Starting phenix.real_space_refine on Thu Mar 5 17:13:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9i_34568/03_2026/8h9i_34568.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9i_34568/03_2026/8h9i_34568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h9i_34568/03_2026/8h9i_34568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9i_34568/03_2026/8h9i_34568.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h9i_34568/03_2026/8h9i_34568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9i_34568/03_2026/8h9i_34568.map" } resolution = 2.77 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= 0.000 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 88 5.16 5 C 15079 2.51 5 N 4158 2.21 5 O 4618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 181 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: 23961 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3830 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 484} Chain breaks: 1 Chain: "A" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3639 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "B" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3714 Classifications: {'peptide': 487} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 468} Chain breaks: 1 Chain: "E" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3522 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 441} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3562 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 444} Chain: "G" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 623 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1437 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "D" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3482 Classifications: {'peptide': 460} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 434} Chain breaks: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.20, per 1000 atoms: 0.26 Number of scatterers: 23961 At special positions: 0 Unit cell: (121.91, 128.48, 133.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 13 15.00 Mg 5 11.99 O 4618 8.00 N 4158 7.00 C 15079 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=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5688 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 19 sheets defined 49.4% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.533A pdb=" N LEU C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.654A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.722A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 194 through 197 removed outlier: 3.647A pdb=" N LYS C 197 " --> pdb=" O ASP C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 239 through 260 Proline residue: C 247 - end of helix removed outlier: 3.979A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.823A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.597A pdb=" N GLY C 317 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.507A pdb=" N ALA C 377 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 401 removed outlier: 4.337A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 411 through 428 Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 460 through 475 Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 508 Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.746A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.599A pdb=" N GLY A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.930A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.691A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 295 through 296 No H-bonds generated for 'chain 'A' and resid 295 through 296' Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.510A pdb=" N HIS A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.688A pdb=" N GLY A 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 380 through 401 removed outlier: 3.819A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.658A pdb=" N LEU A 480 " --> pdb=" O HIS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 507 removed outlier: 3.501A pdb=" N GLY A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 removed outlier: 3.601A pdb=" N LEU B 12 " --> pdb=" O MET B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.666A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.806A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 239 through 260 Proline residue: B 247 - end of helix removed outlier: 4.002A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 removed outlier: 3.619A pdb=" N GLN B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.871A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 374 through 379 Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.979A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 429 removed outlier: 3.710A pdb=" N LYS B 429 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 460 through 475 Processing helix chain 'B' and resid 476 through 487 Processing helix chain 'B' and resid 490 through 508 Processing helix chain 'E' and resid 125 through 129 Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 228 through 251 removed outlier: 4.858A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE E 246 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.804A pdb=" N PHE E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 284 removed outlier: 3.812A pdb=" N TYR E 284 " --> pdb=" O ALA E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.681A pdb=" N MET E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 322 through 330 Processing helix chain 'E' and resid 339 through 345 Processing helix chain 'E' and resid 362 through 392 removed outlier: 7.529A pdb=" N SER E 368 " --> pdb=" O ASN E 364 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N GLU E 369 " --> pdb=" O ILE E 365 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS E 370 " --> pdb=" O VAL E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 417 removed outlier: 3.963A pdb=" N LYS E 404 " --> pdb=" O SER E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 426 removed outlier: 4.484A pdb=" N VAL E 426 " --> pdb=" O VAL E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 450 Processing helix chain 'E' and resid 465 through 476 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 125 through 129 Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 164 through 180 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 228 through 249 removed outlier: 5.103A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 273 removed outlier: 3.734A pdb=" N THR F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA F 273 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 276 No H-bonds generated for 'chain 'F' and resid 274 through 276' Processing helix chain 'F' and resid 287 through 297 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 322 through 330 removed outlier: 4.420A pdb=" N ALA F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 Processing helix chain 'F' and resid 367 through 395 removed outlier: 4.543A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 399 Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.719A pdb=" N SER F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 423 No H-bonds generated for 'chain 'F' and resid 421 through 423' Processing helix chain 'F' and resid 424 through 429 Processing helix chain 'F' and resid 436 through 450 Processing helix chain 'F' and resid 456 through 460 Processing helix chain 'F' and resid 465 through 480 removed outlier: 3.560A pdb=" N ALA F 469 " --> pdb=" O PRO F 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 32 removed outlier: 3.754A pdb=" N ALA G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 271 removed outlier: 3.536A pdb=" N ALA G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 27 Processing helix chain 'O' and resid 31 through 47 Processing helix chain 'O' and resid 48 through 57 Processing helix chain 'O' and resid 61 through 76 Processing helix chain 'O' and resid 79 through 92 Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'O' and resid 97 through 111 Processing helix chain 'O' and resid 128 through 140 removed outlier: 3.577A pdb=" N SER O 140 " --> pdb=" O THR O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 188 removed outlier: 3.719A pdb=" N LYS O 178 " --> pdb=" O SER O 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 164 through 179 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 228 through 249 removed outlier: 4.948A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 removed outlier: 4.067A pdb=" N PHE D 264 " --> pdb=" O ASN D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 280 through 284 Processing helix chain 'D' and resid 287 through 297 Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 339 through 344 Processing helix chain 'D' and resid 367 through 394 removed outlier: 3.811A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 399 Processing helix chain 'D' and resid 400 through 417 removed outlier: 3.567A pdb=" N LYS D 404 " --> pdb=" O SER D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 449 Processing helix chain 'D' and resid 456 through 460 removed outlier: 3.662A pdb=" N PHE D 460 " --> pdb=" O GLU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 480 Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 35 removed outlier: 5.495A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 43 current: chain 'C' and resid 60 through 66 removed outlier: 5.778A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 75 current: chain 'A' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 43 current: chain 'A' and resid 60 through 66 removed outlier: 6.556A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 75 current: chain 'B' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 43 current: chain 'B' and resid 60 through 66 removed outlier: 5.792A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 75 current: chain 'E' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 23 through 28 current: chain 'E' and resid 49 through 57 removed outlier: 6.588A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 60 through 65 current: chain 'F' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 23 through 28 current: chain 'F' and resid 49 through 57 removed outlier: 6.750A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 60 through 65 current: chain 'O' and resid 147 through 151 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 147 through 151 current: chain 'O' and resid 169 through 172 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 169 through 172 current: chain 'D' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 23 through 28 current: chain 'D' and resid 49 through 55 removed outlier: 6.681A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.117A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 107 through 109 Processing sheet with id=AA4, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.625A pdb=" N ILE C 159 " --> pdb=" O MET C 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 326 through 328 removed outlier: 6.462A pdb=" N ILE C 167 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU C 352 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.000A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.694A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 264 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU A 324 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE A 266 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL A 326 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TYR A 268 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLU A 328 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.962A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 109 removed outlier: 3.548A pdb=" N TYR B 268 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 86 through 89 removed outlier: 3.996A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.070A pdb=" N MET E 98 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLN E 224 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE E 155 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY E 156 " --> pdb=" O ALA E 334 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 135 through 136 removed outlier: 4.492A pdb=" N TYR E 149 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.202A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 97 through 98 removed outlier: 6.457A pdb=" N MET F 98 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER F 184 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N VAL F 221 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE F 186 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLY F 223 " --> pdb=" O PHE F 186 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLY F 188 " --> pdb=" O GLY F 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.119A pdb=" N TYR F 149 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 86 through 89 removed outlier: 3.915A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.141A pdb=" N MET D 98 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL D 185 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASP D 259 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA D 187 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 134 through 136 removed outlier: 4.363A pdb=" N GLU D 134 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 334 through 335 1138 hydrogen bonds defined for protein. 3249 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: 4.69 Time building geometry restraints manager: 3.37 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: 5972 1.33 - 1.45: 3971 1.45 - 1.57: 14167 1.57 - 1.69: 21 1.69 - 1.81: 169 Bond restraints: 24300 Sorted by residual: bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.462 -0.125 1.10e-02 8.26e+03 1.28e+02 bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.458 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.458 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" C4 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.374 1.283 0.091 1.00e-02 1.00e+04 8.32e+01 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.285 0.089 1.00e-02 1.00e+04 7.87e+01 ... (remaining 24295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 32691 3.63 - 7.26: 151 7.26 - 10.89: 27 10.89 - 14.52: 3 14.52 - 18.15: 3 Bond angle restraints: 32875 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 121.72 18.15 1.00e+00 1.00e+00 3.30e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 123.53 16.34 1.00e+00 1.00e+00 2.67e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 125.02 14.85 1.00e+00 1.00e+00 2.21e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 123.88 12.95 1.00e+00 1.00e+00 1.68e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 124.96 11.87 1.00e+00 1.00e+00 1.41e+02 ... (remaining 32870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.36: 14532 32.36 - 64.72: 345 64.72 - 97.08: 47 97.08 - 129.43: 1 129.43 - 161.79: 1 Dihedral angle restraints: 14926 sinusoidal: 6030 harmonic: 8896 Sorted by residual: dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 138.20 161.79 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 61.42 -121.42 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 32.51 -92.51 1 2.00e+01 2.50e-03 2.51e+01 ... (remaining 14923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2862 0.050 - 0.101: 794 0.101 - 0.151: 175 0.151 - 0.201: 9 0.201 - 0.252: 3 Chirality restraints: 3843 Sorted by residual: chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.43 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.44 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.47 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 3840 not shown) Planarity restraints: 4244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 174 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ASN F 174 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN F 174 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN F 175 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 417 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C LEU E 417 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU E 417 " 0.015 2.00e-02 2.50e+03 pdb=" N SER E 418 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 174 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ASN D 174 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN D 174 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN D 175 " 0.013 2.00e-02 2.50e+03 ... (remaining 4241 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 185 2.54 - 3.13: 18987 3.13 - 3.72: 36770 3.72 - 4.31: 56181 4.31 - 4.90: 92823 Nonbonded interactions: 204946 Sorted by model distance: nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 1.946 2.170 nonbonded pdb=" O1B ATP A 601 " pdb="MG MG A 602 " model vdw 1.971 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 2.033 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 2.069 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 2.124 2.170 ... (remaining 204941 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 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'B' and resid 24 through 602) selection = (chain 'C' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) } ncs_group { reference = (chain 'D' and (resid 12 through 318 or (resid 319 and (name N or name CA or nam \ e C or name O or name CB )) or resid 320 through 403 or (resid 404 and (name N o \ r name CA or name C or name O or name CB )) or resid 405 through 477)) selection = (chain 'E' and (resid 12 through 420 or resid 431 through 477)) selection = (chain 'F' and (resid 12 through 318 or (resid 319 and (name N or name CA or nam \ e C or name O or name CB )) or resid 320 through 403 or (resid 404 and (name N o \ r name CA or name C or name O or name CB )) or resid 405 through 420 or resid 43 \ 1 through 477)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.760 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 : 0.007 0.143 24300 Z= 0.406 Angle : 0.798 18.154 32875 Z= 0.514 Chirality : 0.047 0.252 3843 Planarity : 0.004 0.041 4244 Dihedral : 14.435 161.794 9238 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: -2.77 (0.13), residues: 3105 helix: -1.56 (0.12), residues: 1333 sheet: -1.63 (0.20), residues: 492 loop : -2.06 (0.15), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 263 TYR 0.019 0.001 TYR O 170 PHE 0.011 0.002 PHE E 264 HIS 0.009 0.001 HIS E 370 Details of bonding type rmsd covalent geometry : bond 0.00736 (24300) covalent geometry : angle 0.79802 (32875) hydrogen bonds : bond 0.15606 ( 1138) hydrogen bonds : angle 7.01246 ( 3249) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 195 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6947 (tp30) REVERT: C 463 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8304 (ttmt) REVERT: C 484 ARG cc_start: 0.7034 (ttt-90) cc_final: 0.6686 (ttm170) REVERT: A 96 ASP cc_start: 0.8239 (p0) cc_final: 0.7936 (p0) REVERT: A 351 PHE cc_start: 0.7941 (m-80) cc_final: 0.7423 (t80) REVERT: A 362 ARG cc_start: 0.7592 (mtt180) cc_final: 0.6590 (mtt90) REVERT: A 422 VAL cc_start: 0.6951 (t) cc_final: 0.6592 (m) REVERT: A 446 TYR cc_start: 0.7713 (t80) cc_final: 0.7359 (t80) REVERT: B 89 LYS cc_start: 0.8727 (mtmm) cc_final: 0.8389 (mtmt) REVERT: F 408 SER cc_start: 0.7877 (m) cc_final: 0.7666 (p) REVERT: F 422 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7593 (tm-30) REVERT: G 229 MET cc_start: 0.7431 (ttp) cc_final: 0.7210 (ptm) REVERT: G 260 LYS cc_start: 0.8719 (tttt) cc_final: 0.8500 (tttp) REVERT: O 33 GLU cc_start: 0.7083 (pt0) cc_final: 0.6608 (pm20) REVERT: O 37 LYS cc_start: 0.7216 (tptm) cc_final: 0.6700 (tppt) REVERT: O 134 LEU cc_start: 0.7772 (tp) cc_final: 0.7465 (mp) REVERT: O 186 MET cc_start: 0.5992 (ptp) cc_final: 0.5474 (pp-130) REVERT: D 59 SER cc_start: 0.8979 (m) cc_final: 0.8752 (p) REVERT: D 149 TYR cc_start: 0.6360 (m-10) cc_final: 0.6126 (m-10) REVERT: D 180 HIS cc_start: 0.7594 (t-90) cc_final: 0.7379 (t-90) REVERT: D 248 ASP cc_start: 0.7190 (m-30) cc_final: 0.6841 (m-30) REVERT: D 462 MET cc_start: 0.5792 (mmt) cc_final: 0.5526 (mmt) outliers start: 0 outliers final: 1 residues processed: 415 average time/residue: 0.7719 time to fit residues: 360.3105 Evaluate side-chains 294 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 380 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN A 396 GLN A 432 GLN B 172 GLN B 466 ASN E 378 GLN E 382 GLN E 419 GLN E 446 GLN F 133 GLN F 180 HIS F 266 GLN O 70 ASN O 84 ASN O 112 HIS D 210 ASN D 249 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103229 restraints weight = 31135.901| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.17 r_work: 0.3100 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 24300 Z= 0.194 Angle : 0.597 7.635 32875 Z= 0.308 Chirality : 0.046 0.210 3843 Planarity : 0.004 0.046 4244 Dihedral : 7.753 133.009 3507 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 2.20 % Allowed : 10.96 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: -1.41 (0.14), residues: 3105 helix: -0.17 (0.14), residues: 1337 sheet: -1.20 (0.21), residues: 484 loop : -1.55 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 373 TYR 0.016 0.001 TYR O 170 PHE 0.027 0.001 PHE D 262 HIS 0.008 0.001 HIS E 370 Details of bonding type rmsd covalent geometry : bond 0.00462 (24300) covalent geometry : angle 0.59704 (32875) hydrogen bonds : bond 0.05114 ( 1138) hydrogen bonds : angle 5.29411 ( 3249) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 317 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: C 143 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.8100 (mmp80) REVERT: C 195 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7062 (tp30) REVERT: C 425 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8505 (m) REVERT: C 484 ARG cc_start: 0.7137 (ttt-90) cc_final: 0.6585 (ttm170) REVERT: A 89 LYS cc_start: 0.8121 (mmtp) cc_final: 0.7908 (mmtt) REVERT: A 96 ASP cc_start: 0.8563 (p0) cc_final: 0.8112 (p0) REVERT: A 226 MET cc_start: 0.9193 (tpt) cc_final: 0.8556 (tpt) REVERT: A 351 PHE cc_start: 0.8131 (m-80) cc_final: 0.7191 (t80) REVERT: A 359 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7110 (mtpt) REVERT: A 362 ARG cc_start: 0.7824 (mtt180) cc_final: 0.6706 (mtt180) REVERT: A 419 SER cc_start: 0.6687 (m) cc_final: 0.6484 (p) REVERT: A 422 VAL cc_start: 0.6606 (t) cc_final: 0.6253 (m) REVERT: A 446 TYR cc_start: 0.6986 (t80) cc_final: 0.6445 (t80) REVERT: B 8 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6297 (mpm) REVERT: B 224 ASP cc_start: 0.8799 (t70) cc_final: 0.8591 (t0) REVERT: E 340 ARG cc_start: 0.7437 (tpp80) cc_final: 0.6888 (tpt170) REVERT: E 344 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7198 (mm-30) REVERT: F 170 MET cc_start: 0.8884 (tpp) cc_final: 0.8603 (mmt) REVERT: F 408 SER cc_start: 0.7738 (m) cc_final: 0.7468 (p) REVERT: F 422 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7712 (tm-30) REVERT: G 229 MET cc_start: 0.7546 (ttp) cc_final: 0.7322 (ptm) REVERT: G 260 LYS cc_start: 0.8941 (tttt) cc_final: 0.8497 (tttp) REVERT: O 33 GLU cc_start: 0.7000 (pt0) cc_final: 0.6418 (pm20) REVERT: O 37 LYS cc_start: 0.7025 (tptm) cc_final: 0.6513 (tppt) REVERT: O 42 VAL cc_start: 0.6855 (t) cc_final: 0.6552 (m) REVERT: O 134 LEU cc_start: 0.7628 (tp) cc_final: 0.7363 (mp) REVERT: O 186 MET cc_start: 0.5859 (ptp) cc_final: 0.5227 (pp-130) REVERT: D 59 SER cc_start: 0.8976 (m) cc_final: 0.8664 (p) REVERT: D 149 TYR cc_start: 0.6463 (m-10) cc_final: 0.6257 (m-10) REVERT: D 180 HIS cc_start: 0.7548 (t-90) cc_final: 0.7073 (t-90) REVERT: D 248 ASP cc_start: 0.7454 (m-30) cc_final: 0.7026 (m-30) REVERT: D 259 ASP cc_start: 0.8711 (t0) cc_final: 0.8281 (t0) REVERT: D 462 MET cc_start: 0.6012 (mmt) cc_final: 0.5810 (mmt) outliers start: 56 outliers final: 21 residues processed: 356 average time/residue: 0.7108 time to fit residues: 288.4247 Evaluate side-chains 304 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 280 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 308 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 109 optimal weight: 4.9990 chunk 309 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 290 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 287 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 110 optimal weight: 0.2980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 ASN A 396 GLN B 466 ASN O 44 GLN D 54 GLN D 210 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.141608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105237 restraints weight = 30817.924| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.19 r_work: 0.3132 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24300 Z= 0.133 Angle : 0.528 8.492 32875 Z= 0.271 Chirality : 0.043 0.167 3843 Planarity : 0.004 0.043 4244 Dihedral : 7.152 112.408 3505 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.26 % Rotamer: Outliers : 2.24 % Allowed : 13.44 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: -0.55 (0.15), residues: 3105 helix: 0.60 (0.14), residues: 1320 sheet: -0.88 (0.22), residues: 494 loop : -1.07 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 373 TYR 0.020 0.001 TYR F 461 PHE 0.028 0.001 PHE D 262 HIS 0.007 0.001 HIS E 370 Details of bonding type rmsd covalent geometry : bond 0.00305 (24300) covalent geometry : angle 0.52819 (32875) hydrogen bonds : bond 0.04267 ( 1138) hydrogen bonds : angle 4.94077 ( 3249) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 322 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 25 LEU cc_start: 0.7609 (mt) cc_final: 0.7393 (mm) REVERT: C 143 ARG cc_start: 0.8395 (tpp-160) cc_final: 0.8122 (mmp80) REVERT: C 373 ARG cc_start: 0.8281 (mtt90) cc_final: 0.8067 (mtt90) REVERT: C 425 THR cc_start: 0.8692 (t) cc_final: 0.8470 (m) REVERT: C 484 ARG cc_start: 0.7124 (ttt-90) cc_final: 0.6710 (ttt-90) REVERT: A 96 ASP cc_start: 0.8589 (p0) cc_final: 0.8115 (p0) REVERT: A 208 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8326 (mt0) REVERT: A 226 MET cc_start: 0.9192 (tpt) cc_final: 0.8652 (tpt) REVERT: A 351 PHE cc_start: 0.7781 (m-80) cc_final: 0.7144 (t80) REVERT: A 356 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7745 (mt) REVERT: A 362 ARG cc_start: 0.7693 (mtt180) cc_final: 0.6604 (mtt180) REVERT: A 422 VAL cc_start: 0.6556 (t) cc_final: 0.6216 (m) REVERT: A 446 TYR cc_start: 0.6866 (t80) cc_final: 0.6281 (t80) REVERT: A 476 HIS cc_start: 0.6685 (m-70) cc_final: 0.6438 (m-70) REVERT: B 24 ASP cc_start: 0.7539 (t70) cc_final: 0.7292 (m-30) REVERT: B 195 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: E 340 ARG cc_start: 0.7474 (tpp80) cc_final: 0.6999 (tpt170) REVERT: E 344 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7234 (mm-30) REVERT: E 431 MET cc_start: 0.8100 (mmm) cc_final: 0.7710 (mtm) REVERT: E 442 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7430 (ttpt) REVERT: F 170 MET cc_start: 0.8886 (tpp) cc_final: 0.8618 (mmt) REVERT: F 171 GLU cc_start: 0.8152 (tp30) cc_final: 0.7867 (tp30) REVERT: F 408 SER cc_start: 0.7725 (m) cc_final: 0.7472 (p) REVERT: F 422 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7624 (tm-30) REVERT: G 229 MET cc_start: 0.7474 (ttp) cc_final: 0.7272 (ptm) REVERT: G 260 LYS cc_start: 0.8892 (tttt) cc_final: 0.8461 (tttp) REVERT: O 33 GLU cc_start: 0.7060 (pt0) cc_final: 0.6448 (pm20) REVERT: O 37 LYS cc_start: 0.7036 (tptm) cc_final: 0.6604 (tppt) REVERT: O 42 VAL cc_start: 0.6861 (t) cc_final: 0.6566 (m) REVERT: O 113 ARG cc_start: 0.5539 (mtm180) cc_final: 0.5322 (mtm-85) REVERT: O 134 LEU cc_start: 0.7648 (tp) cc_final: 0.7379 (mp) REVERT: O 186 MET cc_start: 0.5880 (ptp) cc_final: 0.5237 (pp-130) REVERT: D 59 SER cc_start: 0.8868 (m) cc_final: 0.8583 (p) REVERT: D 170 MET cc_start: 0.6240 (tpp) cc_final: 0.6027 (mmm) REVERT: D 180 HIS cc_start: 0.7419 (t-90) cc_final: 0.6959 (t-90) REVERT: D 248 ASP cc_start: 0.7432 (m-30) cc_final: 0.7008 (m-30) REVERT: D 259 ASP cc_start: 0.8553 (t0) cc_final: 0.8082 (t70) outliers start: 57 outliers final: 22 residues processed: 360 average time/residue: 0.6851 time to fit residues: 282.6934 Evaluate side-chains 303 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 278 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 308 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 232 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN B 385 GLN B 466 ASN B 503 ASN E 445 GLN O 29 GLN O 180 GLN D 54 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103393 restraints weight = 30933.219| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.15 r_work: 0.3102 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24300 Z= 0.185 Angle : 0.567 8.738 32875 Z= 0.289 Chirality : 0.045 0.240 3843 Planarity : 0.004 0.044 4244 Dihedral : 7.244 116.504 3505 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 2.71 % Allowed : 15.05 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: -0.38 (0.15), residues: 3105 helix: 0.73 (0.14), residues: 1331 sheet: -0.77 (0.22), residues: 499 loop : -1.00 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 362 TYR 0.023 0.001 TYR B 446 PHE 0.029 0.001 PHE D 262 HIS 0.008 0.001 HIS E 370 Details of bonding type rmsd covalent geometry : bond 0.00443 (24300) covalent geometry : angle 0.56725 (32875) hydrogen bonds : bond 0.04579 ( 1138) hydrogen bonds : angle 4.93057 ( 3249) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 293 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: C 425 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8484 (m) REVERT: A 89 LYS cc_start: 0.8180 (mmtp) cc_final: 0.7971 (mmmt) REVERT: A 96 ASP cc_start: 0.8592 (p0) cc_final: 0.8138 (p0) REVERT: A 97 VAL cc_start: 0.8981 (p) cc_final: 0.8729 (m) REVERT: A 351 PHE cc_start: 0.7780 (m-80) cc_final: 0.7039 (t80) REVERT: A 362 ARG cc_start: 0.7715 (mtt180) cc_final: 0.6637 (mtt180) REVERT: A 422 VAL cc_start: 0.6636 (t) cc_final: 0.6285 (m) REVERT: A 475 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: B 24 ASP cc_start: 0.7601 (t70) cc_final: 0.7303 (m-30) REVERT: B 195 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: E 340 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7214 (tpt170) REVERT: E 431 MET cc_start: 0.8119 (mmm) cc_final: 0.7811 (mtm) REVERT: F 170 MET cc_start: 0.8906 (tpp) cc_final: 0.8642 (mmt) REVERT: F 217 LYS cc_start: 0.8233 (ptpp) cc_final: 0.7501 (mttp) REVERT: F 408 SER cc_start: 0.7777 (m) cc_final: 0.7523 (p) REVERT: F 422 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7670 (tm-30) REVERT: G 229 MET cc_start: 0.7446 (ttp) cc_final: 0.7246 (ptm) REVERT: G 260 LYS cc_start: 0.8951 (tttt) cc_final: 0.8550 (tttp) REVERT: O 33 GLU cc_start: 0.7070 (pt0) cc_final: 0.6372 (pm20) REVERT: O 37 LYS cc_start: 0.7065 (tptm) cc_final: 0.6620 (tppt) REVERT: O 134 LEU cc_start: 0.7645 (tp) cc_final: 0.7388 (mp) REVERT: O 186 MET cc_start: 0.5918 (ptp) cc_final: 0.5269 (pp-130) REVERT: D 59 SER cc_start: 0.8874 (m) cc_final: 0.8582 (p) REVERT: D 170 MET cc_start: 0.6371 (tpp) cc_final: 0.6168 (mmm) REVERT: D 180 HIS cc_start: 0.7479 (t-90) cc_final: 0.6965 (t-90) REVERT: D 248 ASP cc_start: 0.7417 (m-30) cc_final: 0.7014 (m-30) REVERT: D 259 ASP cc_start: 0.8601 (t0) cc_final: 0.8152 (t70) REVERT: D 396 MET cc_start: 0.2097 (OUTLIER) cc_final: 0.1415 (ppp) REVERT: D 479 GLU cc_start: 0.2993 (OUTLIER) cc_final: 0.2717 (mp0) outliers start: 69 outliers final: 30 residues processed: 342 average time/residue: 0.6565 time to fit residues: 258.4897 Evaluate side-chains 319 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 269 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 294 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN B 466 ASN B 503 ASN E 378 GLN F 388 GLN D 54 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104372 restraints weight = 30895.862| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.18 r_work: 0.3105 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24300 Z= 0.171 Angle : 0.557 9.985 32875 Z= 0.283 Chirality : 0.044 0.167 3843 Planarity : 0.004 0.043 4244 Dihedral : 7.129 115.338 3505 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 2.55 % Allowed : 16.39 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: -0.22 (0.15), residues: 3105 helix: 0.86 (0.14), residues: 1328 sheet: -0.69 (0.23), residues: 488 loop : -0.91 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 373 TYR 0.022 0.001 TYR B 446 PHE 0.030 0.001 PHE D 262 HIS 0.008 0.001 HIS E 370 Details of bonding type rmsd covalent geometry : bond 0.00407 (24300) covalent geometry : angle 0.55719 (32875) hydrogen bonds : bond 0.04424 ( 1138) hydrogen bonds : angle 4.89078 ( 3249) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 284 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: C 143 ARG cc_start: 0.8436 (tpp-160) cc_final: 0.8181 (mmp80) REVERT: C 373 ARG cc_start: 0.8359 (mtt90) cc_final: 0.8144 (mtt90) REVERT: C 425 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8472 (m) REVERT: A 62 MET cc_start: 0.8875 (ttm) cc_final: 0.8539 (ttt) REVERT: A 89 LYS cc_start: 0.8165 (mmtp) cc_final: 0.7869 (mmtm) REVERT: A 96 ASP cc_start: 0.8599 (p0) cc_final: 0.8150 (p0) REVERT: A 97 VAL cc_start: 0.8962 (p) cc_final: 0.8717 (m) REVERT: A 362 ARG cc_start: 0.7700 (mtt180) cc_final: 0.6548 (mtt90) REVERT: A 422 VAL cc_start: 0.6616 (t) cc_final: 0.6260 (m) REVERT: B 24 ASP cc_start: 0.7596 (t70) cc_final: 0.7310 (m-30) REVERT: B 195 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: E 205 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: E 340 ARG cc_start: 0.7541 (tpp80) cc_final: 0.7257 (tpt-90) REVERT: E 431 MET cc_start: 0.8130 (mmm) cc_final: 0.7844 (mtm) REVERT: F 170 MET cc_start: 0.8906 (tpp) cc_final: 0.8652 (mmt) REVERT: F 408 SER cc_start: 0.7771 (m) cc_final: 0.7522 (p) REVERT: F 422 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7633 (tm-30) REVERT: G 260 LYS cc_start: 0.8921 (tttt) cc_final: 0.8522 (tttp) REVERT: O 37 LYS cc_start: 0.7054 (tptm) cc_final: 0.6539 (tppt) REVERT: O 42 VAL cc_start: 0.7079 (t) cc_final: 0.6798 (m) REVERT: O 113 ARG cc_start: 0.6740 (mtm110) cc_final: 0.6528 (mtm110) REVERT: O 134 LEU cc_start: 0.7690 (tp) cc_final: 0.7442 (mp) REVERT: O 186 MET cc_start: 0.5920 (ptp) cc_final: 0.5299 (pp-130) REVERT: D 59 SER cc_start: 0.8848 (m) cc_final: 0.8554 (p) REVERT: D 170 MET cc_start: 0.6400 (tpp) cc_final: 0.6166 (mmm) REVERT: D 180 HIS cc_start: 0.7489 (t-90) cc_final: 0.6924 (t-90) REVERT: D 248 ASP cc_start: 0.7395 (m-30) cc_final: 0.6985 (m-30) REVERT: D 259 ASP cc_start: 0.8570 (t0) cc_final: 0.8122 (t70) outliers start: 65 outliers final: 34 residues processed: 329 average time/residue: 0.6864 time to fit residues: 259.8929 Evaluate side-chains 301 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain O residue 10 GLN Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 435 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 306 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 278 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN E 378 GLN F 388 GLN D 54 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.139882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103050 restraints weight = 30850.674| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.03 r_work: 0.3109 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24300 Z= 0.171 Angle : 0.555 10.018 32875 Z= 0.283 Chirality : 0.044 0.189 3843 Planarity : 0.004 0.042 4244 Dihedral : 7.051 117.517 3505 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 2.59 % Allowed : 16.66 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: -0.15 (0.15), residues: 3105 helix: 0.87 (0.14), residues: 1340 sheet: -0.68 (0.23), residues: 501 loop : -0.82 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 373 TYR 0.031 0.001 TYR A 397 PHE 0.031 0.001 PHE D 262 HIS 0.008 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00407 (24300) covalent geometry : angle 0.55503 (32875) hydrogen bonds : bond 0.04414 ( 1138) hydrogen bonds : angle 4.88331 ( 3249) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 283 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: C 143 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.8178 (mmp80) REVERT: C 373 ARG cc_start: 0.8324 (mtt90) cc_final: 0.8102 (mtt90) REVERT: C 425 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8469 (m) REVERT: A 62 MET cc_start: 0.8871 (ttm) cc_final: 0.8519 (ttt) REVERT: A 96 ASP cc_start: 0.8597 (p0) cc_final: 0.8148 (p0) REVERT: A 97 VAL cc_start: 0.8945 (p) cc_final: 0.8710 (m) REVERT: A 362 ARG cc_start: 0.7722 (mtt180) cc_final: 0.6562 (mtt90) REVERT: A 397 TYR cc_start: 0.7595 (t80) cc_final: 0.7312 (t80) REVERT: A 422 VAL cc_start: 0.6624 (t) cc_final: 0.6243 (m) REVERT: A 498 LYS cc_start: 0.7660 (ptmt) cc_final: 0.7225 (pttm) REVERT: B 24 ASP cc_start: 0.7596 (t70) cc_final: 0.7328 (m-30) REVERT: B 195 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: E 205 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: E 340 ARG cc_start: 0.7513 (tpp80) cc_final: 0.7260 (tpt-90) REVERT: E 431 MET cc_start: 0.8116 (mmm) cc_final: 0.7860 (mtm) REVERT: F 170 MET cc_start: 0.8909 (tpp) cc_final: 0.8655 (mmt) REVERT: F 408 SER cc_start: 0.7749 (m) cc_final: 0.7500 (p) REVERT: F 422 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7635 (tm-30) REVERT: G 260 LYS cc_start: 0.8948 (tttt) cc_final: 0.8538 (tttp) REVERT: O 37 LYS cc_start: 0.7074 (tptm) cc_final: 0.6634 (tppt) REVERT: O 42 VAL cc_start: 0.7072 (t) cc_final: 0.6789 (m) REVERT: O 134 LEU cc_start: 0.7688 (tp) cc_final: 0.7448 (mp) REVERT: O 186 MET cc_start: 0.5949 (ptp) cc_final: 0.5321 (pp-130) REVERT: D 59 SER cc_start: 0.8836 (m) cc_final: 0.8525 (p) REVERT: D 170 MET cc_start: 0.6345 (tpp) cc_final: 0.6119 (mmm) REVERT: D 180 HIS cc_start: 0.7481 (t-90) cc_final: 0.6912 (t-90) REVERT: D 203 MET cc_start: 0.8666 (mtt) cc_final: 0.8194 (mtt) REVERT: D 248 ASP cc_start: 0.7390 (m-30) cc_final: 0.6998 (m-30) REVERT: D 259 ASP cc_start: 0.8570 (t0) cc_final: 0.8113 (t70) outliers start: 66 outliers final: 32 residues processed: 325 average time/residue: 0.6970 time to fit residues: 260.2857 Evaluate side-chains 307 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 272 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 442 LYS Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain O residue 130 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 435 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 191 optimal weight: 5.9990 chunk 140 optimal weight: 0.0270 chunk 248 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 259 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 188 optimal weight: 0.7980 chunk 184 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 HIS A 396 GLN A 475 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN E 378 GLN D 54 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106210 restraints weight = 30861.270| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.03 r_work: 0.3162 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24300 Z= 0.108 Angle : 0.511 10.982 32875 Z= 0.259 Chirality : 0.043 0.322 3843 Planarity : 0.004 0.048 4244 Dihedral : 6.583 116.824 3505 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 1.49 % Allowed : 18.39 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: 0.16 (0.15), residues: 3105 helix: 1.19 (0.15), residues: 1325 sheet: -0.52 (0.23), residues: 486 loop : -0.71 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 113 TYR 0.023 0.001 TYR A 397 PHE 0.024 0.001 PHE D 262 HIS 0.006 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00238 (24300) covalent geometry : angle 0.51123 (32875) hydrogen bonds : bond 0.03762 ( 1138) hydrogen bonds : angle 4.71390 ( 3249) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 312 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 ARG cc_start: 0.8409 (tpp-160) cc_final: 0.8140 (mmp80) REVERT: A 62 MET cc_start: 0.8839 (ttm) cc_final: 0.8550 (ttt) REVERT: A 89 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7887 (mmtm) REVERT: A 96 ASP cc_start: 0.8584 (p0) cc_final: 0.8163 (p0) REVERT: A 97 VAL cc_start: 0.8879 (p) cc_final: 0.8634 (m) REVERT: A 218 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7452 (tttt) REVERT: A 226 MET cc_start: 0.9181 (tpt) cc_final: 0.8732 (tpt) REVERT: A 347 ASP cc_start: 0.8378 (m-30) cc_final: 0.8147 (m-30) REVERT: A 351 PHE cc_start: 0.7558 (m-80) cc_final: 0.6939 (t80) REVERT: A 362 ARG cc_start: 0.7506 (mtt180) cc_final: 0.6489 (mtt90) REVERT: A 397 TYR cc_start: 0.7562 (t80) cc_final: 0.7309 (t80) REVERT: A 422 VAL cc_start: 0.6504 (t) cc_final: 0.6145 (m) REVERT: A 466 ASN cc_start: 0.8157 (m-40) cc_final: 0.7822 (m110) REVERT: A 498 LYS cc_start: 0.7675 (ptmt) cc_final: 0.7263 (pttm) REVERT: B 390 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8618 (tpt) REVERT: E 205 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: E 340 ARG cc_start: 0.7524 (tpp80) cc_final: 0.7184 (tpt-90) REVERT: E 431 MET cc_start: 0.8067 (mmm) cc_final: 0.7861 (mtm) REVERT: E 475 LYS cc_start: 0.7168 (mmmm) cc_final: 0.6891 (mmmm) REVERT: F 170 MET cc_start: 0.8901 (tpp) cc_final: 0.8627 (mmt) REVERT: F 248 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8288 (m-30) REVERT: F 253 ASP cc_start: 0.8656 (m-30) cc_final: 0.8414 (m-30) REVERT: F 408 SER cc_start: 0.7669 (m) cc_final: 0.7426 (p) REVERT: F 422 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7568 (tm-30) REVERT: G 260 LYS cc_start: 0.8869 (tttt) cc_final: 0.8466 (tttp) REVERT: O 37 LYS cc_start: 0.7052 (tptm) cc_final: 0.6643 (tppt) REVERT: O 42 VAL cc_start: 0.6995 (t) cc_final: 0.6721 (m) REVERT: O 109 MET cc_start: 0.5236 (mtp) cc_final: 0.5005 (mtp) REVERT: O 113 ARG cc_start: 0.6818 (mtm110) cc_final: 0.6555 (mtm110) REVERT: O 134 LEU cc_start: 0.7693 (tp) cc_final: 0.7450 (mp) REVERT: O 186 MET cc_start: 0.5942 (ptp) cc_final: 0.5294 (pp-130) REVERT: D 59 SER cc_start: 0.8784 (m) cc_final: 0.8444 (p) REVERT: D 180 HIS cc_start: 0.7349 (t-90) cc_final: 0.6811 (t-90) REVERT: D 203 MET cc_start: 0.8709 (mtt) cc_final: 0.8257 (mtt) REVERT: D 259 ASP cc_start: 0.8433 (t0) cc_final: 0.8004 (t70) REVERT: D 372 ASP cc_start: 0.7365 (t0) cc_final: 0.6839 (m-30) outliers start: 38 outliers final: 15 residues processed: 337 average time/residue: 0.7116 time to fit residues: 274.7095 Evaluate side-chains 299 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 280 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 308 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 191 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 271 optimal weight: 4.9990 chunk 210 optimal weight: 0.4980 chunk 261 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 224 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 378 GLN E 445 GLN D 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104649 restraints weight = 30633.253| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.10 r_work: 0.3143 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24300 Z= 0.135 Angle : 0.537 11.881 32875 Z= 0.271 Chirality : 0.044 0.248 3843 Planarity : 0.004 0.050 4244 Dihedral : 6.593 107.025 3505 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.80 % Favored : 97.17 % Rotamer: Outliers : 1.69 % Allowed : 18.55 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: 0.21 (0.15), residues: 3105 helix: 1.20 (0.15), residues: 1331 sheet: -0.52 (0.23), residues: 497 loop : -0.64 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 373 TYR 0.021 0.001 TYR A 397 PHE 0.027 0.001 PHE D 262 HIS 0.007 0.001 HIS E 370 Details of bonding type rmsd covalent geometry : bond 0.00313 (24300) covalent geometry : angle 0.53690 (32875) hydrogen bonds : bond 0.03990 ( 1138) hydrogen bonds : angle 4.72664 ( 3249) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 291 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 143 ARG cc_start: 0.8419 (tpp-160) cc_final: 0.8180 (mmp80) REVERT: C 373 ARG cc_start: 0.8226 (mtt90) cc_final: 0.7979 (mtt90) REVERT: C 484 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6522 (ttt-90) REVERT: A 62 MET cc_start: 0.8860 (ttm) cc_final: 0.8509 (ttt) REVERT: A 96 ASP cc_start: 0.8605 (p0) cc_final: 0.8183 (p0) REVERT: A 97 VAL cc_start: 0.8888 (p) cc_final: 0.8657 (m) REVERT: A 218 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7384 (tttt) REVERT: A 226 MET cc_start: 0.9195 (tpt) cc_final: 0.8709 (tpt) REVERT: A 351 PHE cc_start: 0.7613 (m-80) cc_final: 0.6935 (t80) REVERT: A 362 ARG cc_start: 0.7316 (mtt180) cc_final: 0.6375 (mtt180) REVERT: A 397 TYR cc_start: 0.7577 (t80) cc_final: 0.7332 (t80) REVERT: A 422 VAL cc_start: 0.6577 (t) cc_final: 0.6217 (m) REVERT: B 89 LYS cc_start: 0.8821 (mtmm) cc_final: 0.8397 (mttp) REVERT: B 195 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: B 390 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8587 (tpt) REVERT: E 205 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: E 340 ARG cc_start: 0.7577 (tpp80) cc_final: 0.7211 (tpt-90) REVERT: E 475 LYS cc_start: 0.7144 (mmmm) cc_final: 0.6853 (mmmm) REVERT: F 170 MET cc_start: 0.8878 (tpp) cc_final: 0.8597 (mmt) REVERT: F 217 LYS cc_start: 0.7907 (ptpp) cc_final: 0.7106 (mttp) REVERT: F 253 ASP cc_start: 0.8657 (m-30) cc_final: 0.8413 (m-30) REVERT: F 408 SER cc_start: 0.7714 (m) cc_final: 0.7455 (p) REVERT: F 422 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7573 (tm-30) REVERT: G 260 LYS cc_start: 0.8881 (tttt) cc_final: 0.8465 (tttp) REVERT: O 37 LYS cc_start: 0.7018 (tptm) cc_final: 0.6650 (tppt) REVERT: O 42 VAL cc_start: 0.7023 (t) cc_final: 0.6743 (m) REVERT: O 113 ARG cc_start: 0.6743 (mtm110) cc_final: 0.6390 (mtm110) REVERT: O 134 LEU cc_start: 0.7683 (tp) cc_final: 0.7449 (mp) REVERT: O 186 MET cc_start: 0.5958 (ptp) cc_final: 0.5306 (pp-130) REVERT: D 59 SER cc_start: 0.8786 (m) cc_final: 0.8441 (p) REVERT: D 180 HIS cc_start: 0.7406 (t-90) cc_final: 0.6837 (t-90) REVERT: D 259 ASP cc_start: 0.8457 (t0) cc_final: 0.8080 (t70) outliers start: 43 outliers final: 23 residues processed: 323 average time/residue: 0.7010 time to fit residues: 259.0886 Evaluate side-chains 306 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 278 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 484 ARG Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 466 ILE Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 308 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 0.0000 chunk 121 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 260 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 251 optimal weight: 0.8980 chunk 270 optimal weight: 9.9990 chunk 262 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN B 70 ASN E 378 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.143619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106837 restraints weight = 30784.562| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.06 r_work: 0.3166 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24300 Z= 0.110 Angle : 0.526 12.626 32875 Z= 0.265 Chirality : 0.043 0.230 3843 Planarity : 0.004 0.052 4244 Dihedral : 6.386 107.937 3505 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 1.38 % Allowed : 19.17 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: 0.31 (0.15), residues: 3105 helix: 1.28 (0.15), residues: 1337 sheet: -0.51 (0.24), residues: 481 loop : -0.57 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 373 TYR 0.023 0.001 TYR A 446 PHE 0.023 0.001 PHE D 262 HIS 0.006 0.001 HIS E 370 Details of bonding type rmsd covalent geometry : bond 0.00243 (24300) covalent geometry : angle 0.52575 (32875) hydrogen bonds : bond 0.03702 ( 1138) hydrogen bonds : angle 4.66557 ( 3249) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 304 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 ARG cc_start: 0.8385 (tpp-160) cc_final: 0.8136 (mmp80) REVERT: C 373 ARG cc_start: 0.8247 (mtt90) cc_final: 0.7988 (mtt90) REVERT: A 62 MET cc_start: 0.8853 (ttm) cc_final: 0.8523 (ttt) REVERT: A 89 LYS cc_start: 0.8176 (mptp) cc_final: 0.7915 (mmpt) REVERT: A 96 ASP cc_start: 0.8607 (p0) cc_final: 0.8201 (p0) REVERT: A 97 VAL cc_start: 0.8863 (p) cc_final: 0.8646 (m) REVERT: A 181 ASP cc_start: 0.8006 (m-30) cc_final: 0.7753 (t0) REVERT: A 226 MET cc_start: 0.9173 (tpt) cc_final: 0.8725 (tpt) REVERT: A 347 ASP cc_start: 0.8349 (m-30) cc_final: 0.8122 (m-30) REVERT: A 351 PHE cc_start: 0.7626 (m-80) cc_final: 0.6939 (t80) REVERT: A 362 ARG cc_start: 0.7249 (mtt180) cc_final: 0.6318 (mtt180) REVERT: A 397 TYR cc_start: 0.7623 (t80) cc_final: 0.7376 (t80) REVERT: A 422 VAL cc_start: 0.6555 (t) cc_final: 0.6200 (m) REVERT: A 498 LYS cc_start: 0.7616 (ptmt) cc_final: 0.7205 (pttm) REVERT: B 89 LYS cc_start: 0.8813 (mtmm) cc_final: 0.8422 (mtpp) REVERT: B 195 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: B 390 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8598 (tpt) REVERT: B 434 SER cc_start: 0.8745 (m) cc_final: 0.8540 (p) REVERT: E 205 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: E 340 ARG cc_start: 0.7561 (tpp80) cc_final: 0.7210 (tpt-90) REVERT: E 475 LYS cc_start: 0.7138 (mmmm) cc_final: 0.6857 (mmmm) REVERT: F 170 MET cc_start: 0.8884 (tpp) cc_final: 0.8590 (mmt) REVERT: F 217 LYS cc_start: 0.8101 (ptpp) cc_final: 0.7345 (mttp) REVERT: F 408 SER cc_start: 0.7702 (m) cc_final: 0.7460 (p) REVERT: F 422 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7589 (tm-30) REVERT: G 260 LYS cc_start: 0.8932 (tttt) cc_final: 0.8510 (tttp) REVERT: O 36 GLU cc_start: 0.6355 (tm-30) cc_final: 0.6153 (mm-30) REVERT: O 37 LYS cc_start: 0.7078 (tptm) cc_final: 0.6765 (tppt) REVERT: O 42 VAL cc_start: 0.7031 (t) cc_final: 0.6753 (m) REVERT: O 113 ARG cc_start: 0.6781 (mtm110) cc_final: 0.6433 (mtm110) REVERT: O 134 LEU cc_start: 0.7702 (tp) cc_final: 0.7448 (mp) REVERT: O 186 MET cc_start: 0.5982 (ptp) cc_final: 0.5322 (pp-130) REVERT: D 59 SER cc_start: 0.8795 (m) cc_final: 0.8465 (p) REVERT: D 180 HIS cc_start: 0.7372 (t-90) cc_final: 0.6810 (t-90) REVERT: D 259 ASP cc_start: 0.8431 (t0) cc_final: 0.8088 (t70) outliers start: 35 outliers final: 19 residues processed: 331 average time/residue: 0.6838 time to fit residues: 259.4014 Evaluate side-chains 308 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 286 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain D residue 37 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 308 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 203 optimal weight: 0.0770 chunk 73 optimal weight: 2.9990 chunk 308 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 183 optimal weight: 7.9990 chunk 299 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 overall best weight: 1.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 396 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN E 378 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.140402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103057 restraints weight = 30931.663| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.07 r_work: 0.3113 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24300 Z= 0.183 Angle : 0.598 13.426 32875 Z= 0.299 Chirality : 0.046 0.364 3843 Planarity : 0.004 0.052 4244 Dihedral : 6.759 112.973 3505 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.19 % Favored : 96.78 % Rotamer: Outliers : 1.18 % Allowed : 19.33 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: 0.13 (0.15), residues: 3105 helix: 1.10 (0.14), residues: 1336 sheet: -0.57 (0.23), residues: 505 loop : -0.64 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 373 TYR 0.024 0.002 TYR A 446 PHE 0.028 0.001 PHE D 262 HIS 0.008 0.001 HIS E 370 Details of bonding type rmsd covalent geometry : bond 0.00440 (24300) covalent geometry : angle 0.59832 (32875) hydrogen bonds : bond 0.04402 ( 1138) hydrogen bonds : angle 4.84122 ( 3249) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 ARG cc_start: 0.8434 (tpp-160) cc_final: 0.8163 (mmp80) REVERT: C 373 ARG cc_start: 0.8268 (mtt90) cc_final: 0.8023 (mtt90) REVERT: A 89 LYS cc_start: 0.8258 (mptp) cc_final: 0.7995 (mmmt) REVERT: A 96 ASP cc_start: 0.8603 (p0) cc_final: 0.8170 (p0) REVERT: A 97 VAL cc_start: 0.8920 (p) cc_final: 0.8707 (m) REVERT: A 181 ASP cc_start: 0.7965 (m-30) cc_final: 0.7715 (t0) REVERT: A 351 PHE cc_start: 0.7619 (m-80) cc_final: 0.6935 (t80) REVERT: A 362 ARG cc_start: 0.7323 (mtt180) cc_final: 0.6250 (mtt180) REVERT: A 397 TYR cc_start: 0.7562 (t80) cc_final: 0.7275 (t80) REVERT: B 195 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: B 390 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8587 (tpt) REVERT: E 205 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: E 340 ARG cc_start: 0.7630 (tpp80) cc_final: 0.7235 (tpt-90) REVERT: E 375 ARG cc_start: 0.8290 (mmp-170) cc_final: 0.8062 (mmp-170) REVERT: E 475 LYS cc_start: 0.7181 (mmmm) cc_final: 0.6895 (mmmm) REVERT: F 170 MET cc_start: 0.8804 (tpp) cc_final: 0.8488 (mmt) REVERT: F 253 ASP cc_start: 0.8669 (m-30) cc_final: 0.8436 (m-30) REVERT: F 422 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7591 (tm-30) REVERT: G 260 LYS cc_start: 0.8904 (tttt) cc_final: 0.8479 (tttp) REVERT: O 37 LYS cc_start: 0.7055 (tptm) cc_final: 0.6482 (tppt) REVERT: O 40 LEU cc_start: 0.6923 (mm) cc_final: 0.6396 (pt) REVERT: O 134 LEU cc_start: 0.7639 (tp) cc_final: 0.7427 (mp) REVERT: O 186 MET cc_start: 0.5997 (ptp) cc_final: 0.5341 (pp-130) REVERT: D 59 SER cc_start: 0.8789 (m) cc_final: 0.8439 (p) REVERT: D 180 HIS cc_start: 0.7469 (t-90) cc_final: 0.6885 (t-90) REVERT: D 259 ASP cc_start: 0.8580 (t0) cc_final: 0.8253 (t70) outliers start: 30 outliers final: 20 residues processed: 294 average time/residue: 0.7240 time to fit residues: 243.5020 Evaluate side-chains 287 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 264 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain A residue 143 ARG Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain O residue 121 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 308 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 20 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 218 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 299 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 282 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN A 471 HIS ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN E 378 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.142122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105132 restraints weight = 30696.405| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.06 r_work: 0.3142 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24300 Z= 0.133 Angle : 0.571 13.560 32875 Z= 0.283 Chirality : 0.044 0.345 3843 Planarity : 0.004 0.059 4244 Dihedral : 6.569 112.365 3505 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 1.18 % Allowed : 19.65 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % 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: 0.23 (0.15), residues: 3105 helix: 1.17 (0.15), residues: 1341 sheet: -0.50 (0.23), residues: 490 loop : -0.58 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG O 113 TYR 0.031 0.001 TYR A 446 PHE 0.026 0.001 PHE D 262 HIS 0.007 0.001 HIS E 370 Details of bonding type rmsd covalent geometry : bond 0.00309 (24300) covalent geometry : angle 0.57068 (32875) hydrogen bonds : bond 0.04016 ( 1138) hydrogen bonds : angle 4.78353 ( 3249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9439.85 seconds wall clock time: 161 minutes 20.54 seconds (9680.54 seconds total)