Starting phenix.real_space_refine on Fri Jun 20 20:03:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9i_34568/06_2025/8h9i_34568.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9i_34568/06_2025/8h9i_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h9i_34568/06_2025/8h9i_34568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9i_34568/06_2025/8h9i_34568.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9i_34568/06_2025/8h9i_34568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9i_34568/06_2025/8h9i_34568.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.40, per 1000 atoms: 0.73 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: 6.37 Conformation dependent library (CDL) restraints added in 3.4 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: 2.84 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: 9.12 Time building geometry restraints manager: 7.51 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 508 or resid 601 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: 37.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 60.140 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.120 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:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.650 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (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 HIS 0.009 0.001 HIS E 370 PHE 0.011 0.002 PHE E 264 TYR 0.019 0.001 TYR O 170 ARG 0.008 0.000 ARG E 263 Details of bonding type rmsd hydrogen bonds : bond 0.15606 ( 1138) hydrogen bonds : angle 7.01246 ( 3249) covalent geometry : bond 0.00736 (24300) covalent geometry : angle 0.79802 (32875) *********************** 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 : 2.993 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: 0.6593 (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: 1.6220 time to fit residues: 760.5634 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 : 2.706 ------------------------------------------------------------------------------- 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 261 optimal weight: 7.9990 chunk 234 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 281 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 385 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 Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103671 restraints weight = 30876.443| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.14 r_work: 0.3117 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1314 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= 0.149 Angle : 0.565 7.566 32875 Z= 0.291 Chirality : 0.044 0.210 3843 Planarity : 0.004 0.044 4244 Dihedral : 7.595 129.474 3507 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 1.85 % Allowed : 11.20 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3105 helix: -0.02 (0.14), residues: 1330 sheet: -1.12 (0.22), residues: 472 loop : -1.49 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 370 PHE 0.025 0.001 PHE D 262 TYR 0.015 0.001 TYR O 170 ARG 0.007 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 1138) hydrogen bonds : angle 5.18812 ( 3249) covalent geometry : bond 0.00345 (24300) covalent geometry : angle 0.56451 (32875) *********************** 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 384 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 337 time to evaluate : 2.977 Fit side-chains revert: symmetry clash REVERT: C 25 LEU cc_start: 0.7696 (mt) cc_final: 0.7479 (mm) REVERT: C 143 ARG cc_start: 0.8440 (tpp-160) cc_final: 0.8111 (mmp80) REVERT: C 195 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7069 (tp30) REVERT: C 425 THR cc_start: 0.8731 (t) cc_final: 0.8483 (m) REVERT: C 484 ARG cc_start: 0.7111 (ttt-90) cc_final: 0.6568 (ttm170) REVERT: A 96 ASP cc_start: 0.8555 (p0) cc_final: 0.8146 (p0) REVERT: A 226 MET cc_start: 0.9185 (tpt) cc_final: 0.8592 (tpt) REVERT: A 351 PHE cc_start: 0.8112 (m-80) cc_final: 0.7206 (t80) REVERT: A 359 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.7032 (mtpt) REVERT: A 362 ARG cc_start: 0.7814 (mtt180) cc_final: 0.6678 (mtt180) REVERT: A 422 VAL cc_start: 0.6532 (t) cc_final: 0.6186 (m) REVERT: A 446 TYR cc_start: 0.6923 (t80) cc_final: 0.6305 (t80) REVERT: B 8 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6418 (mpm) REVERT: B 24 ASP cc_start: 0.7586 (t70) cc_final: 0.7210 (m-30) REVERT: B 89 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8461 (mtmt) REVERT: E 340 ARG cc_start: 0.7409 (tpp80) cc_final: 0.6893 (tpt170) REVERT: E 344 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7233 (mm-30) REVERT: E 438 LYS cc_start: 0.7742 (pttm) cc_final: 0.7508 (pttp) REVERT: E 442 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7422 (ttpt) REVERT: F 170 MET cc_start: 0.8841 (tpp) cc_final: 0.8544 (mmt) REVERT: F 408 SER cc_start: 0.7725 (m) cc_final: 0.7457 (p) REVERT: F 422 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7670 (tm-30) REVERT: G 229 MET cc_start: 0.7560 (ttp) cc_final: 0.7335 (ptm) REVERT: G 260 LYS cc_start: 0.8928 (tttt) cc_final: 0.8503 (tttp) REVERT: O 33 GLU cc_start: 0.6971 (pt0) cc_final: 0.6398 (pm20) REVERT: O 37 LYS cc_start: 0.7037 (tptm) cc_final: 0.6570 (tppt) REVERT: O 42 VAL cc_start: 0.6860 (t) cc_final: 0.6556 (m) REVERT: O 134 LEU cc_start: 0.7632 (tp) cc_final: 0.7351 (mp) REVERT: O 186 MET cc_start: 0.5872 (ptp) cc_final: 0.5233 (pp-130) REVERT: D 59 SER cc_start: 0.8930 (m) cc_final: 0.8635 (p) REVERT: D 180 HIS cc_start: 0.7476 (t-90) cc_final: 0.7045 (t-90) REVERT: D 248 ASP cc_start: 0.7441 (m-30) cc_final: 0.7008 (m-30) REVERT: D 259 ASP cc_start: 0.8644 (t0) cc_final: 0.8193 (t0) outliers start: 47 outliers final: 16 residues processed: 369 average time/residue: 1.4388 time to fit residues: 607.0616 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 : 2.644 ------------------------------------------------------------------------------- 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 475 GLN 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 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 D residue 37 ASN 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 167 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 E 378 GLN O 29 GLN O 44 GLN D 210 ASN D 249 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 = 0.140425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103232 restraints weight = 30740.774| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.07 r_work: 0.3102 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24300 Z= 0.183 Angle : 0.568 8.095 32875 Z= 0.291 Chirality : 0.045 0.176 3843 Planarity : 0.004 0.042 4244 Dihedral : 7.371 114.116 3505 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 2.87 % Allowed : 13.24 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3105 helix: 0.45 (0.14), residues: 1326 sheet: -0.95 (0.22), residues: 509 loop : -1.14 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 370 PHE 0.025 0.001 PHE D 262 TYR 0.021 0.001 TYR A 397 ARG 0.005 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 1138) hydrogen bonds : angle 5.05243 ( 3249) covalent geometry : bond 0.00437 (24300) covalent geometry : angle 0.56751 (32875) *********************** 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 378 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 305 time to evaluate : 4.125 Fit side-chains revert: symmetry clash REVERT: C 195 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7034 (tp30) REVERT: C 425 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8491 (m) REVERT: A 89 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7886 (mmmt) REVERT: A 96 ASP cc_start: 0.8618 (p0) cc_final: 0.8137 (p0) REVERT: A 226 MET cc_start: 0.9203 (tpt) cc_final: 0.8602 (tpt) REVERT: A 351 PHE cc_start: 0.7856 (m-80) cc_final: 0.7213 (t80) REVERT: A 356 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7854 (mp) REVERT: A 362 ARG cc_start: 0.7799 (mtt180) cc_final: 0.6647 (mtt180) REVERT: A 422 VAL cc_start: 0.6675 (t) cc_final: 0.6315 (m) REVERT: A 476 HIS cc_start: 0.6644 (m-70) cc_final: 0.6377 (m-70) REVERT: B 8 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6364 (mpm) REVERT: B 24 ASP cc_start: 0.7659 (t70) cc_final: 0.7279 (m-30) REVERT: B 195 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: E 340 ARG cc_start: 0.7529 (tpp80) cc_final: 0.6982 (tpt170) REVERT: E 344 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7151 (mm-30) REVERT: E 431 MET cc_start: 0.8135 (mmm) cc_final: 0.7762 (mtm) REVERT: E 442 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7483 (ttpt) REVERT: E 445 GLN cc_start: 0.8025 (tt0) cc_final: 0.7793 (tt0) REVERT: F 170 MET cc_start: 0.8936 (tpp) cc_final: 0.8654 (mmt) REVERT: F 171 GLU cc_start: 0.8155 (tp30) cc_final: 0.7875 (tp30) REVERT: F 217 LYS cc_start: 0.8147 (ptpp) cc_final: 0.7442 (mttp) REVERT: F 408 SER cc_start: 0.7790 (m) cc_final: 0.7543 (p) REVERT: F 422 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7659 (tm-30) REVERT: G 229 MET cc_start: 0.7559 (ttp) cc_final: 0.7351 (ptm) REVERT: G 260 LYS cc_start: 0.8948 (tttt) cc_final: 0.8524 (tttp) REVERT: O 33 GLU cc_start: 0.7047 (pt0) cc_final: 0.6436 (pm20) REVERT: O 37 LYS cc_start: 0.7055 (tptm) cc_final: 0.6598 (tppt) REVERT: O 42 VAL cc_start: 0.6891 (t) cc_final: 0.6595 (m) REVERT: O 113 ARG cc_start: 0.5595 (mtm180) cc_final: 0.5383 (mtm-85) REVERT: O 134 LEU cc_start: 0.7659 (tp) cc_final: 0.7390 (mp) REVERT: O 186 MET cc_start: 0.5912 (ptp) cc_final: 0.5259 (pp-130) REVERT: D 59 SER cc_start: 0.8923 (m) cc_final: 0.8639 (p) REVERT: D 170 MET cc_start: 0.6271 (tpp) cc_final: 0.6026 (mmm) REVERT: D 180 HIS cc_start: 0.7501 (t-90) cc_final: 0.7033 (t-90) REVERT: D 248 ASP cc_start: 0.7440 (m-30) cc_final: 0.7015 (m-30) REVERT: D 259 ASP cc_start: 0.8620 (t0) cc_final: 0.8158 (t70) outliers start: 73 outliers final: 28 residues processed: 352 average time/residue: 1.8660 time to fit residues: 759.0421 Evaluate side-chains 316 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 283 time to evaluate : 2.945 ------------------------------------------------------------------------------- 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 155 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 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 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 G residue 12 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 270 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 97 optimal weight: 0.0270 chunk 69 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN A 475 GLN B 466 ASN F 388 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 = 0.3678 r_free = 0.3678 target = 0.140243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.103158 restraints weight = 31039.039| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.06 r_work: 0.3101 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24300 Z= 0.187 Angle : 0.569 8.646 32875 Z= 0.290 Chirality : 0.045 0.179 3843 Planarity : 0.004 0.045 4244 Dihedral : 7.301 112.640 3505 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 2.91 % Allowed : 14.93 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3105 helix: 0.65 (0.14), residues: 1330 sheet: -0.79 (0.23), residues: 487 loop : -1.03 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 370 PHE 0.030 0.001 PHE D 262 TYR 0.023 0.001 TYR A 397 ARG 0.006 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 1138) hydrogen bonds : angle 4.97980 ( 3249) covalent geometry : bond 0.00448 (24300) covalent geometry : angle 0.56935 (32875) *********************** 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 374 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 300 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 425 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8454 (m) REVERT: A 89 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7880 (mmtm) REVERT: A 96 ASP cc_start: 0.8573 (p0) cc_final: 0.8126 (p0) REVERT: A 97 VAL cc_start: 0.8971 (p) cc_final: 0.8718 (m) REVERT: A 351 PHE cc_start: 0.7754 (m-80) cc_final: 0.7020 (t80) REVERT: A 362 ARG cc_start: 0.7701 (mtt180) cc_final: 0.6589 (mtt180) REVERT: A 422 VAL cc_start: 0.6604 (t) cc_final: 0.6257 (m) REVERT: A 475 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7294 (pm20) REVERT: B 8 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6401 (mpm) REVERT: B 24 ASP cc_start: 0.7563 (t70) cc_final: 0.7265 (m-30) REVERT: B 195 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: E 340 ARG cc_start: 0.7545 (tpp80) cc_final: 0.6931 (tpt170) REVERT: E 344 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7174 (mm-30) REVERT: E 431 MET cc_start: 0.8091 (mmm) cc_final: 0.7772 (mtm) REVERT: E 445 GLN cc_start: 0.7977 (tt0) cc_final: 0.7746 (tt0) REVERT: F 170 MET cc_start: 0.8882 (tpp) cc_final: 0.8624 (mmt) REVERT: F 217 LYS cc_start: 0.8053 (ptpp) cc_final: 0.7303 (mttp) REVERT: F 408 SER cc_start: 0.7735 (m) cc_final: 0.7481 (p) REVERT: F 422 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7664 (tm-30) REVERT: G 229 MET cc_start: 0.7447 (ttp) cc_final: 0.7242 (ptm) REVERT: G 260 LYS cc_start: 0.8929 (tttt) cc_final: 0.8521 (tttp) REVERT: O 33 GLU cc_start: 0.7056 (pt0) cc_final: 0.6377 (pm20) REVERT: O 37 LYS cc_start: 0.7071 (tptm) cc_final: 0.6617 (tppt) REVERT: O 113 ARG cc_start: 0.5484 (mtm180) cc_final: 0.5256 (mtm-85) REVERT: O 134 LEU cc_start: 0.7640 (tp) cc_final: 0.7396 (mp) REVERT: O 186 MET cc_start: 0.5858 (ptp) cc_final: 0.5241 (pp-130) REVERT: D 59 SER cc_start: 0.8888 (m) cc_final: 0.8584 (p) REVERT: D 170 MET cc_start: 0.6362 (tpp) cc_final: 0.6140 (mmm) REVERT: D 180 HIS cc_start: 0.7475 (t-90) cc_final: 0.6924 (t-90) REVERT: D 248 ASP cc_start: 0.7371 (m-30) cc_final: 0.6926 (m-30) REVERT: D 259 ASP cc_start: 0.8607 (t0) cc_final: 0.8150 (t70) REVERT: D 322 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7650 (t70) REVERT: D 396 MET cc_start: 0.2036 (OUTLIER) cc_final: 0.1400 (ppp) REVERT: D 479 GLU cc_start: 0.3066 (OUTLIER) cc_final: 0.2785 (mp0) outliers start: 74 outliers final: 32 residues processed: 354 average time/residue: 1.3690 time to fit residues: 556.6057 Evaluate side-chains 317 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 278 time to evaluate : 2.718 ------------------------------------------------------------------------------- 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 393 GLU 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 21 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 195 GLU 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 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 G residue 12 SER 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 322 ASP 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 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 276 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 149 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN D 210 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.141211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104223 restraints weight = 30851.856| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.05 r_work: 0.3141 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1873 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= 0.122 Angle : 0.521 10.065 32875 Z= 0.265 Chirality : 0.043 0.164 3843 Planarity : 0.004 0.043 4244 Dihedral : 6.952 107.488 3505 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.13 % Rotamer: Outliers : 2.20 % Allowed : 16.54 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 3105 helix: 0.96 (0.14), residues: 1324 sheet: -0.68 (0.23), residues: 486 loop : -0.85 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 370 PHE 0.028 0.001 PHE D 262 TYR 0.025 0.001 TYR A 397 ARG 0.006 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 1138) hydrogen bonds : angle 4.81546 ( 3249) covalent geometry : bond 0.00276 (24300) covalent geometry : angle 0.52076 (32875) *********************** 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 360 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 304 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 ARG cc_start: 0.8438 (tpp-160) cc_final: 0.8174 (mmp80) REVERT: C 373 ARG cc_start: 0.8279 (mtt90) cc_final: 0.7875 (mtt90) REVERT: C 425 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8439 (m) REVERT: A 62 MET cc_start: 0.8851 (ttm) cc_final: 0.8562 (ttt) REVERT: A 96 ASP cc_start: 0.8583 (p0) cc_final: 0.8152 (p0) REVERT: A 97 VAL cc_start: 0.8926 (p) cc_final: 0.8674 (m) REVERT: A 208 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8322 (mt0) REVERT: A 226 MET cc_start: 0.9186 (tpt) cc_final: 0.8700 (tpt) REVERT: A 351 PHE cc_start: 0.7545 (m-80) cc_final: 0.7004 (t80) REVERT: A 362 ARG cc_start: 0.7629 (mtt180) cc_final: 0.6445 (mtt90) REVERT: A 422 VAL cc_start: 0.6571 (t) cc_final: 0.6227 (m) REVERT: B 24 ASP cc_start: 0.7591 (t70) cc_final: 0.7323 (m-30) REVERT: B 195 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: B 381 ARG cc_start: 0.7703 (tpt170) cc_final: 0.7475 (tpt170) REVERT: E 205 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7661 (tp30) REVERT: E 340 ARG cc_start: 0.7482 (tpp80) cc_final: 0.7241 (tpt170) REVERT: E 431 MET cc_start: 0.8122 (mmm) cc_final: 0.7836 (mtm) REVERT: F 170 MET cc_start: 0.8879 (tpp) cc_final: 0.8631 (mmt) REVERT: F 217 LYS cc_start: 0.8134 (ptpp) cc_final: 0.7369 (mttp) REVERT: F 408 SER cc_start: 0.7677 (m) cc_final: 0.7433 (p) REVERT: F 422 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7662 (tm-30) REVERT: G 260 LYS cc_start: 0.8885 (tttt) cc_final: 0.8486 (tttp) REVERT: O 37 LYS cc_start: 0.7081 (tptm) cc_final: 0.6601 (tppt) REVERT: O 42 VAL cc_start: 0.7045 (t) cc_final: 0.6762 (m) REVERT: O 134 LEU cc_start: 0.7655 (tp) cc_final: 0.7389 (mp) REVERT: O 186 MET cc_start: 0.5889 (ptp) cc_final: 0.5260 (pp-130) REVERT: D 59 SER cc_start: 0.8820 (m) cc_final: 0.8507 (p) REVERT: D 170 MET cc_start: 0.6327 (tpp) cc_final: 0.6079 (mmm) REVERT: D 180 HIS cc_start: 0.7410 (t-90) cc_final: 0.6885 (t-90) REVERT: D 248 ASP cc_start: 0.7383 (m-30) cc_final: 0.6980 (m-30) REVERT: D 259 ASP cc_start: 0.8499 (t0) cc_final: 0.8043 (t0) REVERT: D 479 GLU cc_start: 0.2852 (OUTLIER) cc_final: 0.2532 (mp0) outliers start: 56 outliers final: 24 residues processed: 346 average time/residue: 1.4268 time to fit residues: 570.3503 Evaluate side-chains 310 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 2.489 ------------------------------------------------------------------------------- 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 380 THR Chi-restraints excluded: chain A residue 393 GLU 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 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 F residue 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 131 VAL 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 Chi-restraints excluded: chain D residue 479 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 130 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 260 optimal weight: 20.0000 chunk 228 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 270 optimal weight: 9.9990 chunk 203 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 173 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 503 ASN E 378 GLN E 445 GLN F 388 GLN O 180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.140722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.103544 restraints weight = 30840.214| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.06 r_work: 0.3106 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24300 Z= 0.182 Angle : 0.562 9.739 32875 Z= 0.287 Chirality : 0.045 0.279 3843 Planarity : 0.004 0.042 4244 Dihedral : 7.085 112.822 3505 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % Rotamer: Outliers : 2.44 % Allowed : 16.97 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3105 helix: 0.90 (0.14), residues: 1339 sheet: -0.68 (0.23), residues: 501 loop : -0.82 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 476 PHE 0.030 0.001 PHE D 262 TYR 0.029 0.002 TYR A 397 ARG 0.005 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 1138) hydrogen bonds : angle 4.88763 ( 3249) covalent geometry : bond 0.00438 (24300) covalent geometry : angle 0.56249 (32875) *********************** 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 351 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 289 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 ARG cc_start: 0.8454 (tpp-160) cc_final: 0.8159 (mmp80) REVERT: C 196 LYS cc_start: 0.8330 (mtmm) cc_final: 0.7645 (mmpt) REVERT: C 425 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8464 (m) REVERT: A 96 ASP cc_start: 0.8593 (p0) cc_final: 0.8158 (p0) REVERT: A 97 VAL cc_start: 0.8938 (p) cc_final: 0.8709 (m) REVERT: A 208 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8408 (mt0) REVERT: A 362 ARG cc_start: 0.7695 (mtt180) cc_final: 0.6513 (mtt90) REVERT: A 397 TYR cc_start: 0.7625 (t80) cc_final: 0.7412 (t80) REVERT: A 422 VAL cc_start: 0.6588 (t) cc_final: 0.6222 (m) REVERT: A 498 LYS cc_start: 0.7677 (ptmt) cc_final: 0.7233 (pttm) REVERT: B 24 ASP cc_start: 0.7646 (t70) cc_final: 0.7341 (m-30) REVERT: B 89 LYS cc_start: 0.8821 (mtmm) cc_final: 0.8428 (mttp) REVERT: B 195 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: E 205 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: E 340 ARG cc_start: 0.7564 (tpp80) cc_final: 0.7260 (tpt-90) REVERT: E 431 MET cc_start: 0.8118 (mmm) cc_final: 0.7854 (mtm) REVERT: E 442 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7387 (ttpt) REVERT: F 170 MET cc_start: 0.8900 (tpp) cc_final: 0.8650 (mmt) REVERT: F 408 SER cc_start: 0.7762 (m) cc_final: 0.7512 (p) REVERT: F 422 GLN cc_start: 0.8048 (tm-30) cc_final: 0.7666 (tm-30) REVERT: G 260 LYS cc_start: 0.8921 (tttt) cc_final: 0.8521 (tttp) REVERT: G 262 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8626 (tt) REVERT: O 37 LYS cc_start: 0.7078 (tptm) cc_final: 0.6651 (tppt) REVERT: O 42 VAL cc_start: 0.7073 (t) cc_final: 0.6790 (m) REVERT: O 113 ARG cc_start: 0.6167 (mtm-85) cc_final: 0.5924 (mtm-85) REVERT: O 134 LEU cc_start: 0.7696 (tp) cc_final: 0.7455 (mp) REVERT: O 186 MET cc_start: 0.5920 (ptp) cc_final: 0.5294 (pp-130) REVERT: D 59 SER cc_start: 0.8851 (m) cc_final: 0.8539 (p) REVERT: D 170 MET cc_start: 0.6330 (tpp) cc_final: 0.6088 (mmm) REVERT: D 180 HIS cc_start: 0.7460 (t-90) cc_final: 0.6900 (t-90) REVERT: D 248 ASP cc_start: 0.7376 (m-30) cc_final: 0.6992 (m-30) REVERT: D 259 ASP cc_start: 0.8598 (t0) cc_final: 0.8200 (t70) outliers start: 62 outliers final: 29 residues processed: 334 average time/residue: 1.3824 time to fit residues: 532.7755 Evaluate side-chains 309 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 275 time to evaluate : 2.654 ------------------------------------------------------------------------------- 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 380 THR Chi-restraints excluded: chain A residue 393 GLU 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 56 SER 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 301 THR Chi-restraints excluded: chain E residue 344 GLU 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 G residue 12 SER Chi-restraints excluded: chain G residue 262 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 1 optimal weight: 9.9990 chunk 113 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 chunk 271 optimal weight: 4.9990 chunk 59 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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** F 388 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.143651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106835 restraints weight = 30787.562| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.03 r_work: 0.3156 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24300 Z= 0.103 Angle : 0.509 10.773 32875 Z= 0.258 Chirality : 0.042 0.185 3843 Planarity : 0.003 0.042 4244 Dihedral : 6.533 106.153 3505 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 1.49 % Allowed : 18.31 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3105 helix: 1.24 (0.15), residues: 1325 sheet: -0.57 (0.23), residues: 489 loop : -0.68 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 370 PHE 0.024 0.001 PHE D 262 TYR 0.026 0.001 TYR F 461 ARG 0.007 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 1138) hydrogen bonds : angle 4.69847 ( 3249) covalent geometry : bond 0.00223 (24300) covalent geometry : angle 0.50863 (32875) *********************** 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 362 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 324 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 143 ARG cc_start: 0.8429 (tpp-160) cc_final: 0.8179 (mmp80) REVERT: C 196 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7670 (mmpt) REVERT: C 415 GLN cc_start: 0.5795 (mt0) cc_final: 0.5496 (mt0) REVERT: C 425 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8422 (m) REVERT: A 62 MET cc_start: 0.8829 (ttm) cc_final: 0.8585 (ttt) REVERT: A 89 LYS cc_start: 0.8064 (mptt) cc_final: 0.7750 (mmpt) REVERT: A 96 ASP cc_start: 0.8611 (p0) cc_final: 0.8203 (p0) REVERT: A 97 VAL cc_start: 0.8877 (p) cc_final: 0.8641 (m) REVERT: A 226 MET cc_start: 0.9194 (tpt) cc_final: 0.8761 (tpt) REVERT: A 347 ASP cc_start: 0.8344 (m-30) cc_final: 0.8119 (m-30) REVERT: A 351 PHE cc_start: 0.7600 (m-80) cc_final: 0.7032 (t80) REVERT: A 362 ARG cc_start: 0.7535 (mtt180) cc_final: 0.6656 (mtt180) REVERT: A 397 TYR cc_start: 0.7596 (t80) cc_final: 0.7215 (t80) REVERT: A 422 VAL cc_start: 0.6555 (t) cc_final: 0.6183 (m) REVERT: A 466 ASN cc_start: 0.8178 (m-40) cc_final: 0.7873 (m110) REVERT: A 498 LYS cc_start: 0.7693 (ptmt) cc_final: 0.7265 (pttm) REVERT: B 24 ASP cc_start: 0.7590 (t70) cc_final: 0.7381 (m-30) REVERT: B 89 LYS cc_start: 0.8769 (mtmm) cc_final: 0.8373 (mtpp) REVERT: B 423 ARG cc_start: 0.8055 (mpt180) cc_final: 0.7845 (mmt-90) REVERT: E 205 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: E 227 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8260 (mp0) REVERT: E 340 ARG cc_start: 0.7471 (tpp80) cc_final: 0.7239 (tpt-90) REVERT: E 431 MET cc_start: 0.8094 (mmm) cc_final: 0.7876 (mtm) REVERT: F 170 MET cc_start: 0.8950 (tpp) cc_final: 0.8688 (mmt) REVERT: F 248 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8313 (m-30) REVERT: F 408 SER cc_start: 0.7710 (m) cc_final: 0.7472 (p) REVERT: F 422 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7604 (tm-30) REVERT: G 260 LYS cc_start: 0.8906 (tttt) cc_final: 0.8510 (tttp) REVERT: O 37 LYS cc_start: 0.7049 (tptm) cc_final: 0.6692 (tppt) REVERT: O 42 VAL cc_start: 0.6971 (t) cc_final: 0.6695 (m) REVERT: O 134 LEU cc_start: 0.7703 (tp) cc_final: 0.7443 (mp) REVERT: O 186 MET cc_start: 0.5956 (ptp) cc_final: 0.5310 (pp-130) REVERT: D 59 SER cc_start: 0.8811 (m) cc_final: 0.8481 (p) REVERT: D 170 MET cc_start: 0.6303 (tpp) cc_final: 0.6075 (mmm) REVERT: D 180 HIS cc_start: 0.7341 (t-90) cc_final: 0.6833 (t-90) REVERT: D 203 MET cc_start: 0.8740 (mtt) cc_final: 0.8385 (mtt) REVERT: D 259 ASP cc_start: 0.8434 (t0) cc_final: 0.8055 (t0) outliers start: 38 outliers final: 15 residues processed: 352 average time/residue: 1.4119 time to fit residues: 570.5058 Evaluate side-chains 307 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 288 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 458 GLN 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 128 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 275 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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** D 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.138968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101800 restraints weight = 30974.159| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.08 r_work: 0.3099 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 24300 Z= 0.229 Angle : 0.614 12.161 32875 Z= 0.310 Chirality : 0.047 0.402 3843 Planarity : 0.004 0.049 4244 Dihedral : 7.051 108.850 3505 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 2.12 % Allowed : 18.00 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3105 helix: 0.94 (0.14), residues: 1342 sheet: -0.61 (0.23), residues: 499 loop : -0.75 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 370 PHE 0.034 0.002 PHE D 262 TYR 0.021 0.002 TYR A 397 ARG 0.010 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.04701 ( 1138) hydrogen bonds : angle 4.94167 ( 3249) covalent geometry : bond 0.00555 (24300) covalent geometry : angle 0.61389 (32875) *********************** 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 336 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 282 time to evaluate : 4.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 196 LYS cc_start: 0.8347 (mtmm) cc_final: 0.7683 (mmpt) REVERT: C 373 ARG cc_start: 0.8316 (mtt90) cc_final: 0.8063 (mtt90) REVERT: C 415 GLN cc_start: 0.5864 (mt0) cc_final: 0.5589 (mt0) REVERT: C 425 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8504 (m) REVERT: A 96 ASP cc_start: 0.8641 (p0) cc_final: 0.8210 (p0) REVERT: A 97 VAL cc_start: 0.8962 (p) cc_final: 0.8755 (m) REVERT: A 218 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7487 (tttt) REVERT: A 351 PHE cc_start: 0.7661 (m-80) cc_final: 0.7055 (t80) REVERT: A 362 ARG cc_start: 0.7496 (mtt180) cc_final: 0.6571 (mtt180) REVERT: A 397 TYR cc_start: 0.7670 (t80) cc_final: 0.7428 (t80) REVERT: B 24 ASP cc_start: 0.7688 (t70) cc_final: 0.7377 (m-30) REVERT: B 89 LYS cc_start: 0.8850 (mtmm) cc_final: 0.8448 (mtpp) REVERT: B 195 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: E 205 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: E 340 ARG cc_start: 0.7669 (tpp80) cc_final: 0.7320 (tpt-90) REVERT: E 431 MET cc_start: 0.8138 (mmm) cc_final: 0.7901 (mtm) REVERT: E 475 LYS cc_start: 0.7250 (mmmm) cc_final: 0.6973 (mmmm) REVERT: F 170 MET cc_start: 0.8911 (tpp) cc_final: 0.8659 (mmt) REVERT: F 422 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7690 (tm-30) REVERT: G 260 LYS cc_start: 0.8968 (tttt) cc_final: 0.8564 (tttp) REVERT: O 33 GLU cc_start: 0.7188 (pt0) cc_final: 0.6480 (pm20) REVERT: O 36 GLU cc_start: 0.6453 (tm-30) cc_final: 0.6211 (mt-10) REVERT: O 37 LYS cc_start: 0.7184 (tptm) cc_final: 0.6746 (tppt) REVERT: O 109 MET cc_start: 0.5823 (mtp) cc_final: 0.4949 (mtp) REVERT: O 134 LEU cc_start: 0.7664 (tp) cc_final: 0.7442 (mp) REVERT: O 186 MET cc_start: 0.5992 (ptp) cc_final: 0.5340 (pp-130) REVERT: D 59 SER cc_start: 0.8835 (m) cc_final: 0.8515 (p) REVERT: D 170 MET cc_start: 0.6362 (tpp) cc_final: 0.6114 (mmm) REVERT: D 180 HIS cc_start: 0.7483 (t-90) cc_final: 0.6955 (t-90) REVERT: D 203 MET cc_start: 0.8754 (mtt) cc_final: 0.8393 (mtt) REVERT: D 259 ASP cc_start: 0.8676 (t0) cc_final: 0.8333 (t0) outliers start: 54 outliers final: 27 residues processed: 323 average time/residue: 2.2938 time to fit residues: 872.8214 Evaluate side-chains 305 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 274 time to evaluate : 4.515 ------------------------------------------------------------------------------- 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 218 LYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 393 GLU 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 56 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU 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 46 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain G residue 12 SER 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 Chi-restraints excluded: chain D residue 435 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 90 optimal weight: 0.8980 chunk 193 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 244 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 259 optimal weight: 10.0000 chunk 243 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 B 432 GLN D 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.142873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104802 restraints weight = 30801.861| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.00 r_work: 0.3147 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24300 Z= 0.113 Angle : 0.549 13.339 32875 Z= 0.275 Chirality : 0.044 0.230 3843 Planarity : 0.004 0.051 4244 Dihedral : 6.568 107.493 3505 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.80 % Favored : 97.17 % Rotamer: Outliers : 1.30 % Allowed : 19.29 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3105 helix: 1.19 (0.15), residues: 1333 sheet: -0.53 (0.23), residues: 483 loop : -0.65 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 370 PHE 0.025 0.001 PHE D 262 TYR 0.024 0.001 TYR B 433 ARG 0.009 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 1138) hydrogen bonds : angle 4.77078 ( 3249) covalent geometry : bond 0.00253 (24300) covalent geometry : angle 0.54937 (32875) *********************** 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 319 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 3.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 143 ARG cc_start: 0.8413 (tpp-160) cc_final: 0.8184 (mmp80) REVERT: C 373 ARG cc_start: 0.8275 (mtt90) cc_final: 0.8063 (mtt90) REVERT: C 415 GLN cc_start: 0.5809 (mt0) cc_final: 0.5513 (mt0) REVERT: C 425 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8438 (m) REVERT: A 62 MET cc_start: 0.8819 (ttm) cc_final: 0.8581 (ttt) REVERT: A 96 ASP cc_start: 0.8642 (p0) cc_final: 0.8212 (p0) REVERT: A 97 VAL cc_start: 0.8897 (p) cc_final: 0.8670 (m) REVERT: A 218 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7473 (tttt) REVERT: A 226 MET cc_start: 0.9198 (tpt) cc_final: 0.8754 (tpt) REVERT: A 351 PHE cc_start: 0.7676 (m-80) cc_final: 0.7002 (t80) REVERT: A 362 ARG cc_start: 0.7381 (mtt180) cc_final: 0.6469 (mtt180) REVERT: A 397 TYR cc_start: 0.7574 (t80) cc_final: 0.7268 (t80) REVERT: B 24 ASP cc_start: 0.7620 (t70) cc_final: 0.7383 (m-30) REVERT: B 89 LYS cc_start: 0.8806 (mtmm) cc_final: 0.8422 (mtpp) REVERT: B 195 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: B 381 ARG cc_start: 0.7679 (tpt170) cc_final: 0.7286 (tpm170) REVERT: B 385 GLN cc_start: 0.7318 (mt0) cc_final: 0.7089 (mt0) REVERT: B 396 GLN cc_start: 0.7399 (mt0) cc_final: 0.7173 (mt0) REVERT: E 205 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: E 340 ARG cc_start: 0.7584 (tpp80) cc_final: 0.7260 (tpt-90) REVERT: E 475 LYS cc_start: 0.7192 (mmmm) cc_final: 0.6931 (mmmm) REVERT: F 170 MET cc_start: 0.8892 (tpp) cc_final: 0.8614 (mmt) REVERT: F 253 ASP cc_start: 0.8601 (m-30) cc_final: 0.8363 (m-30) REVERT: F 408 SER cc_start: 0.7752 (m) cc_final: 0.7515 (p) REVERT: F 422 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7628 (tm-30) REVERT: G 260 LYS cc_start: 0.8920 (tttt) cc_final: 0.8523 (tttp) REVERT: O 37 LYS cc_start: 0.7076 (tptm) cc_final: 0.6504 (tppt) REVERT: O 40 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6422 (pt) REVERT: O 42 VAL cc_start: 0.6996 (t) cc_final: 0.6747 (m) REVERT: O 134 LEU cc_start: 0.7671 (tp) cc_final: 0.7440 (mp) REVERT: O 186 MET cc_start: 0.5985 (ptp) cc_final: 0.5321 (pp-130) REVERT: D 59 SER cc_start: 0.8828 (m) cc_final: 0.8497 (p) REVERT: D 180 HIS cc_start: 0.7397 (t-90) cc_final: 0.6873 (t-90) REVERT: D 203 MET cc_start: 0.8731 (mtt) cc_final: 0.8347 (mtt) REVERT: D 259 ASP cc_start: 0.8486 (t0) cc_final: 0.8115 (t70) outliers start: 33 outliers final: 18 residues processed: 311 average time/residue: 1.3853 time to fit residues: 494.5357 Evaluate side-chains 303 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 280 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 73 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 466 ILE Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain O residue 40 LEU 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 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 272 optimal weight: 0.4980 chunk 226 optimal weight: 4.9990 chunk 290 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 217 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 238 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 chunk 224 optimal weight: 0.0870 chunk 172 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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** D 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.144317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107464 restraints weight = 30861.613| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.05 r_work: 0.3177 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24300 Z= 0.107 Angle : 0.538 14.139 32875 Z= 0.268 Chirality : 0.043 0.362 3843 Planarity : 0.004 0.054 4244 Dihedral : 6.304 108.030 3505 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 1.06 % Allowed : 19.41 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3105 helix: 1.35 (0.15), residues: 1332 sheet: -0.50 (0.24), residues: 476 loop : -0.52 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 370 PHE 0.022 0.001 PHE D 262 TYR 0.021 0.001 TYR E 384 ARG 0.009 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 1138) hydrogen bonds : angle 4.64975 ( 3249) covalent geometry : bond 0.00237 (24300) covalent geometry : angle 0.53798 (32875) ********************** 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 330 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 303 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 143 ARG cc_start: 0.8390 (tpp-160) cc_final: 0.8147 (mmp80) REVERT: C 373 ARG cc_start: 0.8211 (mtt90) cc_final: 0.8009 (mtt90) REVERT: C 415 GLN cc_start: 0.5759 (mt0) cc_final: 0.5477 (mt0) REVERT: A 62 MET cc_start: 0.8791 (ttm) cc_final: 0.8544 (ttt) REVERT: A 96 ASP cc_start: 0.8609 (p0) cc_final: 0.8191 (p0) REVERT: A 97 VAL cc_start: 0.8842 (p) cc_final: 0.8617 (m) REVERT: A 218 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7451 (tttt) REVERT: A 226 MET cc_start: 0.9160 (tpt) cc_final: 0.8754 (tpt) REVERT: A 347 ASP cc_start: 0.8275 (m-30) cc_final: 0.8051 (m-30) REVERT: A 351 PHE cc_start: 0.7604 (m-80) cc_final: 0.6912 (t80) REVERT: A 362 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6107 (mtt180) REVERT: A 397 TYR cc_start: 0.7540 (t80) cc_final: 0.7271 (t80) REVERT: B 89 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8322 (mtpp) REVERT: B 195 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: B 489 ILE cc_start: 0.7493 (pt) cc_final: 0.6607 (pp) REVERT: E 205 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: E 340 ARG cc_start: 0.7548 (tpp80) cc_final: 0.7196 (tpt-90) REVERT: F 291 ASP cc_start: 0.8363 (m-30) cc_final: 0.8130 (m-30) REVERT: F 408 SER cc_start: 0.7650 (m) cc_final: 0.7404 (p) REVERT: F 422 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7556 (tm-30) REVERT: G 260 LYS cc_start: 0.8853 (tttt) cc_final: 0.8439 (tttp) REVERT: O 36 GLU cc_start: 0.6602 (tm-30) cc_final: 0.6321 (tt0) REVERT: O 37 LYS cc_start: 0.6936 (tptm) cc_final: 0.6733 (tppt) REVERT: O 42 VAL cc_start: 0.6967 (t) cc_final: 0.6717 (m) REVERT: O 134 LEU cc_start: 0.7514 (tp) cc_final: 0.7270 (mp) REVERT: O 186 MET cc_start: 0.5942 (ptp) cc_final: 0.5269 (pp-130) REVERT: D 59 SER cc_start: 0.8756 (m) cc_final: 0.8405 (p) REVERT: D 180 HIS cc_start: 0.7393 (t-90) cc_final: 0.6846 (t-90) REVERT: D 203 MET cc_start: 0.8735 (mtt) cc_final: 0.8346 (mtt) REVERT: D 259 ASP cc_start: 0.8435 (t0) cc_final: 0.8066 (t0) outliers start: 27 outliers final: 17 residues processed: 324 average time/residue: 1.3873 time to fit residues: 516.6094 Evaluate side-chains 301 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 281 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 505 LEU 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 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 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 252 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 161 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 A 475 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 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 = 0.3732 r_free = 0.3732 target = 0.144051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.106838 restraints weight = 30690.095| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.16 r_work: 0.3160 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24300 Z= 0.116 Angle : 0.560 15.847 32875 Z= 0.276 Chirality : 0.044 0.265 3843 Planarity : 0.004 0.056 4244 Dihedral : 6.280 109.968 3505 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.61 % Favored : 97.36 % Rotamer: Outliers : 1.02 % Allowed : 19.96 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 3105 helix: 1.40 (0.15), residues: 1325 sheet: -0.48 (0.24), residues: 482 loop : -0.47 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 370 PHE 0.022 0.001 PHE D 262 TYR 0.020 0.001 TYR A 397 ARG 0.009 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 1138) hydrogen bonds : angle 4.64379 ( 3249) covalent geometry : bond 0.00264 (24300) covalent geometry : angle 0.55994 (32875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20440.53 seconds wall clock time: 355 minutes 20.98 seconds (21320.98 seconds total)