometry : angle 0.64909 (26938) hydrogen bonds : bond 0.03895 ( 775) hydrogen bonds : angle 4.87975 ( 2328) Misc. bond : bond 0.00027 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 ILE cc_start: 0.8198 (mp) cc_final: 0.7832 (mm) REVERT: A 215 LEU cc_start: 0.7663 (pp) cc_final: 0.7403 (mt) REVERT: A 241 MET cc_start: 0.8534 (ttp) cc_final: 0.8207 (ttt) REVERT: A 311 LYS cc_start: 0.9077 (tttp) cc_final: 0.8722 (ttpt) REVERT: A 378 ARG cc_start: 0.7812 (ppp-140) cc_final: 0.7586 (ttm-80) REVERT: A 392 ASN cc_start: 0.8039 (t0) cc_final: 0.7801 (t0) REVERT: A 416 ASN cc_start: 0.8587 (m-40) cc_final: 0.8277 (m110) REVERT: B 80 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8749 (pp) REVERT: B 162 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8328 (t0) REVERT: B 348 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: B 394 GLU cc_start: 0.7903 (pt0) cc_final: 0.7512 (tt0) REVERT: B 407 ASP cc_start: 0.7016 (t70) cc_final: 0.6617 (t70) REVERT: C 35 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: C 54 ARG cc_start: 0.8334 (mmt90) cc_final: 0.7912 (mmm-85) REVERT: C 116 ASP cc_start: 0.8177 (t0) cc_final: 0.7916 (t0) REVERT: C 151 ASP cc_start: 0.8507 (p0) cc_final: 0.8288 (p0) REVERT: C 260 ASN cc_start: 0.8207 (m-40) cc_final: 0.7197 (t0) REVERT: C 378 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7998 (mtm110) REVERT: D 126 ILE cc_start: 0.6057 (OUTLIER) cc_final: 0.5811 (pp) REVERT: D 346 THR cc_start: 0.8871 (m) cc_final: 0.8611 (p) REVERT: D 348 GLU cc_start: 0.8426 (pp20) cc_final: 0.8069 (pm20) REVERT: E 74 ASP cc_start: 0.7819 (t70) cc_final: 0.7539 (t70) REVERT: E 238 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8093 (pt) REVERT: E 329 ASP cc_start: 0.7679 (t70) cc_final: 0.6986 (m-30) REVERT: E 411 ASP cc_start: 0.8189 (t0) cc_final: 0.7505 (m-30) REVERT: E 433 SER cc_start: 0.8512 (t) cc_final: 0.8194 (p) REVERT: F 54 ARG cc_start: 0.7574 (mtp-110) cc_final: 0.7208 (ttt180) REVERT: F 131 LEU cc_start: 0.6142 (mt) cc_final: 0.5651 (mt) REVERT: F 386 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.6033 (mp) outliers start: 54 outliers final: 19 residues processed: 320 average time/residue: 0.1617 time to fit residues: 76.4337 Evaluate side-chains 255 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 444 VAL Chi-restraints excluded: chain G residue 2 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN F 98 GLN F 426 GLN G 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.132228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107553 restraints weight = 26523.517| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.38 r_work: 0.3022 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19907 Z= 0.144 Angle : 0.652 9.137 26938 Z= 0.317 Chirality : 0.046 0.169 3119 Planarity : 0.005 0.046 3473 Dihedral : 7.156 131.321 2810 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.43 % Allowed : 11.20 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.16), residues: 2512 helix: -0.49 (0.17), residues: 981 sheet: -1.24 (0.25), residues: 418 loop : -1.98 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 288 TYR 0.019 0.002 TYR F 390 PHE 0.024 0.001 PHE D 58 TRP 0.005 0.001 TRP F 94 HIS 0.006 0.001 HIS F 354 Details of bonding type rmsd covalent geometry : bond 0.00346 (19905) covalent geometry : angle 0.65167 (26938) hydrogen bonds : bond 0.03929 ( 775) hydrogen bonds : angle 4.50183 ( 2328) Misc. bond : bond 0.00053 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 243 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8369 (tt) REVERT: A 90 TYR cc_start: 0.6633 (m-80) cc_final: 0.6082 (m-80) REVERT: A 155 ILE cc_start: 0.8101 (mp) cc_final: 0.7874 (mm) REVERT: A 215 LEU cc_start: 0.7753 (pp) cc_final: 0.7450 (mt) REVERT: A 217 LEU cc_start: 0.8687 (tt) cc_final: 0.8348 (tp) REVERT: A 241 MET cc_start: 0.8657 (ttp) cc_final: 0.8336 (ttt) REVERT: A 317 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8459 (mt) REVERT: B 37 LYS cc_start: 0.8566 (mttm) cc_final: 0.8338 (mmtp) REVERT: B 162 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8492 (t0) REVERT: B 348 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: B 394 GLU cc_start: 0.7917 (pt0) cc_final: 0.7702 (pt0) REVERT: B 407 ASP cc_start: 0.7198 (t70) cc_final: 0.6810 (t70) REVERT: C 35 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: C 54 ARG cc_start: 0.8393 (mmt90) cc_final: 0.8049 (mmm-85) REVERT: C 116 ASP cc_start: 0.8039 (t0) cc_final: 0.7766 (t0) REVERT: C 151 ASP cc_start: 0.8547 (p0) cc_final: 0.8293 (p0) REVERT: C 260 ASN cc_start: 0.8316 (m-40) cc_final: 0.7301 (t0) REVERT: C 378 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7994 (mtm110) REVERT: C 431 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7342 (mm) REVERT: D 348 GLU cc_start: 0.8441 (pp20) cc_final: 0.8198 (pm20) REVERT: E 89 MET cc_start: 0.8611 (mtt) cc_final: 0.8219 (mtt) REVERT: E 401 GLU cc_start: 0.7749 (pt0) cc_final: 0.7505 (pt0) REVERT: E 411 ASP cc_start: 0.8074 (t0) cc_final: 0.7793 (m-30) REVERT: F 375 GLU cc_start: 0.7820 (pt0) cc_final: 0.7614 (pt0) REVERT: F 377 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6442 (pp) REVERT: F 418 LYS cc_start: 0.7318 (tppt) cc_final: 0.7019 (tppt) outliers start: 72 outliers final: 33 residues processed: 304 average time/residue: 0.1542 time to fit residues: 70.2372 Evaluate side-chains 263 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 98 GLN Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain G residue 2 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 46 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN G 24 ASN G 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.125751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.101794 restraints weight = 26736.306| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.35 r_work: 0.2932 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.007 0.051 19907 Z= 0.278 Angle : 0.780 10.943 26938 Z= 0.381 Chirality : 0.052 0.219 3119 Planarity : 0.006 0.049 3473 Dihedral : 7.593 133.109 2810 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.86 % Allowed : 13.35 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.16), residues: 2512 helix: -0.61 (0.16), residues: 991 sheet: -1.27 (0.25), residues: 441 loop : -1.96 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 66 TYR 0.018 0.002 TYR C 402 PHE 0.035 0.002 PHE F 58 TRP 0.007 0.001 TRP D 94 HIS 0.009 0.002 HIS D 342 Details of bonding type rmsd covalent geometry : bond 0.00691 (19905) covalent geometry : angle 0.77976 (26938) hydrogen bonds : bond 0.04999 ( 775) hydrogen bonds : angle 4.73324 ( 2328) Misc. bond : bond 0.00160 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 235 time to evaluate : 0.746 Fit side-chains REVERT: A 66 ARG cc_start: 0.7272 (ttm110) cc_final: 0.7055 (tpp80) REVERT: A 80 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8382 (tp) REVERT: A 102 PHE cc_start: 0.8194 (t80) cc_final: 0.7841 (t80) REVERT: A 215 LEU cc_start: 0.8111 (pp) cc_final: 0.7667 (mt) REVERT: A 241 MET cc_start: 0.8634 (ttp) cc_final: 0.8355 (ttt) REVERT: A 317 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8520 (mt) REVERT: B 41 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8816 (mt) REVERT: B 286 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8123 (t0) REVERT: B 348 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: B 407 ASP cc_start: 0.7219 (t70) cc_final: 0.6849 (t70) REVERT: C 54 ARG cc_start: 0.8579 (mmt90) cc_final: 0.8262 (mmm-85) REVERT: C 116 ASP cc_start: 0.8239 (t0) cc_final: 0.7954 (t0) REVERT: C 151 ASP cc_start: 0.8650 (p0) cc_final: 0.8446 (p0) REVERT: C 378 ARG cc_start: 0.8414 (ttp80) cc_final: 0.7995 (mtm110) REVERT: C 431 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7579 (mm) REVERT: E 74 ASP cc_start: 0.8153 (t70) cc_final: 0.7847 (t70) REVERT: E 77 GLU cc_start: 0.8391 (pm20) cc_final: 0.8092 (pt0) REVERT: E 89 MET cc_start: 0.8790 (mtt) cc_final: 0.8457 (mtt) REVERT: E 404 MET cc_start: 0.7567 (tpp) cc_final: 0.6923 (tpp) REVERT: E 411 ASP cc_start: 0.8156 (t0) cc_final: 0.7954 (t0) REVERT: F 132 PRO cc_start: 0.8572 (Cg_endo) cc_final: 0.8216 (Cg_exo) REVERT: F 375 GLU cc_start: 0.7843 (pt0) cc_final: 0.7631 (pt0) REVERT: F 390 TYR cc_start: 0.6670 (t80) cc_final: 0.6328 (t80) REVERT: F 404 MET cc_start: 0.3986 (mmp) cc_final: 0.3761 (mmm) REVERT: F 418 LYS cc_start: 0.7251 (tppt) cc_final: 0.6912 (tppt) outliers start: 81 outliers final: 47 residues processed: 305 average time/residue: 0.1694 time to fit residues: 75.6404 Evaluate side-chains 271 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 3 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.103580 restraints weight = 26621.659| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.50 r_work: 0.2945 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19907 Z= 0.191 Angle : 0.684 8.962 26938 Z= 0.332 Chirality : 0.048 0.174 3119 Planarity : 0.005 0.048 3473 Dihedral : 7.102 132.843 2805 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.81 % Allowed : 14.39 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.16), residues: 2512 helix: -0.24 (0.17), residues: 964 sheet: -1.23 (0.25), residues: 436 loop : -1.77 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 66 TYR 0.017 0.002 TYR A 390 PHE 0.023 0.002 PHE D 58 TRP 0.004 0.001 TRP F 94 HIS 0.007 0.001 HIS F 354 Details of bonding type rmsd covalent geometry : bond 0.00471 (19905) covalent geometry : angle 0.68351 (26938) hydrogen bonds : bond 0.04214 ( 775) hydrogen bonds : angle 4.51325 ( 2328) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 228 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.7202 (ttm110) cc_final: 0.6857 (mtp180) REVERT: A 80 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8339 (tp) REVERT: A 102 PHE cc_start: 0.8207 (t80) cc_final: 0.7940 (t80) REVERT: A 215 LEU cc_start: 0.7878 (pp) cc_final: 0.7494 (mt) REVERT: A 241 MET cc_start: 0.8717 (ttp) cc_final: 0.8405 (ttt) REVERT: A 317 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8455 (mt) REVERT: B 280 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8873 (mp) REVERT: B 286 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8041 (t0) REVERT: C 54 ARG cc_start: 0.8518 (mmt90) cc_final: 0.8118 (mmm-85) REVERT: C 77 GLU cc_start: 0.8128 (mp0) cc_final: 0.7436 (pt0) REVERT: C 116 ASP cc_start: 0.8175 (t0) cc_final: 0.7831 (t0) REVERT: C 151 ASP cc_start: 0.8624 (p0) cc_final: 0.8396 (p0) REVERT: C 378 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8041 (mtm110) REVERT: C 431 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7539 (mm) REVERT: D 378 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7376 (tpp-160) REVERT: E 74 ASP cc_start: 0.8177 (t70) cc_final: 0.7896 (t70) REVERT: E 77 GLU cc_start: 0.8325 (pm20) cc_final: 0.7770 (pt0) REVERT: E 89 MET cc_start: 0.8707 (mtt) cc_final: 0.8342 (mtt) REVERT: E 401 GLU cc_start: 0.7780 (pt0) cc_final: 0.7453 (pt0) REVERT: F 132 PRO cc_start: 0.8581 (Cg_endo) cc_final: 0.8243 (Cg_exo) REVERT: F 375 GLU cc_start: 0.7976 (pt0) cc_final: 0.7717 (pt0) REVERT: F 390 TYR cc_start: 0.6542 (t80) cc_final: 0.6230 (t80) REVERT: F 404 MET cc_start: 0.3880 (mmp) cc_final: 0.3634 (mmm) outliers start: 80 outliers final: 50 residues processed: 296 average time/residue: 0.1584 time to fit residues: 69.2923 Evaluate side-chains 264 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 90 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 147 optimal weight: 0.4980 chunk 211 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN F 353 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.104791 restraints weight = 26454.391| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.42 r_work: 0.2969 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19907 Z= 0.165 Angle : 0.657 10.002 26938 Z= 0.318 Chirality : 0.047 0.182 3119 Planarity : 0.005 0.047 3473 Dihedral : 6.870 130.290 2805 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.72 % Allowed : 14.82 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.16), residues: 2512 helix: -0.05 (0.17), residues: 965 sheet: -1.25 (0.25), residues: 427 loop : -1.58 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 66 TYR 0.016 0.002 TYR C 97 PHE 0.022 0.001 PHE D 58 TRP 0.004 0.001 TRP F 94 HIS 0.006 0.001 HIS F 354 Details of bonding type rmsd covalent geometry : bond 0.00405 (19905) covalent geometry : angle 0.65715 (26938) hydrogen bonds : bond 0.03934 ( 775) hydrogen bonds : angle 4.39191 ( 2328) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 224 time to evaluate : 0.852 Fit side-chains REVERT: A 215 LEU cc_start: 0.7832 (pp) cc_final: 0.7522 (mt) REVERT: A 241 MET cc_start: 0.8690 (ttp) cc_final: 0.8373 (ttt) REVERT: A 317 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8433 (mt) REVERT: B 280 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8866 (mp) REVERT: B 286 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7980 (t0) REVERT: B 414 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8266 (mp) REVERT: C 54 ARG cc_start: 0.8496 (mmt90) cc_final: 0.8113 (mmm-85) REVERT: C 77 GLU cc_start: 0.8154 (mp0) cc_final: 0.7480 (pt0) REVERT: C 116 ASP cc_start: 0.8155 (t0) cc_final: 0.7836 (t0) REVERT: C 151 ASP cc_start: 0.8581 (p0) cc_final: 0.8361 (p0) REVERT: C 378 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8047 (mtm110) REVERT: C 431 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7637 (mm) REVERT: D 378 ARG cc_start: 0.8123 (ttm110) cc_final: 0.7383 (tpp-160) REVERT: E 74 ASP cc_start: 0.8163 (t70) cc_final: 0.7857 (t70) REVERT: E 89 MET cc_start: 0.8728 (mtt) cc_final: 0.8323 (mtt) REVERT: E 401 GLU cc_start: 0.7643 (pt0) cc_final: 0.7380 (pt0) REVERT: F 375 GLU cc_start: 0.7852 (pt0) cc_final: 0.7607 (pt0) REVERT: F 404 MET cc_start: 0.4029 (mmp) cc_final: 0.3744 (mmm) outliers start: 78 outliers final: 56 residues processed: 290 average time/residue: 0.1648 time to fit residues: 71.0621 Evaluate side-chains 271 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 210 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 237 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 10 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 246 optimal weight: 4.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105174 restraints weight = 26569.710| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.43 r_work: 0.2975 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19907 Z= 0.154 Angle : 0.650 10.623 26938 Z= 0.314 Chirality : 0.046 0.177 3119 Planarity : 0.005 0.051 3473 Dihedral : 6.678 126.768 2805 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.67 % Allowed : 15.63 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.17), residues: 2512 helix: 0.12 (0.17), residues: 961 sheet: -1.18 (0.25), residues: 427 loop : -1.55 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 113 TYR 0.017 0.002 TYR C 402 PHE 0.021 0.001 PHE D 58 TRP 0.004 0.001 TRP C 94 HIS 0.006 0.001 HIS F 354 Details of bonding type rmsd covalent geometry : bond 0.00378 (19905) covalent geometry : angle 0.64959 (26938) hydrogen bonds : bond 0.03809 ( 775) hydrogen bonds : angle 4.31908 ( 2328) Misc. bond : bond 0.00076 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 224 time to evaluate : 0.685 Fit side-chains REVERT: A 215 LEU cc_start: 0.7854 (pp) cc_final: 0.7525 (mt) REVERT: A 241 MET cc_start: 0.8628 (ttp) cc_final: 0.8300 (ttt) REVERT: A 317 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8423 (mt) REVERT: B 41 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8713 (mt) REVERT: B 280 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8845 (mp) REVERT: B 286 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7970 (t0) REVERT: B 414 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8188 (mp) REVERT: C 54 ARG cc_start: 0.8467 (mmt90) cc_final: 0.8085 (mmm-85) REVERT: C 77 GLU cc_start: 0.8122 (mp0) cc_final: 0.7512 (pt0) REVERT: C 116 ASP cc_start: 0.8152 (t0) cc_final: 0.7847 (t0) REVERT: C 151 ASP cc_start: 0.8565 (p0) cc_final: 0.8344 (p0) REVERT: C 264 MET cc_start: 0.9058 (mtm) cc_final: 0.8779 (mtp) REVERT: C 378 ARG cc_start: 0.8386 (ttp80) cc_final: 0.8030 (mtm110) REVERT: C 431 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7680 (mm) REVERT: D 96 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8692 (p) REVERT: D 378 ARG cc_start: 0.8128 (ttm110) cc_final: 0.7385 (tpp-160) REVERT: E 74 ASP cc_start: 0.8178 (t70) cc_final: 0.7844 (t70) REVERT: E 85 HIS cc_start: 0.7464 (p90) cc_final: 0.7102 (m-70) REVERT: E 89 MET cc_start: 0.8726 (mtt) cc_final: 0.8313 (mtt) REVERT: E 401 GLU cc_start: 0.7611 (pt0) cc_final: 0.7355 (pt0) REVERT: F 159 ARG cc_start: 0.7774 (ttp80) cc_final: 0.7479 (ttm110) REVERT: F 299 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8722 (tp) REVERT: F 404 MET cc_start: 0.4248 (mmp) cc_final: 0.3945 (mmm) REVERT: F 418 LYS cc_start: 0.7540 (tppt) cc_final: 0.7332 (tppt) outliers start: 77 outliers final: 58 residues processed: 291 average time/residue: 0.1621 time to fit residues: 69.8351 Evaluate side-chains 280 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 214 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 393 VAL Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 247 optimal weight: 2.9990 chunk 241 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 112 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN F 98 GLN F 257 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.108097 restraints weight = 26430.502| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.39 r_work: 0.3029 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19907 Z= 0.111 Angle : 0.608 11.727 26938 Z= 0.292 Chirality : 0.045 0.207 3119 Planarity : 0.004 0.051 3473 Dihedral : 6.099 118.897 2805 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.38 % Allowed : 16.35 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.17), residues: 2512 helix: 0.43 (0.17), residues: 968 sheet: -1.11 (0.25), residues: 418 loop : -1.55 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 113 TYR 0.017 0.001 TYR D 390 PHE 0.021 0.001 PHE D 58 TRP 0.003 0.001 TRP F 94 HIS 0.006 0.001 HIS F 354 Details of bonding type rmsd covalent geometry : bond 0.00261 (19905) covalent geometry : angle 0.60795 (26938) hydrogen bonds : bond 0.03248 ( 775) hydrogen bonds : angle 4.14757 ( 2328) Misc. bond : bond 0.00041 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 229 time to evaluate : 0.545 Fit side-chains REVERT: A 241 MET cc_start: 0.8589 (ttp) cc_final: 0.8199 (ttt) REVERT: A 317 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8390 (mt) REVERT: B 286 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7831 (t0) REVERT: B 414 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7972 (mp) REVERT: C 54 ARG cc_start: 0.8399 (mmt90) cc_final: 0.8011 (mmm-85) REVERT: C 77 GLU cc_start: 0.8059 (mp0) cc_final: 0.7424 (pt0) REVERT: C 113 ARG cc_start: 0.8296 (ptp-110) cc_final: 0.7449 (mtm-85) REVERT: C 151 ASP cc_start: 0.8515 (p0) cc_final: 0.8279 (p0) REVERT: C 378 ARG cc_start: 0.8329 (ttp80) cc_final: 0.7960 (mtm110) REVERT: C 431 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7693 (mm) REVERT: C 435 GLU cc_start: 0.8007 (pm20) cc_final: 0.7546 (pm20) REVERT: D 378 ARG cc_start: 0.8060 (ttm110) cc_final: 0.7339 (tpp-160) REVERT: E 85 HIS cc_start: 0.7294 (p90) cc_final: 0.7061 (m-70) REVERT: E 89 MET cc_start: 0.8578 (mtt) cc_final: 0.8156 (mtt) REVERT: E 401 GLU cc_start: 0.7446 (pt0) cc_final: 0.7237 (pt0) REVERT: F 69 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6518 (mt-10) REVERT: F 159 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7390 (ttm110) REVERT: F 265 MET cc_start: 0.7429 (ttm) cc_final: 0.7158 (tmm) REVERT: F 385 LYS cc_start: 0.8002 (ptpp) cc_final: 0.7478 (mmtt) REVERT: F 404 MET cc_start: 0.4266 (mmp) cc_final: 0.3915 (mmm) outliers start: 71 outliers final: 46 residues processed: 289 average time/residue: 0.1482 time to fit residues: 63.8660 Evaluate side-chains 265 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 38 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 205 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 217 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 59 optimal weight: 0.4980 chunk 69 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 416 ASN ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN F 98 GLN F 257 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.104405 restraints weight = 26351.536| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.36 r_work: 0.2989 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19907 Z= 0.163 Angle : 0.666 12.082 26938 Z= 0.319 Chirality : 0.047 0.204 3119 Planarity : 0.005 0.052 3473 Dihedral : 6.240 120.229 2805 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.19 % Allowed : 16.59 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.17), residues: 2512 helix: 0.37 (0.17), residues: 966 sheet: -1.03 (0.26), residues: 416 loop : -1.51 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 417 TYR 0.017 0.002 TYR C 402 PHE 0.032 0.001 PHE G 117 TRP 0.004 0.001 TRP C 94 HIS 0.006 0.001 HIS F 354 Details of bonding type rmsd covalent geometry : bond 0.00400 (19905) covalent geometry : angle 0.66553 (26938) hydrogen bonds : bond 0.03791 ( 775) hydrogen bonds : angle 4.26580 ( 2328) Misc. bond : bond 0.00075 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 215 time to evaluate : 0.761 Fit side-chains REVERT: A 102 PHE cc_start: 0.7962 (t80) cc_final: 0.7570 (t80) REVERT: A 241 MET cc_start: 0.8561 (ttp) cc_final: 0.8232 (ttt) REVERT: A 317 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8403 (mt) REVERT: B 41 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8655 (mt) REVERT: B 286 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7929 (t0) REVERT: B 348 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7741 (pm20) REVERT: B 414 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8077 (mp) REVERT: B 417 ARG cc_start: 0.7684 (ttt90) cc_final: 0.7257 (ttt90) REVERT: B 421 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: C 54 ARG cc_start: 0.8418 (mmt90) cc_final: 0.8050 (mmm-85) REVERT: C 77 GLU cc_start: 0.8083 (mp0) cc_final: 0.7445 (pt0) REVERT: C 151 ASP cc_start: 0.8568 (p0) cc_final: 0.8350 (p0) REVERT: C 264 MET cc_start: 0.9066 (mtm) cc_final: 0.8804 (mtp) REVERT: C 378 ARG cc_start: 0.8337 (ttp80) cc_final: 0.7980 (mtm110) REVERT: C 382 GLU cc_start: 0.8193 (tt0) cc_final: 0.7955 (tt0) REVERT: C 431 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7713 (mm) REVERT: C 435 GLU cc_start: 0.8075 (pm20) cc_final: 0.7605 (pm20) REVERT: D 378 ARG cc_start: 0.8088 (ttm110) cc_final: 0.7392 (tpp-160) REVERT: E 74 ASP cc_start: 0.8141 (t70) cc_final: 0.7786 (t70) REVERT: E 85 HIS cc_start: 0.7415 (p90) cc_final: 0.7089 (m-70) REVERT: E 89 MET cc_start: 0.8648 (mtt) cc_final: 0.8223 (mtt) REVERT: E 401 GLU cc_start: 0.7539 (pt0) cc_final: 0.7294 (pt0) REVERT: F 159 ARG cc_start: 0.7710 (ttp80) cc_final: 0.7370 (ttm110) REVERT: F 377 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6480 (pp) REVERT: F 385 LYS cc_start: 0.7975 (ptpp) cc_final: 0.7447 (mmtt) REVERT: F 404 MET cc_start: 0.4197 (mmp) cc_final: 0.3837 (mmm) outliers start: 67 outliers final: 52 residues processed: 274 average time/residue: 0.1498 time to fit residues: 61.3384 Evaluate side-chains 266 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 206 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 98 GLN Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 28 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 203 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 169 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN B 421 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN F 98 GLN F 257 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.112271 restraints weight = 26334.896| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.08 r_work: 0.3018 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 19907 Z= 0.196 Angle : 0.881 59.094 26938 Z= 0.477 Chirality : 0.048 0.442 3119 Planarity : 0.005 0.137 3473 Dihedral : 6.251 120.396 2805 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 3.24 % Allowed : 16.68 % Favored : 80.08 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.17), residues: 2512 helix: 0.35 (0.17), residues: 967 sheet: -1.02 (0.26), residues: 416 loop : -1.51 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 417 TYR 0.017 0.002 TYR C 402 PHE 0.029 0.002 PHE G 117 TRP 0.021 0.002 TRP B 94 HIS 0.006 0.001 HIS F 354 Details of bonding type rmsd covalent geometry : bond 0.00478 (19905) covalent geometry : angle 0.88076 (26938) hydrogen bonds : bond 0.03826 ( 775) hydrogen bonds : angle 4.26633 ( 2328) Misc. bond : bond 0.00079 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5024 Ramachandran restraints generated. 2512 Oldfield, 0 Emsley, 2512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 208 time to evaluate : 0.740 Fit side-chains REVERT: A 102 PHE cc_start: 0.7959 (t80) cc_final: 0.7621 (t80) REVERT: A 241 MET cc_start: 0.8491 (ttp) cc_final: 0.8160 (ttt) REVERT: A 317 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8421 (mt) REVERT: B 41 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8757 (mt) REVERT: B 286 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7878 (t0) REVERT: B 414 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8265 (mp) REVERT: C 54 ARG cc_start: 0.8464 (mmt90) cc_final: 0.8179 (mmm-85) REVERT: C 77 GLU cc_start: 0.8047 (mp0) cc_final: 0.7538 (pt0) REVERT: C 264 MET cc_start: 0.8967 (mtm) cc_final: 0.8705 (mtp) REVERT: C 378 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7963 (mtm110) REVERT: C 431 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7753 (mm) REVERT: C 435 GLU cc_start: 0.8081 (pm20) cc_final: 0.7629 (pm20) REVERT: D 378 ARG cc_start: 0.8048 (ttm110) cc_final: 0.7575 (tpp-160) REVERT: E 74 ASP cc_start: 0.8114 (t70) cc_final: 0.7809 (t70) REVERT: E 89 MET cc_start: 0.8644 (mtt) cc_final: 0.8241 (mtt) REVERT: E 329 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: E 401 GLU cc_start: 0.7444 (pt0) cc_final: 0.7188 (pt0) REVERT: F 159 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7497 (ttm110) REVERT: F 377 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6684 (pp) REVERT: F 385 LYS cc_start: 0.8027 (ptpp) cc_final: 0.7490 (mmtt) REVERT: F 404 MET cc_start: 0.4186 (mmp) cc_final: 0.3804 (mmm) outliers start: 68 outliers final: 56 residues processed: 267 average time/residue: 0.1547 time to fit residues: 61.9637 Evaluate side-chains 272 residues out of total 2101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 191 CYS Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 261 VAL Chi-restraints excluded: chain E residue 267 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 98 GLN Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 370 ASN Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 393 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 119 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 HIS E 152 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.111669 restraints weight = 26180.762| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.14 r_work: 0.3009 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.520 19907 Z= 0.342 Angle : 0.837 41.449 26938 Z= 0.446 Chirality : 0.048 0.427 3119 Planarity : 0.006 0.207 3473 Dihedral : 6.251 120.397 2805 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 3.00 % Allowed : 16.83 % Favored : 80.17 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.17), residues: 2512 helix: 0.35 (0.17), residues: 967 sheet: -1.03 (0.26), residues: 416 loop : -1.51 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 113 TYR 0.017 0.002 TYR C 402 PHE 0.029 0.002 PHE G 117 TRP 0.021 0.002 TRP B 94 HIS 0.006 0.001 HIS F 354 Details of bonding type rmsd covalent geometry : bond 0.00771 (19905) covalent geometry : angle 0.83726 (26938) hydrogen bonds : bond 0.03826 ( 775) hydrogen bonds : angle 4.26618 ( 2328) Misc. bond : bond 0.00080 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4983.75 seconds wall clock time: 86 minutes 4.60 seconds (5164.60 seconds total)