Starting phenix.real_space_refine on Sun Aug 24 22:54:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9p_34576/08_2025/8h9p_34576.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9p_34576/08_2025/8h9p_34576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h9p_34576/08_2025/8h9p_34576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9p_34576/08_2025/8h9p_34576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h9p_34576/08_2025/8h9p_34576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9p_34576/08_2025/8h9p_34576.map" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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 84 5.16 5 C 14744 2.51 5 N 4077 2.21 5 O 4495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 157 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23418 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3706 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 467} Chain: "B" 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: "C" Number of atoms: 3587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3587 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 451} Chain breaks: 1 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3458 Classifications: {'peptide': 456} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3529 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain: "D" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3287 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "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: "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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.03, per 1000 atoms: 0.26 Number of scatterers: 23418 At special positions: 0 Unit cell: (129.21, 123.37, 134.32, 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 84 16.00 P 13 15.00 Mg 5 11.99 O 4495 8.00 N 4077 7.00 C 14744 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: 1.74 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5548 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 20 sheets defined 47.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.548A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.827A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.920A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.698A 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 297 through 307 Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 380 through 399 removed outlier: 4.115A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 411 through 429 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 476 Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 490 through 508 removed outlier: 3.560A pdb=" N GLY A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.694A 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 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 239 through 259 Proline residue: B 247 - end of helix removed outlier: 3.970A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 284 removed outlier: 3.776A 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: 4.080A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 346 removed outlier: 3.545A pdb=" N THR B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 380 through 401 removed outlier: 4.376A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 429 removed outlier: 3.966A pdb=" N GLN B 416 " --> pdb=" O ALA B 412 " (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 476 Processing helix chain 'B' and resid 476 through 487 Processing helix chain 'B' and resid 490 through 507 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.765A pdb=" N ILE C 82 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.787A 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 209 through 223 Processing helix chain 'C' and resid 239 through 259 Proline residue: C 247 - end of helix removed outlier: 4.070A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.945A 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 removed outlier: 3.835A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.835A pdb=" N ALA C 377 " --> pdb=" O VAL C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 401 removed outlier: 4.195A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 429 removed outlier: 3.618A pdb=" N LYS C 429 " --> pdb=" O THR C 425 " (cutoff:3.500A) 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 476 Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 507 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.642A pdb=" N MET E 129 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 164 through 180 Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 228 through 249 removed outlier: 4.847A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 275 Processing helix chain 'E' and resid 280 through 284 removed outlier: 3.946A pdb=" N GLY E 283 " --> pdb=" O SER E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 322 through 329 Processing helix chain 'E' and resid 340 through 345 Processing helix chain 'E' and resid 362 through 391 removed outlier: 7.505A pdb=" N SER E 368 " --> pdb=" O ASN E 364 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLU E 369 " --> pdb=" O ILE E 365 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS E 370 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.764A pdb=" N SER E 418 " --> pdb=" O GLN E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 423 No H-bonds generated for 'chain 'E' and resid 421 through 423' Processing helix chain 'E' and resid 424 through 429 Processing helix chain 'E' and resid 436 through 449 Processing helix chain 'E' and resid 456 through 461 removed outlier: 3.538A pdb=" N PHE E 460 " --> pdb=" O GLU E 457 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR E 461 " --> pdb=" O GLN E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 475 removed outlier: 3.500A pdb=" N ALA E 469 " --> pdb=" O PRO E 465 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS E 475 " --> pdb=" O ALA E 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 164 through 176 Processing helix chain 'F' and resid 192 through 206 removed outlier: 3.571A pdb=" N GLY F 196 " --> pdb=" O ARG F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 249 removed outlier: 4.687A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 273 removed outlier: 3.991A 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 287 through 297 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 322 through 329 Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 339 through 344 Processing helix chain 'F' and resid 362 through 394 removed outlier: 7.196A pdb=" N SER F 368 " --> pdb=" O ASN F 364 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N GLU F 369 " --> pdb=" O ILE F 365 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N HIS F 370 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 399 removed outlier: 3.956A pdb=" N GLU F 398 " --> pdb=" O GLY F 395 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU F 399 " --> pdb=" O MET F 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 395 through 399' Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.802A pdb=" N SER F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 428 removed outlier: 3.639A pdb=" N PHE F 427 " --> pdb=" O ALA F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 449 Processing helix chain 'F' and resid 456 through 460 Processing helix chain 'F' and resid 465 through 476 Processing helix chain 'D' and resid 165 through 180 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 228 through 251 removed outlier: 4.917A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 275 removed outlier: 3.755A pdb=" N PHE D 264 " --> pdb=" O ASN D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 339 through 345 removed outlier: 3.584A pdb=" N ALA D 343 " --> pdb=" O SER D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 388 removed outlier: 3.548A pdb=" N TYR D 371 " --> pdb=" O GLY D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 436 through 449 Processing helix chain 'D' and resid 456 through 460 removed outlier: 3.645A pdb=" N ALA D 459 " --> pdb=" O PRO D 456 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE D 460 " --> pdb=" O GLU D 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 456 through 460' Processing helix chain 'D' and resid 465 through 475 removed outlier: 3.572A pdb=" N ALA D 469 " --> pdb=" O PRO D 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 30 Processing helix chain 'G' and resid 224 through 270 Processing helix chain 'O' and resid 12 through 28 Processing helix chain 'O' and resid 31 through 47 Processing helix chain 'O' and resid 48 through 57 removed outlier: 4.232A pdb=" N LEU O 56 " --> pdb=" O ALA O 52 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 75 removed outlier: 3.763A pdb=" N LYS O 75 " --> pdb=" O ASP O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 92 removed outlier: 3.533A pdb=" N THR O 83 " --> pdb=" O SER O 79 " (cutoff:3.500A) 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 113 Processing helix chain 'O' and resid 127 through 140 Processing helix chain 'O' and resid 155 through 159 removed outlier: 3.754A pdb=" N ILE O 158 " --> pdb=" O ASP O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 33 removed outlier: 6.508A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) 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: 6.466A 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 '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: 6.734A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.065A 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 'O' and resid 147 through 150 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 147 through 150 current: chain 'O' and resid 169 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.211A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 8.786A pdb=" N ILE A 230 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR A 200 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE A 267 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 202 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ASP A 269 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 204 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 328 removed outlier: 6.595A pdb=" N ILE A 167 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N GLN A 349 " --> pdb=" O GLY A 368 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N GLY A 368 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE A 351 " --> pdb=" O ASN A 366 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 28 through 35 removed outlier: 6.824A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) 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: 6.439A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 75 current: chain 'C' and resid 38 through 43 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: 5.563A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.838A 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 70 through 75 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: 6.694A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.074A 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 'D' and resid 23 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 23 through 27 current: chain 'D' and resid 49 through 55 removed outlier: 6.715A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.257A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.188A pdb=" N TYR B 200 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE B 267 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 202 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASP B 269 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL B 204 " --> pdb=" O ASP B 269 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 264 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 326 through 328 removed outlier: 6.466A pdb=" N ILE B 167 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.277A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.361A pdb=" N VAL C 108 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N ILE C 230 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 326 through 328 removed outlier: 6.483A pdb=" N ILE C 167 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 168 " --> pdb=" O LEU C 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.059A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.105A pdb=" N MET E 98 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLN E 224 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL E 254 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL E 310 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU E 256 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA E 312 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE E 258 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE E 155 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS E 154 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR E 336 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY E 156 " --> pdb=" O THR E 336 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 135 through 136 removed outlier: 4.348A pdb=" N TYR E 149 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.229A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 97 through 98 removed outlier: 6.603A pdb=" N SER F 184 " --> pdb=" O ALA F 219 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL F 221 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE F 186 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLY F 223 " --> pdb=" O PHE F 186 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLY F 188 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL F 254 " --> pdb=" O THR F 308 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL F 310 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU F 256 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ALA F 312 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE F 258 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N TYR F 314 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS F 154 " --> pdb=" O ALA F 334 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N THR F 336 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY F 156 " --> pdb=" O THR F 336 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.204A pdb=" N TYR F 149 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 86 through 89 removed outlier: 4.064A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 97 through 98 removed outlier: 5.995A pdb=" N MET D 98 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLN D 224 " --> pdb=" O MET D 98 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 155 " --> pdb=" O GLN D 311 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 334 through 335 1037 hydrogen bonds defined for protein. 2991 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.33 Time building geometry restraints manager: 2.26 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: 5294 1.33 - 1.45: 4409 1.45 - 1.57: 13866 1.57 - 1.69: 21 1.69 - 1.81: 161 Bond restraints: 23751 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 1.29e+02 bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.461 -0.124 1.10e-02 8.26e+03 1.26e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.460 -0.123 1.10e-02 8.26e+03 1.25e+02 bond pdb=" C4 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.374 1.285 0.089 1.00e-02 1.00e+04 7.87e+01 bond pdb=" C4 ATP B 601 " pdb=" N9 ATP B 601 " ideal model delta sigma weight residual 1.374 1.286 0.088 1.00e-02 1.00e+04 7.71e+01 ... (remaining 23746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 31951 3.58 - 7.16: 138 7.16 - 10.73: 29 10.73 - 14.31: 4 14.31 - 17.89: 2 Bond angle restraints: 32124 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 121.98 17.89 1.00e+00 1.00e+00 3.20e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 122.43 17.44 1.00e+00 1.00e+00 3.04e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 125.84 14.03 1.00e+00 1.00e+00 1.97e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 123.16 13.67 1.00e+00 1.00e+00 1.87e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 123.40 13.43 1.00e+00 1.00e+00 1.80e+02 ... (remaining 32119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.05: 14044 29.05 - 58.10: 473 58.10 - 87.16: 54 87.16 - 116.21: 5 116.21 - 145.26: 2 Dihedral angle restraints: 14578 sinusoidal: 5899 harmonic: 8679 Sorted by residual: dihedral pdb=" CD ARG C 373 " pdb=" NE ARG C 373 " pdb=" CZ ARG C 373 " pdb=" NH1 ARG C 373 " ideal model delta sinusoidal sigma weight residual 0.00 70.48 -70.48 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual 300.00 154.74 145.26 1 2.00e+01 2.50e-03 4.37e+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 59.26 -119.25 1 2.00e+01 2.50e-03 3.57e+01 ... (remaining 14575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2823 0.050 - 0.100: 740 0.100 - 0.150: 172 0.150 - 0.200: 10 0.200 - 0.250: 3 Chirality restraints: 3748 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 1.56e+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 -2.44 -0.24 2.00e-01 2.50e+01 1.42e+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 -2.46 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 3745 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 373 " 1.023 9.50e-02 1.11e+02 4.58e-01 1.27e+02 pdb=" NE ARG C 373 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG C 373 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 373 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 373 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 277 " -0.274 9.50e-02 1.11e+02 1.23e-01 9.22e+00 pdb=" NE ARG D 277 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 277 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 277 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 277 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 322 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO E 323 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 323 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 323 " 0.025 5.00e-02 4.00e+02 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 207 2.56 - 3.15: 19482 3.15 - 3.73: 35884 3.73 - 4.32: 53475 4.32 - 4.90: 88513 Nonbonded interactions: 197561 Sorted by model distance: nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 1.976 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 1.982 2.170 nonbonded pdb=" O3G ATP A 601 " pdb="MG MG A 602 " model vdw 1.983 2.170 nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 602 " model vdw 2.144 2.170 ... (remaining 197556 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 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 12 through 475) selection = (chain 'E' and (resid 12 through 160 or resid 162 through 312 or resid 330 throu \ gh 389 or (resid 404 and (name N or name CA or name C or name O or name CB )) or \ resid 405 through 475)) selection = (chain 'F' and (resid 12 through 160 or resid 162 through 312 or resid 330 throu \ gh 389 or (resid 404 and (name N or name CA or name C or name O or name CB )) or \ resid 405 through 475)) } 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: 15.180 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: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 22.480 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.006 0.147 23751 Z= 0.392 Angle : 0.793 17.889 32124 Z= 0.520 Chirality : 0.046 0.250 3748 Planarity : 0.008 0.458 4144 Dihedral : 14.266 145.261 9030 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.13), residues: 3027 helix: -1.47 (0.12), residues: 1259 sheet: -2.12 (0.20), residues: 492 loop : -2.27 (0.15), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 373 TYR 0.015 0.001 TYR C 446 PHE 0.017 0.001 PHE D 444 HIS 0.003 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00643 (23751) covalent geometry : angle 0.79251 (32124) hydrogen bonds : bond 0.13855 ( 1037) hydrogen bonds : angle 6.74242 ( 2991) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 420 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7744 (ttmt) REVERT: A 475 GLN cc_start: 0.6701 (mp10) cc_final: 0.6434 (mp10) REVERT: B 89 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7625 (mtpt) REVERT: B 226 MET cc_start: 0.8227 (mmm) cc_final: 0.7848 (tpt) REVERT: B 396 GLN cc_start: 0.8196 (mt0) cc_final: 0.7933 (mm-40) REVERT: B 418 LEU cc_start: 0.8081 (mp) cc_final: 0.7725 (tt) REVERT: B 477 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7187 (tm-30) REVERT: E 347 ILE cc_start: 0.9261 (mm) cc_final: 0.8886 (mm) REVERT: D 62 ARG cc_start: 0.7924 (ttm170) cc_final: 0.7677 (ttm-80) REVERT: D 128 GLU cc_start: 0.8248 (tt0) cc_final: 0.7946 (mt-10) REVERT: D 339 SER cc_start: 0.8174 (t) cc_final: 0.7762 (p) REVERT: D 433 LYS cc_start: 0.6842 (mmtm) cc_final: 0.6288 (mptt) REVERT: D 445 GLN cc_start: 0.6212 (tm-30) cc_final: 0.5883 (pt0) REVERT: D 455 LEU cc_start: 0.6748 (mm) cc_final: 0.6503 (mm) REVERT: D 460 PHE cc_start: 0.6978 (m-10) cc_final: 0.6777 (m-10) REVERT: D 462 MET cc_start: 0.8140 (tpt) cc_final: 0.7575 (tpp) REVERT: D 467 GLU cc_start: 0.7027 (tt0) cc_final: 0.6804 (mp0) REVERT: G 229 MET cc_start: 0.7549 (ttp) cc_final: 0.7166 (ttm) REVERT: O 33 GLU cc_start: 0.6064 (mp0) cc_final: 0.4520 (tp30) outliers start: 3 outliers final: 1 residues processed: 421 average time/residue: 0.1749 time to fit residues: 108.7871 Evaluate side-chains 289 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 284 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 349 GLN A 385 GLN A 396 GLN A 476 HIS B 65 ASN B 475 GLN C 78 ASN C 208 GLN C 385 GLN C 471 HIS C 475 GLN E 224 GLN E 370 HIS F 133 GLN F 174 ASN F 197 ASN F 311 GLN F 331 HIS D 260 ASN D 285 GLN D 378 GLN D 382 GLN D 419 GLN O 10 GLN O 92 ASN O 99 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097526 restraints weight = 34094.004| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.21 r_work: 0.3077 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23751 Z= 0.161 Angle : 0.598 14.237 32124 Z= 0.302 Chirality : 0.045 0.149 3748 Planarity : 0.004 0.041 4144 Dihedral : 7.701 127.730 3428 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.13 % Rotamer: Outliers : 1.17 % Allowed : 9.21 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.14), residues: 3027 helix: -0.01 (0.14), residues: 1269 sheet: -1.62 (0.21), residues: 483 loop : -1.52 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 375 TYR 0.025 0.002 TYR E 384 PHE 0.020 0.001 PHE D 444 HIS 0.009 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00375 (23751) covalent geometry : angle 0.59779 (32124) hydrogen bonds : bond 0.04662 ( 1037) hydrogen bonds : angle 5.00359 ( 2991) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 332 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8800 (ttp80) cc_final: 0.8398 (ttp-110) REVERT: A 208 GLN cc_start: 0.7603 (mt0) cc_final: 0.7266 (mt0) REVERT: A 226 MET cc_start: 0.8818 (mmm) cc_final: 0.8523 (mmm) REVERT: A 330 GLN cc_start: 0.8937 (mp10) cc_final: 0.8721 (mp10) REVERT: A 460 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7518 (ttmt) REVERT: A 475 GLN cc_start: 0.6708 (mp10) cc_final: 0.6454 (mp10) REVERT: B 89 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7736 (mtpt) REVERT: B 396 GLN cc_start: 0.7814 (mt0) cc_final: 0.7593 (mm-40) REVERT: B 415 GLN cc_start: 0.7420 (mt0) cc_final: 0.7173 (mt0) REVERT: B 418 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7559 (tt) REVERT: B 477 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7042 (tm-30) REVERT: E 263 ARG cc_start: 0.7638 (mtt180) cc_final: 0.7408 (mtm-85) REVERT: E 347 ILE cc_start: 0.9291 (mm) cc_final: 0.8889 (mm) REVERT: E 427 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8209 (t80) REVERT: D 62 ARG cc_start: 0.8348 (ttm170) cc_final: 0.8004 (ttm-80) REVERT: D 128 GLU cc_start: 0.8272 (tt0) cc_final: 0.7936 (mt-10) REVERT: D 339 SER cc_start: 0.8179 (t) cc_final: 0.7757 (p) REVERT: D 433 LYS cc_start: 0.6585 (mmtm) cc_final: 0.5966 (mptt) REVERT: D 445 GLN cc_start: 0.6116 (tm-30) cc_final: 0.5652 (pt0) REVERT: D 460 PHE cc_start: 0.7136 (m-10) cc_final: 0.6877 (m-10) REVERT: D 462 MET cc_start: 0.8160 (tpt) cc_final: 0.7265 (tpp) REVERT: D 467 GLU cc_start: 0.7059 (tt0) cc_final: 0.6728 (mp0) REVERT: O 33 GLU cc_start: 0.6023 (mp0) cc_final: 0.4541 (tp30) REVERT: O 163 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8168 (mm) outliers start: 29 outliers final: 12 residues processed: 351 average time/residue: 0.1590 time to fit residues: 85.7994 Evaluate side-chains 305 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 290 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 163 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 42 optimal weight: 6.9990 chunk 21 optimal weight: 0.0470 chunk 178 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 99 optimal weight: 0.4980 chunk 296 optimal weight: 30.0000 chunk 55 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 216 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.6482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN A 302 HIS E 174 ASN E 210 ASN F 174 ASN F 175 ASN D 296 GLN O 10 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101007 restraints weight = 33572.342| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.24 r_work: 0.3140 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23751 Z= 0.107 Angle : 0.535 11.976 32124 Z= 0.269 Chirality : 0.043 0.149 3748 Planarity : 0.004 0.040 4144 Dihedral : 7.043 112.847 3428 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.05 % Favored : 97.89 % Rotamer: Outliers : 1.41 % Allowed : 11.14 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.15), residues: 3027 helix: 0.65 (0.15), residues: 1271 sheet: -1.32 (0.22), residues: 470 loop : -1.08 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 375 TYR 0.029 0.001 TYR E 384 PHE 0.025 0.001 PHE C 464 HIS 0.009 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00232 (23751) covalent geometry : angle 0.53529 (32124) hydrogen bonds : bond 0.04051 ( 1037) hydrogen bonds : angle 4.68595 ( 2991) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 346 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.7519 (mt0) cc_final: 0.7197 (mt0) REVERT: A 226 MET cc_start: 0.8892 (mmm) cc_final: 0.8551 (mmm) REVERT: A 330 GLN cc_start: 0.9082 (mp10) cc_final: 0.8852 (mp10) REVERT: A 460 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7664 (ttmt) REVERT: A 475 GLN cc_start: 0.6816 (mp10) cc_final: 0.6609 (mp10) REVERT: B 67 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8559 (mm-30) REVERT: B 89 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7846 (mtpt) REVERT: B 396 GLN cc_start: 0.7823 (mt0) cc_final: 0.7586 (mm-40) REVERT: B 415 GLN cc_start: 0.7386 (mt0) cc_final: 0.7140 (mt0) REVERT: B 418 LEU cc_start: 0.7936 (mp) cc_final: 0.7577 (tt) REVERT: B 477 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7079 (tm-30) REVERT: C 218 LYS cc_start: 0.8415 (tttm) cc_final: 0.8025 (tppt) REVERT: E 255 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8661 (tp) REVERT: E 263 ARG cc_start: 0.7723 (mtt180) cc_final: 0.7430 (mtm-85) REVERT: E 347 ILE cc_start: 0.9307 (mm) cc_final: 0.8894 (mm) REVERT: E 427 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8152 (t80) REVERT: E 458 GLN cc_start: 0.8009 (tp40) cc_final: 0.7397 (tp40) REVERT: D 62 ARG cc_start: 0.8377 (ttm170) cc_final: 0.8089 (ttm-80) REVERT: D 128 GLU cc_start: 0.8334 (tt0) cc_final: 0.8086 (mt-10) REVERT: D 433 LYS cc_start: 0.6693 (mmtm) cc_final: 0.6034 (mptt) REVERT: D 460 PHE cc_start: 0.7069 (m-10) cc_final: 0.6738 (m-10) REVERT: D 462 MET cc_start: 0.8155 (tpt) cc_final: 0.7228 (tpp) REVERT: D 467 GLU cc_start: 0.6976 (tt0) cc_final: 0.6726 (mp0) REVERT: O 33 GLU cc_start: 0.5950 (mp0) cc_final: 0.4547 (tp30) REVERT: O 163 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8157 (mm) outliers start: 35 outliers final: 19 residues processed: 369 average time/residue: 0.1626 time to fit residues: 92.5351 Evaluate side-chains 326 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 304 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 163 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 40 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 chunk 180 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 228 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 274 GLN A 476 HIS B 476 HIS F 311 GLN O 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.132770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.102541 restraints weight = 33883.656| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.14 r_work: 0.3175 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23751 Z= 0.111 Angle : 0.524 10.470 32124 Z= 0.263 Chirality : 0.043 0.194 3748 Planarity : 0.004 0.038 4144 Dihedral : 6.632 105.881 3428 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.05 % Favored : 97.89 % Rotamer: Outliers : 1.73 % Allowed : 12.59 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.15), residues: 3027 helix: 1.00 (0.15), residues: 1272 sheet: -1.16 (0.23), residues: 458 loop : -0.83 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 359 TYR 0.023 0.001 TYR E 384 PHE 0.024 0.001 PHE A 464 HIS 0.009 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00245 (23751) covalent geometry : angle 0.52392 (32124) hydrogen bonds : bond 0.03900 ( 1037) hydrogen bonds : angle 4.52961 ( 2991) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 330 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7855 (tm-30) cc_final: 0.6982 (tm-30) REVERT: A 208 GLN cc_start: 0.7736 (mt0) cc_final: 0.7441 (mt0) REVERT: A 226 MET cc_start: 0.8896 (mmm) cc_final: 0.8600 (mmm) REVERT: A 460 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7676 (ttmt) REVERT: B 396 GLN cc_start: 0.7946 (mt0) cc_final: 0.7719 (mm-40) REVERT: B 415 GLN cc_start: 0.7518 (mt0) cc_final: 0.7303 (mt0) REVERT: B 418 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7648 (tt) REVERT: B 475 GLN cc_start: 0.7409 (mp10) cc_final: 0.6957 (mp10) REVERT: B 477 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7174 (tm-30) REVERT: C 218 LYS cc_start: 0.8495 (tttm) cc_final: 0.8168 (tppt) REVERT: C 420 ARG cc_start: 0.7077 (tpp80) cc_final: 0.6230 (tpp-160) REVERT: E 347 ILE cc_start: 0.9335 (mm) cc_final: 0.8945 (mm) REVERT: E 427 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8166 (t80) REVERT: E 458 GLN cc_start: 0.7961 (tp40) cc_final: 0.7372 (tp40) REVERT: F 191 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7959 (tp30) REVERT: D 128 GLU cc_start: 0.8458 (tt0) cc_final: 0.8241 (mt-10) REVERT: D 296 GLN cc_start: 0.8497 (mm-40) cc_final: 0.7877 (tt0) REVERT: D 433 LYS cc_start: 0.6753 (mmtm) cc_final: 0.6297 (mptt) REVERT: D 460 PHE cc_start: 0.6900 (m-10) cc_final: 0.6659 (m-10) REVERT: D 462 MET cc_start: 0.8134 (tpt) cc_final: 0.7128 (tpp) REVERT: O 33 GLU cc_start: 0.5968 (mp0) cc_final: 0.4530 (tp30) REVERT: O 113 ARG cc_start: 0.6376 (ptp-170) cc_final: 0.5985 (ptp-110) REVERT: O 163 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8184 (mm) outliers start: 43 outliers final: 22 residues processed: 358 average time/residue: 0.1659 time to fit residues: 91.8184 Evaluate side-chains 326 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 301 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 163 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 180 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 220 optimal weight: 0.5980 chunk 178 optimal weight: 0.9980 chunk 273 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 238 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN F 311 GLN D 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.132820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102591 restraints weight = 33755.720| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.13 r_work: 0.3180 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23751 Z= 0.112 Angle : 0.520 9.643 32124 Z= 0.261 Chirality : 0.043 0.168 3748 Planarity : 0.003 0.036 4144 Dihedral : 6.416 104.431 3428 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.02 % Favored : 97.92 % Rotamer: Outliers : 1.97 % Allowed : 12.99 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.15), residues: 3027 helix: 1.17 (0.15), residues: 1270 sheet: -1.01 (0.24), residues: 452 loop : -0.66 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 359 TYR 0.028 0.001 TYR C 397 PHE 0.016 0.001 PHE A 464 HIS 0.009 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00252 (23751) covalent geometry : angle 0.52028 (32124) hydrogen bonds : bond 0.03818 ( 1037) hydrogen bonds : angle 4.45171 ( 2991) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 322 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.7734 (mt0) cc_final: 0.7429 (mt0) REVERT: A 226 MET cc_start: 0.8912 (mmm) cc_final: 0.8608 (mmm) REVERT: A 335 SER cc_start: 0.9198 (m) cc_final: 0.8910 (t) REVERT: B 396 GLN cc_start: 0.7941 (mt0) cc_final: 0.7717 (mm-40) REVERT: B 415 GLN cc_start: 0.7484 (mt0) cc_final: 0.7261 (mt0) REVERT: B 418 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7616 (tt) REVERT: B 475 GLN cc_start: 0.7279 (mp10) cc_final: 0.6822 (mp10) REVERT: B 477 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7171 (tm-30) REVERT: C 45 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.8018 (mmm160) REVERT: C 420 ARG cc_start: 0.6989 (tpp80) cc_final: 0.6233 (tpp-160) REVERT: E 347 ILE cc_start: 0.9329 (mm) cc_final: 0.8948 (mm) REVERT: E 427 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8180 (t80) REVERT: E 458 GLN cc_start: 0.7946 (tp40) cc_final: 0.7346 (tp40) REVERT: F 191 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7977 (tp30) REVERT: D 128 GLU cc_start: 0.8454 (tt0) cc_final: 0.8249 (mt-10) REVERT: D 414 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.5656 (mt0) REVERT: D 460 PHE cc_start: 0.6892 (m-10) cc_final: 0.6661 (m-10) REVERT: D 462 MET cc_start: 0.8112 (tpt) cc_final: 0.7220 (tpp) REVERT: O 33 GLU cc_start: 0.6002 (mp0) cc_final: 0.4546 (tp30) REVERT: O 113 ARG cc_start: 0.6388 (ptp-170) cc_final: 0.5980 (ptp-110) REVERT: O 163 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8172 (mm) outliers start: 49 outliers final: 24 residues processed: 354 average time/residue: 0.1647 time to fit residues: 90.4093 Evaluate side-chains 326 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 298 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 124 SER Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 163 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 22 optimal weight: 0.6980 chunk 217 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 GLN F 311 GLN D 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.100010 restraints weight = 34292.377| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.14 r_work: 0.3136 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23751 Z= 0.181 Angle : 0.560 9.208 32124 Z= 0.281 Chirality : 0.045 0.173 3748 Planarity : 0.004 0.041 4144 Dihedral : 6.484 103.452 3428 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 1.97 % Allowed : 13.68 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.15), residues: 3027 helix: 1.13 (0.15), residues: 1274 sheet: -0.88 (0.24), residues: 457 loop : -0.66 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 45 TYR 0.027 0.002 TYR C 397 PHE 0.020 0.001 PHE C 468 HIS 0.009 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00432 (23751) covalent geometry : angle 0.56033 (32124) hydrogen bonds : bond 0.04254 ( 1037) hydrogen bonds : angle 4.52618 ( 2991) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 299 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.7836 (mt0) cc_final: 0.7627 (mt0) REVERT: A 226 MET cc_start: 0.8944 (mmm) cc_final: 0.8604 (mmm) REVERT: A 335 SER cc_start: 0.9227 (m) cc_final: 0.8907 (t) REVERT: B 396 GLN cc_start: 0.7891 (mt0) cc_final: 0.7641 (mm-40) REVERT: B 415 GLN cc_start: 0.7471 (mt0) cc_final: 0.7256 (mt0) REVERT: B 418 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7589 (tt) REVERT: B 475 GLN cc_start: 0.7220 (mp10) cc_final: 0.6777 (mp10) REVERT: B 477 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7134 (tm-30) REVERT: C 393 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7775 (mt-10) REVERT: C 420 ARG cc_start: 0.6982 (tpp80) cc_final: 0.6122 (tpp-160) REVERT: E 347 ILE cc_start: 0.9346 (mm) cc_final: 0.8966 (mm) REVERT: E 427 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.8184 (t80) REVERT: F 191 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8162 (tp30) REVERT: F 359 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7983 (ttm110) REVERT: D 128 GLU cc_start: 0.8407 (tt0) cc_final: 0.8205 (mt-10) REVERT: D 263 ARG cc_start: 0.8659 (mmt-90) cc_final: 0.8244 (mpt180) REVERT: D 414 GLN cc_start: 0.6460 (OUTLIER) cc_final: 0.5692 (mt0) REVERT: D 460 PHE cc_start: 0.6990 (m-10) cc_final: 0.6732 (m-10) REVERT: D 462 MET cc_start: 0.8185 (tpt) cc_final: 0.7234 (tpp) REVERT: O 33 GLU cc_start: 0.6043 (mp0) cc_final: 0.4535 (tp30) REVERT: O 113 ARG cc_start: 0.6385 (ptp-170) cc_final: 0.5964 (ptp-110) REVERT: O 163 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8132 (mm) outliers start: 49 outliers final: 32 residues processed: 331 average time/residue: 0.1629 time to fit residues: 83.3938 Evaluate side-chains 321 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 124 SER Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 163 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 251 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 199 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 265 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.097686 restraints weight = 34388.843| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.14 r_work: 0.3110 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 23751 Z= 0.233 Angle : 0.603 8.967 32124 Z= 0.303 Chirality : 0.047 0.154 3748 Planarity : 0.004 0.039 4144 Dihedral : 6.648 99.307 3428 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.03 % Rotamer: Outliers : 1.93 % Allowed : 14.44 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.15), residues: 3027 helix: 1.05 (0.15), residues: 1272 sheet: -0.97 (0.24), residues: 453 loop : -0.73 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 45 TYR 0.030 0.002 TYR C 397 PHE 0.015 0.001 PHE A 464 HIS 0.009 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00559 (23751) covalent geometry : angle 0.60290 (32124) hydrogen bonds : bond 0.04634 ( 1037) hydrogen bonds : angle 4.66757 ( 2991) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 286 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.7922 (mt0) cc_final: 0.7718 (mt0) REVERT: A 226 MET cc_start: 0.8950 (mmm) cc_final: 0.8645 (mmm) REVERT: A 335 SER cc_start: 0.9260 (m) cc_final: 0.8938 (t) REVERT: B 224 ASP cc_start: 0.8808 (t0) cc_final: 0.8565 (t0) REVERT: B 396 GLN cc_start: 0.7958 (mt0) cc_final: 0.7714 (mm-40) REVERT: B 418 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7640 (tt) REVERT: B 475 GLN cc_start: 0.7237 (mp10) cc_final: 0.6807 (mp10) REVERT: B 477 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7150 (tm-30) REVERT: C 420 ARG cc_start: 0.7043 (tpp80) cc_final: 0.6240 (tpp-160) REVERT: E 347 ILE cc_start: 0.9355 (mm) cc_final: 0.8972 (mm) REVERT: E 427 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8180 (t80) REVERT: F 191 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8232 (tp30) REVERT: F 398 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: D 263 ARG cc_start: 0.8735 (mmt-90) cc_final: 0.8306 (mpt180) REVERT: D 414 GLN cc_start: 0.6564 (OUTLIER) cc_final: 0.5785 (mt0) REVERT: D 433 LYS cc_start: 0.6891 (mmtt) cc_final: 0.6437 (mptt) REVERT: D 445 GLN cc_start: 0.6070 (tm-30) cc_final: 0.5626 (pt0) REVERT: D 460 PHE cc_start: 0.6963 (m-10) cc_final: 0.6738 (m-10) REVERT: D 462 MET cc_start: 0.8216 (tpt) cc_final: 0.7179 (tpp) REVERT: G 23 MET cc_start: 0.6738 (ttm) cc_final: 0.6486 (ttm) REVERT: O 33 GLU cc_start: 0.6102 (mp0) cc_final: 0.4595 (tp30) REVERT: O 113 ARG cc_start: 0.6452 (ptp-170) cc_final: 0.6027 (ptp-110) REVERT: O 127 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6489 (pm20) REVERT: O 163 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8106 (mm) outliers start: 48 outliers final: 34 residues processed: 318 average time/residue: 0.1791 time to fit residues: 87.4526 Evaluate side-chains 318 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 278 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 463 LYS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 241 GLU Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 124 SER Chi-restraints excluded: chain O residue 127 GLU Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 163 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 191 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 163 optimal weight: 0.0870 chunk 58 optimal weight: 5.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 ASN D 296 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101715 restraints weight = 33969.286| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.14 r_work: 0.3164 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23751 Z= 0.117 Angle : 0.534 8.768 32124 Z= 0.268 Chirality : 0.043 0.154 3748 Planarity : 0.003 0.038 4144 Dihedral : 6.169 83.406 3428 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.75 % Rotamer: Outliers : 1.85 % Allowed : 14.64 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.16), residues: 3027 helix: 1.25 (0.15), residues: 1274 sheet: -0.91 (0.25), residues: 432 loop : -0.55 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 45 TYR 0.023 0.001 TYR C 397 PHE 0.014 0.001 PHE A 464 HIS 0.009 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00265 (23751) covalent geometry : angle 0.53361 (32124) hydrogen bonds : bond 0.03906 ( 1037) hydrogen bonds : angle 4.47259 ( 2991) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 302 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.7759 (mt0) cc_final: 0.7549 (mt0) REVERT: A 226 MET cc_start: 0.8921 (mmm) cc_final: 0.8643 (mmm) REVERT: A 335 SER cc_start: 0.9239 (m) cc_final: 0.8929 (t) REVERT: A 373 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7873 (ttm-80) REVERT: B 396 GLN cc_start: 0.7947 (mt0) cc_final: 0.7683 (mm-40) REVERT: B 415 GLN cc_start: 0.7424 (mt0) cc_final: 0.6774 (mm-40) REVERT: B 418 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7571 (tt) REVERT: B 475 GLN cc_start: 0.7230 (mp10) cc_final: 0.6773 (mp10) REVERT: B 477 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7152 (tm-30) REVERT: C 45 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7997 (mmm160) REVERT: C 393 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7690 (mt-10) REVERT: E 347 ILE cc_start: 0.9323 (mm) cc_final: 0.8931 (mm) REVERT: E 427 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8201 (t80) REVERT: F 191 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8043 (tp30) REVERT: F 398 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: D 270 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8196 (mt-10) REVERT: D 347 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6597 (mp) REVERT: D 414 GLN cc_start: 0.6447 (OUTLIER) cc_final: 0.5691 (mt0) REVERT: D 462 MET cc_start: 0.8177 (tpt) cc_final: 0.7287 (tpp) REVERT: O 33 GLU cc_start: 0.6019 (mp0) cc_final: 0.4524 (tp30) REVERT: O 113 ARG cc_start: 0.6411 (ptp-170) cc_final: 0.6006 (ptp-110) REVERT: O 163 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8092 (mm) outliers start: 46 outliers final: 30 residues processed: 331 average time/residue: 0.1860 time to fit residues: 94.3118 Evaluate side-chains 322 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 286 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 463 LYS Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain F residue 463 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 124 SER Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 294 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 231 optimal weight: 0.4980 chunk 190 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 270 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 299 optimal weight: 20.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.131582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.100827 restraints weight = 34078.512| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.16 r_work: 0.3152 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23751 Z= 0.131 Angle : 0.548 9.126 32124 Z= 0.274 Chirality : 0.044 0.167 3748 Planarity : 0.004 0.040 4144 Dihedral : 6.036 79.297 3428 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.01 % Allowed : 14.48 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.16), residues: 3027 helix: 1.30 (0.15), residues: 1270 sheet: -0.89 (0.25), residues: 432 loop : -0.50 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 359 TYR 0.024 0.001 TYR C 397 PHE 0.026 0.001 PHE D 460 HIS 0.009 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00302 (23751) covalent geometry : angle 0.54775 (32124) hydrogen bonds : bond 0.03981 ( 1037) hydrogen bonds : angle 4.45622 ( 2991) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 292 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.7762 (mt0) cc_final: 0.7520 (mt0) REVERT: A 226 MET cc_start: 0.8922 (mmm) cc_final: 0.8588 (mmm) REVERT: A 335 SER cc_start: 0.9196 (m) cc_final: 0.8868 (t) REVERT: B 224 ASP cc_start: 0.8743 (t0) cc_final: 0.8501 (t0) REVERT: B 396 GLN cc_start: 0.7891 (mt0) cc_final: 0.7643 (mm-40) REVERT: B 415 GLN cc_start: 0.7445 (mt0) cc_final: 0.6770 (mm-40) REVERT: B 418 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7597 (tt) REVERT: B 475 GLN cc_start: 0.7220 (mp10) cc_final: 0.6749 (mp10) REVERT: B 477 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7078 (tm-30) REVERT: C 45 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7904 (mmm160) REVERT: E 347 ILE cc_start: 0.9336 (mm) cc_final: 0.8947 (mm) REVERT: E 384 TYR cc_start: 0.8227 (t80) cc_final: 0.7836 (t80) REVERT: E 427 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8208 (t80) REVERT: F 191 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8136 (tp30) REVERT: F 398 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: D 263 ARG cc_start: 0.8550 (mmt-90) cc_final: 0.8168 (mpt180) REVERT: D 270 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8153 (mt-10) REVERT: D 347 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6590 (mp) REVERT: D 414 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.5693 (mt0) REVERT: D 445 GLN cc_start: 0.5985 (tm-30) cc_final: 0.5560 (pt0) REVERT: D 462 MET cc_start: 0.8185 (tpt) cc_final: 0.7256 (tpp) REVERT: G 25 MET cc_start: 0.7978 (mmm) cc_final: 0.7409 (ttm) REVERT: O 33 GLU cc_start: 0.6008 (mp0) cc_final: 0.4538 (tp30) REVERT: O 113 ARG cc_start: 0.6411 (ptp-170) cc_final: 0.5980 (ptp-110) REVERT: O 163 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8053 (mm) outliers start: 50 outliers final: 36 residues processed: 326 average time/residue: 0.1758 time to fit residues: 89.1634 Evaluate side-chains 327 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 463 LYS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 124 SER Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 270 optimal weight: 6.9990 chunk 296 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 222 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.130292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099541 restraints weight = 34123.713| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.17 r_work: 0.3133 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23751 Z= 0.163 Angle : 0.571 9.474 32124 Z= 0.286 Chirality : 0.045 0.192 3748 Planarity : 0.004 0.036 4144 Dihedral : 6.095 83.109 3428 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.81 % Allowed : 14.84 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.16), residues: 3027 helix: 1.28 (0.15), residues: 1270 sheet: -0.91 (0.24), residues: 444 loop : -0.50 (0.18), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 373 TYR 0.029 0.001 TYR C 397 PHE 0.025 0.001 PHE D 460 HIS 0.009 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00388 (23751) covalent geometry : angle 0.57135 (32124) hydrogen bonds : bond 0.04201 ( 1037) hydrogen bonds : angle 4.53077 ( 2991) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6054 Ramachandran restraints generated. 3027 Oldfield, 0 Emsley, 3027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 208 GLN cc_start: 0.7804 (mt0) cc_final: 0.7544 (mt0) REVERT: A 226 MET cc_start: 0.8920 (mmm) cc_final: 0.8580 (mmm) REVERT: A 335 SER cc_start: 0.9222 (m) cc_final: 0.8890 (t) REVERT: B 224 ASP cc_start: 0.8809 (t0) cc_final: 0.8578 (t0) REVERT: B 392 LEU cc_start: 0.7773 (tt) cc_final: 0.7523 (mt) REVERT: B 396 GLN cc_start: 0.7868 (mt0) cc_final: 0.7595 (mm-40) REVERT: B 415 GLN cc_start: 0.7445 (mt0) cc_final: 0.6765 (mm-40) REVERT: B 418 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7569 (tt) REVERT: B 475 GLN cc_start: 0.7210 (mp10) cc_final: 0.6728 (mp10) REVERT: B 477 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7062 (tm-30) REVERT: C 45 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.7930 (mmm160) REVERT: C 146 MET cc_start: 0.8646 (tmm) cc_final: 0.8444 (tmm) REVERT: E 347 ILE cc_start: 0.9343 (mm) cc_final: 0.8957 (mm) REVERT: E 384 TYR cc_start: 0.8240 (t80) cc_final: 0.7869 (t80) REVERT: E 427 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8194 (t80) REVERT: F 191 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8174 (tp30) REVERT: F 398 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: D 263 ARG cc_start: 0.8640 (mmt-90) cc_final: 0.8212 (mpt180) REVERT: D 270 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8190 (mt-10) REVERT: D 347 ILE cc_start: 0.6802 (OUTLIER) cc_final: 0.6542 (mp) REVERT: D 414 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.5642 (mt0) REVERT: D 445 GLN cc_start: 0.5914 (tm-30) cc_final: 0.5471 (pt0) REVERT: D 462 MET cc_start: 0.8196 (tpt) cc_final: 0.7251 (tpp) REVERT: G 21 LYS cc_start: 0.7577 (mtmm) cc_final: 0.6997 (mtmm) REVERT: G 25 MET cc_start: 0.8009 (mmm) cc_final: 0.7381 (ttm) REVERT: O 33 GLU cc_start: 0.6010 (mp0) cc_final: 0.4520 (tp30) REVERT: O 113 ARG cc_start: 0.6419 (ptp-170) cc_final: 0.5964 (ptp-110) REVERT: O 163 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8042 (mm) outliers start: 45 outliers final: 34 residues processed: 318 average time/residue: 0.1760 time to fit residues: 86.9487 Evaluate side-chains 322 residues out of total 2487 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 282 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 358 TYR Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 463 LYS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 427 PHE Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 398 GLU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 124 SER Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 275 optimal weight: 0.8980 chunk 128 optimal weight: 0.0470 chunk 167 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 226 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 295 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.132448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101802 restraints weight = 33835.842| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.17 r_work: 0.3166 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23751 Z= 0.117 Angle : 0.544 9.267 32124 Z= 0.272 Chirality : 0.044 0.186 3748 Planarity : 0.003 0.037 4144 Dihedral : 5.867 80.209 3428 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.73 % Allowed : 14.96 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.16), residues: 3027 helix: 1.37 (0.15), residues: 1276 sheet: -0.77 (0.25), residues: 427 loop : -0.43 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 373 TYR 0.026 0.001 TYR C 397 PHE 0.025 0.001 PHE D 460 HIS 0.008 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00268 (23751) covalent geometry : angle 0.54438 (32124) hydrogen bonds : bond 0.03818 ( 1037) hydrogen bonds : angle 4.43548 ( 2991) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6347.77 seconds wall clock time: 109 minutes 27.64 seconds (6567.64 seconds total)