Starting phenix.real_space_refine on Sat Mar 7 03:13:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p3n_13181/03_2026/7p3n_13181.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p3n_13181/03_2026/7p3n_13181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p3n_13181/03_2026/7p3n_13181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p3n_13181/03_2026/7p3n_13181.map" model { file = "/net/cci-nas-00/data/ceres_data/7p3n_13181/03_2026/7p3n_13181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p3n_13181/03_2026/7p3n_13181.cif" } resolution = 4.6 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= 0.007 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 11 5.49 5 Mg 4 5.21 5 S 147 5.16 5 C 23633 2.51 5 N 6307 2.21 5 O 7012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37114 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3875 Classifications: {'peptide': 512} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Chain: "B" Number of atoms: 3892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3892 Classifications: {'peptide': 514} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 495} Chain: "C" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3821 Classifications: {'peptide': 506} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 488} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3533 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 441} Chain: "E" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 440} Chain: "G" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "H" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "J" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "K" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "L" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "O" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "P" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "Q" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "R" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 585 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "S" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 577 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2104 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 15, 'TRANS': 261} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 3, 'HIS:plan': 3, 'PHE:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "b" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1112 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "d" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1347 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1010 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "g" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2243 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain: "p" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1185 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} 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: "E" 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: 8.17, per 1000 atoms: 0.22 Number of scatterers: 37114 At special positions: 0 Unit cell: (135.15, 138.55, 239.7, 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 147 16.00 P 11 15.00 Mg 4 11.99 O 7012 8.00 N 6307 7.00 C 23633 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: 3.59 Conformation dependent library (CDL) restraints added in 1.5 seconds 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8914 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 30 sheets defined 60.4% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 17 through 26 removed outlier: 3.660A pdb=" N THR A 25 " --> pdb=" O ASP A 21 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.705A pdb=" N ASP A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.760A pdb=" N GLN A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Proline residue: A 240 - end of helix removed outlier: 3.727A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 283 through 288 Proline residue: A 288 - end of helix Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.858A pdb=" N TYR A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 removed outlier: 3.610A pdb=" N VAL A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 350 removed outlier: 3.841A pdb=" N SER A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 removed outlier: 3.733A pdb=" N PHE A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 384 through 404 removed outlier: 4.720A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLY A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.953A pdb=" N GLN A 409 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 433 removed outlier: 3.785A pdb=" N LYS A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 454 Processing helix chain 'A' and resid 464 through 480 Processing helix chain 'A' and resid 480 through 491 Processing helix chain 'A' and resid 494 through 511 Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.530A pdb=" N ALA B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASN B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.606A pdb=" N ILE B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 3.657A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 removed outlier: 3.927A pdb=" N GLN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 288 through 289 No H-bonds generated for 'chain 'B' and resid 288 through 289' Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 379 through 383 removed outlier: 3.691A pdb=" N ALA B 382 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 405 removed outlier: 4.110A pdb=" N GLY B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY B 393 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 415 through 430 Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 464 through 480 Processing helix chain 'B' and resid 480 through 491 Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'C' and resid 7 through 18 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 176 through 191 removed outlier: 4.090A pdb=" N ALA C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 232 through 252 removed outlier: 4.094A pdb=" N GLN C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Proline residue: C 240 - end of helix removed outlier: 3.589A pdb=" N TYR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.876A pdb=" N GLN C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.589A pdb=" N ALA C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 289 No H-bonds generated for 'chain 'C' and resid 288 through 289' Processing helix chain 'C' and resid 290 through 301 removed outlier: 4.042A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 334 through 337 Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 363 removed outlier: 3.739A pdb=" N PHE C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.584A pdb=" N ILE C 373 " --> pdb=" O ASN C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 391 Processing helix chain 'C' and resid 393 through 408 Processing helix chain 'C' and resid 415 through 432 Processing helix chain 'C' and resid 441 through 454 removed outlier: 3.957A pdb=" N GLN C 445 " --> pdb=" O SER C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 480 removed outlier: 4.633A pdb=" N ASP C 467 " --> pdb=" O LYS C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 491 Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 129 through 136 Processing helix chain 'D' and resid 153 through 169 Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 211 through 232 removed outlier: 3.544A pdb=" N ARG D 215 " --> pdb=" O PRO D 211 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 263 removed outlier: 3.622A pdb=" N TYR D 252 " --> pdb=" O ASN D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 286 removed outlier: 3.640A pdb=" N ARG D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 310 through 318 removed outlier: 3.641A pdb=" N ALA D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D 318 " --> pdb=" O ALA D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.539A pdb=" N ALA D 331 " --> pdb=" O SER D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 355 through 383 removed outlier: 4.119A pdb=" N ASP D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 387 Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'D' and resid 409 through 416 removed outlier: 3.514A pdb=" N VAL D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 437 removed outlier: 4.124A pdb=" N GLY D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 449 Processing helix chain 'D' and resid 453 through 464 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.583A pdb=" N GLN E 118 " --> pdb=" O TYR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 153 through 169 removed outlier: 3.568A pdb=" N MET E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 195 removed outlier: 3.570A pdb=" N GLY E 185 " --> pdb=" O ARG E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 217 removed outlier: 3.969A pdb=" N ARG E 217 " --> pdb=" O GLY E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 232 removed outlier: 4.167A pdb=" N GLY E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 261 removed outlier: 3.966A pdb=" N TYR E 252 " --> pdb=" O ASN E 248 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 264 No H-bonds generated for 'chain 'E' and resid 262 through 264' Processing helix chain 'E' and resid 275 through 286 removed outlier: 3.534A pdb=" N ARG E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 310 through 318 removed outlier: 3.796A pdb=" N ALA E 318 " --> pdb=" O ALA E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 333 removed outlier: 3.851A pdb=" N ALA E 331 " --> pdb=" O SER E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 355 Processing helix chain 'E' and resid 355 through 382 removed outlier: 4.368A pdb=" N ASP E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 removed outlier: 3.783A pdb=" N LEU E 387 " --> pdb=" O MET E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'E' and resid 411 through 415 Processing helix chain 'E' and resid 424 through 437 Processing helix chain 'E' and resid 444 through 449 Processing helix chain 'E' and resid 453 through 464 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 129 through 136 Processing helix chain 'F' and resid 153 through 169 removed outlier: 3.896A pdb=" N ASN F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 196 removed outlier: 3.836A pdb=" N GLY F 185 " --> pdb=" O ARG F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 201 Processing helix chain 'F' and resid 211 through 232 removed outlier: 4.917A pdb=" N ALA F 219 " --> pdb=" O ARG F 215 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 263 removed outlier: 3.686A pdb=" N TYR F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 263 " --> pdb=" O VAL F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 286 Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.590A pdb=" N ASP F 306 " --> pdb=" O VAL F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 318 removed outlier: 3.805A pdb=" N ALA F 314 " --> pdb=" O ASP F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 333 Processing helix chain 'F' and resid 355 through 383 removed outlier: 4.325A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 405 Processing helix chain 'F' and resid 424 through 438 Processing helix chain 'F' and resid 444 through 449 removed outlier: 3.959A pdb=" N PHE F 448 " --> pdb=" O PRO F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 464 Processing helix chain 'G' and resid 3 through 41 removed outlier: 3.690A pdb=" N ARG G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 60 removed outlier: 3.577A pdb=" N LEU G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 76 Processing helix chain 'H' and resid 2 through 41 removed outlier: 3.840A pdb=" N ARG H 40 " --> pdb=" O GLU H 36 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 60 removed outlier: 3.626A pdb=" N LEU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 76 Processing helix chain 'J' and resid 2 through 41 removed outlier: 3.619A pdb=" N GLY J 28 " --> pdb=" O ALA J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 60 removed outlier: 3.562A pdb=" N ASP J 60 " --> pdb=" O ALA J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 76 Processing helix chain 'K' and resid 3 through 39 removed outlier: 3.579A pdb=" N ALA K 39 " --> pdb=" O LEU K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 43 No H-bonds generated for 'chain 'K' and resid 41 through 43' Processing helix chain 'K' and resid 44 through 60 removed outlier: 3.573A pdb=" N LEU K 48 " --> pdb=" O LEU K 44 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP K 60 " --> pdb=" O ALA K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 76 Processing helix chain 'L' and resid 3 through 41 Processing helix chain 'L' and resid 44 through 58 Processing helix chain 'L' and resid 60 through 77 Processing helix chain 'O' and resid 2 through 41 removed outlier: 3.677A pdb=" N GLY O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 60 Processing helix chain 'O' and resid 60 through 75 Processing helix chain 'P' and resid 2 through 41 removed outlier: 3.850A pdb=" N ARG P 33 " --> pdb=" O LEU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 60 Processing helix chain 'P' and resid 60 through 77 Processing helix chain 'Q' and resid 2 through 41 removed outlier: 3.982A pdb=" N ARG Q 33 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 76 removed outlier: 3.575A pdb=" N GLY Q 57 " --> pdb=" O PHE Q 53 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU Q 58 " --> pdb=" O LEU Q 54 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP Q 60 " --> pdb=" O ALA Q 56 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA Q 61 " --> pdb=" O GLY Q 57 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL Q 62 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Proline residue: Q 63 - end of helix Processing helix chain 'R' and resid 2 through 41 Processing helix chain 'R' and resid 44 through 58 Processing helix chain 'R' and resid 60 through 76 Processing helix chain 'S' and resid 3 through 41 Processing helix chain 'S' and resid 44 through 58 Processing helix chain 'S' and resid 60 through 76 Processing helix chain 'a' and resid 16 through 24 Processing helix chain 'a' and resid 52 through 72 removed outlier: 4.234A pdb=" N SER a 56 " --> pdb=" O SER a 52 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL a 70 " --> pdb=" O LEU a 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 101 removed outlier: 3.765A pdb=" N PHE a 101 " --> pdb=" O VAL a 97 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 125 Processing helix chain 'a' and resid 126 through 128 No H-bonds generated for 'chain 'a' and resid 126 through 128' Processing helix chain 'a' and resid 129 through 130 No H-bonds generated for 'chain 'a' and resid 129 through 130' Processing helix chain 'a' and resid 131 through 144 removed outlier: 4.127A pdb=" N PHE a 139 " --> pdb=" O GLN a 135 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL a 140 " --> pdb=" O VAL a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 147 through 154 removed outlier: 4.351A pdb=" N TYR a 153 " --> pdb=" O PRO a 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 161 through 181 removed outlier: 3.716A pdb=" N THR a 165 " --> pdb=" O ASP a 161 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 191 Processing helix chain 'a' and resid 202 through 210 removed outlier: 3.877A pdb=" N ILE a 210 " --> pdb=" O LYS a 206 " (cutoff:3.500A) Processing helix chain 'a' and resid 210 through 220 removed outlier: 4.236A pdb=" N LEU a 214 " --> pdb=" O ILE a 210 " (cutoff:3.500A) Processing helix chain 'a' and resid 222 through 247 removed outlier: 4.039A pdb=" N ILE a 226 " --> pdb=" O LEU a 222 " (cutoff:3.500A) Processing helix chain 'a' and resid 257 through 289 removed outlier: 4.668A pdb=" N TRP a 261 " --> pdb=" O LEU a 257 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 23 Processing helix chain 'b' and resid 25 through 132 removed outlier: 4.345A pdb=" N LEU b 29 " --> pdb=" O VAL b 25 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE b 33 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER b 34 " --> pdb=" O ILE b 30 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU b 35 " --> pdb=" O ASN b 31 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA b 52 " --> pdb=" O GLU b 48 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP b 53 " --> pdb=" O LYS b 49 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU b 54 " --> pdb=" O ALA b 50 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN b 58 " --> pdb=" O LEU b 54 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA b 59 " --> pdb=" O ALA b 55 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN b 60 " --> pdb=" O ASP b 56 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA b 67 " --> pdb=" O GLN b 63 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA b 68 " --> pdb=" O GLU b 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS b 69 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU b 112 " --> pdb=" O ALA b 108 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 134 through 139 Processing helix chain 'd' and resid 4 through 23 Proline residue: d 10 - end of helix Processing helix chain 'd' and resid 24 through 41 Processing helix chain 'd' and resid 41 through 49 Processing helix chain 'd' and resid 54 through 67 Processing helix chain 'd' and resid 71 through 84 Processing helix chain 'd' and resid 89 through 105 Processing helix chain 'd' and resid 119 through 132 Processing helix chain 'd' and resid 165 through 176 removed outlier: 4.124A pdb=" N LEU d 169 " --> pdb=" O ALA d 165 " (cutoff:3.500A) Processing helix chain 'e' and resid 91 through 125 removed outlier: 4.285A pdb=" N ALA e 97 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA e 119 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA e 125 " --> pdb=" O LEU e 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 135 removed outlier: 3.815A pdb=" N ILE e 134 " --> pdb=" O THR e 130 " (cutoff:3.500A) Processing helix chain 'g' and resid 3 through 42 removed outlier: 4.507A pdb=" N ILE g 7 " --> pdb=" O ASN g 3 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA g 40 " --> pdb=" O GLN g 36 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN g 41 " --> pdb=" O GLU g 37 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY g 42 " --> pdb=" O ARG g 38 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 60 removed outlier: 3.857A pdb=" N ALA g 46 " --> pdb=" O GLY g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 108 removed outlier: 3.567A pdb=" N GLU g 108 " --> pdb=" O LYS g 104 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 130 Processing helix chain 'g' and resid 145 through 162 removed outlier: 3.735A pdb=" N LEU g 149 " --> pdb=" O SER g 145 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER g 152 " --> pdb=" O GLN g 148 " (cutoff:3.500A) Processing helix chain 'g' and resid 213 through 287 Processing helix chain 'p' and resid 3 through 139 Proline residue: p 27 - end of helix removed outlier: 4.320A pdb=" N ARG p 121 " --> pdb=" O ARG p 117 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN p 123 " --> pdb=" O GLU p 119 " (cutoff:3.500A) Processing helix chain 'p' and resid 141 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 36 removed outlier: 6.017A pdb=" N ILE A 32 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS A 43 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N MET A 53 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 92 " --> pdb=" O MET A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 4.301A pdb=" N LEU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.483A pdb=" N ARG A 107 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ALA A 226 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ALA A 228 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 223 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 193 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 260 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 197 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 removed outlier: 4.340A pdb=" N VAL A 160 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 330 through 332 removed outlier: 3.574A pdb=" N ILE A 331 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 167 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 36 removed outlier: 5.644A pdb=" N ILE B 32 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS B 43 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU B 67 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 89 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 100 removed outlier: 3.752A pdb=" N LEU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.633A pdb=" N ARG B 107 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ALA B 226 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL B 109 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS B 194 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA B 257 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N LEU B 328 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE B 259 " --> pdb=" O LEU B 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 removed outlier: 4.546A pdb=" N VAL B 160 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 332 removed outlier: 8.009A pdb=" N ILE B 331 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE B 168 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 28 removed outlier: 4.299A pdb=" N THR C 25 " --> pdb=" O ASP d 162 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP d 162 " --> pdb=" O THR C 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 31 through 36 removed outlier: 5.324A pdb=" N ILE C 32 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N HIS C 43 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 64 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N GLU C 52 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG C 94 " --> pdb=" O MET C 53 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU C 55 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR C 92 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.037A pdb=" N LEU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.934A pdb=" N VAL C 109 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ALA C 228 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR C 223 " --> pdb=" O CYS C 194 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 330 through 332 removed outlier: 5.778A pdb=" N ILE C 168 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU C 167 " --> pdb=" O ILE C 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.610A pdb=" N ILE D 6 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL D 16 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL D 49 " --> pdb=" O GLN D 44 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN D 44 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG D 51 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 53 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR D 38 " --> pdb=" O MET D 55 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASP D 28 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALA D 72 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N GLN D 31 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N THR D 70 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AB9, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.839A pdb=" N TYR D 205 " --> pdb=" O MET D 87 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N SER D 173 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N VAL D 204 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE D 175 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLY D 206 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLY D 177 " --> pdb=" O GLY D 206 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU D 172 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N PHE D 245 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL D 174 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL D 242 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE D 298 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU D 244 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ALA D 300 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 246 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL D 144 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 322 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 124 through 125 removed outlier: 3.585A pdb=" N PHE D 138 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 10 removed outlier: 6.283A pdb=" N ILE E 6 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU E 17 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN E 8 " --> pdb=" O ASP E 15 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP E 15 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE E 10 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN E 43 " --> pdb=" O ARG E 51 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE E 53 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL E 41 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N MET E 55 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU E 39 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 77 Processing sheet with id=AC4, first strand: chain 'E' and resid 86 through 87 removed outlier: 5.715A pdb=" N GLY E 177 " --> pdb=" O GLY E 206 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 241 through 246 removed outlier: 6.245A pdb=" N VAL E 144 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL E 301 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU E 146 " --> pdb=" O VAL E 301 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 10 removed outlier: 6.134A pdb=" N ILE F 6 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLU F 17 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG F 51 " --> pdb=" O GLN F 42 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE F 53 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR F 38 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL F 41 " --> pdb=" O ASP F 28 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASP F 28 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ALA F 72 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N GLN F 31 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR F 70 " --> pdb=" O GLN F 31 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 75 through 77 Processing sheet with id=AC8, first strand: chain 'F' and resid 124 through 125 Processing sheet with id=AC9, first strand: chain 'F' and resid 173 through 176 removed outlier: 5.875A pdb=" N VAL F 242 " --> pdb=" O THR F 296 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE F 298 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU F 244 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA F 300 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL F 246 " --> pdb=" O ALA F 300 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL F 144 " --> pdb=" O GLN F 299 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL F 301 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU F 146 " --> pdb=" O VAL F 301 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS F 143 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL F 324 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY F 145 " --> pdb=" O VAL F 324 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'e' and resid 14 through 20 removed outlier: 4.553A pdb=" N SER e 14 " --> pdb=" O SER e 10 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N SER e 10 " --> pdb=" O SER e 14 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLY e 66 " --> pdb=" O ASP e 81 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ALA e 83 " --> pdb=" O VAL e 64 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL e 64 " --> pdb=" O ALA e 83 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS e 26 " --> pdb=" O PRO e 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'e' and resid 14 through 20 removed outlier: 4.553A pdb=" N SER e 14 " --> pdb=" O SER e 10 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N SER e 10 " --> pdb=" O SER e 14 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLY e 66 " --> pdb=" O ASP e 81 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ALA e 83 " --> pdb=" O VAL e 64 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL e 64 " --> pdb=" O ALA e 83 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY e 67 " --> pdb=" O LEU e 45 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'g' and resid 132 through 137 removed outlier: 5.760A pdb=" N VAL g 133 " --> pdb=" O VAL g 113 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N PHE g 115 " --> pdb=" O VAL g 133 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY g 135 " --> pdb=" O PHE g 115 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG g 75 " --> pdb=" O LEU g 165 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG g 167 " --> pdb=" O ARG g 75 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASN g 173 " --> pdb=" O VAL g 81 " (cutoff:3.500A) 2335 hydrogen bonds defined for protein. 6801 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: 8.04 Time building geometry restraints manager: 4.65 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: 11040 1.33 - 1.45: 5110 1.45 - 1.57: 21254 1.57 - 1.69: 19 1.69 - 1.81: 277 Bond restraints: 37700 Sorted by residual: bond pdb=" C1' ADP E 601 " pdb=" N9 ADP E 601 " ideal model delta sigma weight residual 1.485 1.339 0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 1.592 1.663 -0.071 1.10e-02 8.26e+03 4.19e+01 bond pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 1.592 1.663 -0.071 1.10e-02 8.26e+03 4.19e+01 bond pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 1.592 1.663 -0.071 1.10e-02 8.26e+03 4.15e+01 bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.336 0.051 1.00e-02 1.00e+04 2.65e+01 ... (remaining 37695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 50632 3.44 - 6.88: 432 6.88 - 10.32: 38 10.32 - 13.75: 8 13.75 - 17.19: 1 Bond angle restraints: 51111 Sorted by residual: angle pdb=" N ALA b 57 " pdb=" CA ALA b 57 " pdb=" C ALA b 57 " ideal model delta sigma weight residual 111.07 122.09 -11.02 1.07e+00 8.73e-01 1.06e+02 angle pdb=" N LYS b 51 " pdb=" CA LYS b 51 " pdb=" C LYS b 51 " ideal model delta sigma weight residual 111.07 120.88 -9.81 1.07e+00 8.73e-01 8.41e+01 angle pdb=" C ALA b 57 " pdb=" N GLN b 58 " pdb=" CA GLN b 58 " ideal model delta sigma weight residual 120.38 131.05 -10.67 1.37e+00 5.33e-01 6.06e+01 angle pdb=" C5 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 126.80 119.29 7.51 1.00e+00 1.00e+00 5.64e+01 angle pdb=" C5 ATP C 601 " pdb=" C4 ATP C 601 " pdb=" N3 ATP C 601 " ideal model delta sigma weight residual 126.80 119.33 7.47 1.00e+00 1.00e+00 5.58e+01 ... (remaining 51106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.20: 21882 25.20 - 50.41: 788 50.41 - 75.61: 110 75.61 - 100.82: 36 100.82 - 126.02: 1 Dihedral angle restraints: 22817 sinusoidal: 8898 harmonic: 13919 Sorted by residual: dihedral pdb=" C THR B 513 " pdb=" N THR B 513 " pdb=" CA THR B 513 " pdb=" CB THR B 513 " ideal model delta harmonic sigma weight residual -122.00 -139.85 17.85 0 2.50e+00 1.60e-01 5.10e+01 dihedral pdb=" O2A ADP E 601 " pdb=" O3A ADP E 601 " pdb=" PA ADP E 601 " pdb=" PB ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 66.03 -126.02 1 2.00e+01 2.50e-03 3.81e+01 dihedral pdb=" CA MET B 49 " pdb=" C MET B 49 " pdb=" N TYR B 50 " pdb=" CA TYR B 50 " ideal model delta harmonic sigma weight residual 180.00 150.66 29.34 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 22814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 5954 0.138 - 0.275: 32 0.275 - 0.413: 1 0.413 - 0.551: 0 0.551 - 0.688: 1 Chirality restraints: 5988 Sorted by residual: chirality pdb=" CA THR B 513 " pdb=" N THR B 513 " pdb=" C THR B 513 " pdb=" CB THR B 513 " both_signs ideal model delta sigma weight residual False 2.53 1.84 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CA ILE b 40 " pdb=" N ILE b 40 " pdb=" C ILE b 40 " pdb=" CB ILE b 40 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C1' ADP E 601 " pdb=" C2' ADP E 601 " pdb=" N9 ADP E 601 " pdb=" O4' ADP E 601 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 5985 not shown) Planarity restraints: 6628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 18 " 0.036 2.00e-02 2.50e+03 2.63e-02 1.21e+01 pdb=" CG PHE J 18 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE J 18 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE J 18 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE J 18 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE J 18 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE J 18 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 18 " 0.024 2.00e-02 2.50e+03 2.49e-02 1.08e+01 pdb=" CG PHE H 18 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE H 18 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE H 18 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE H 18 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE H 18 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE H 18 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 18 " 0.035 2.00e-02 2.50e+03 2.48e-02 1.08e+01 pdb=" CG PHE Q 18 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 18 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 18 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 18 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 18 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE Q 18 " 0.018 2.00e-02 2.50e+03 ... (remaining 6625 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 285 2.40 - 3.03: 26830 3.03 - 3.65: 63797 3.65 - 4.28: 90249 4.28 - 4.90: 139166 Nonbonded interactions: 320327 Sorted by model distance: nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 1.777 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.958 2.170 nonbonded pdb=" O PRO E 267 " pdb=" O SER E 268 " model vdw 2.061 3.040 nonbonded pdb=" OD1 ASP E 88 " pdb=" N VAL E 89 " model vdw 2.129 3.120 nonbonded pdb=" OD1 ASP D 88 " pdb=" N VAL D 89 " model vdw 2.172 3.120 ... (remaining 320322 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 6 through 511 or resid 601 through 602)) selection = (chain 'B' and (resid 6 through 511 or resid 601 through 602)) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 2 through 464) selection = (chain 'E' and resid 2 through 464) selection = chain 'F' } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 2 through 80) selection = (chain 'J' and resid 2 through 80) selection = chain 'K' selection = chain 'L' selection = (chain 'O' and resid 2 through 80) selection = (chain 'P' and resid 2 through 80) selection = (chain 'Q' and resid 2 through 80) selection = (chain 'R' and resid 2 through 80) selection = chain 'S' } ncs_group { reference = chain 'b' selection = (chain 'p' and resid 12 through 156) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.960 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: 0.050 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 33.780 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 : 0.005 0.146 37700 Z= 0.285 Angle : 0.851 17.193 51111 Z= 0.499 Chirality : 0.046 0.688 5988 Planarity : 0.005 0.050 6628 Dihedral : 13.803 126.024 13903 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 31.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.44 % Favored : 92.43 % Rotamer: Outliers : 0.21 % Allowed : 0.84 % Favored : 98.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.12), residues: 4851 helix: 0.11 (0.10), residues: 2567 sheet: -1.12 (0.21), residues: 551 loop : -1.91 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 279 TYR 0.024 0.002 TYR a 283 PHE 0.058 0.002 PHE J 18 TRP 0.031 0.002 TRP a 118 HIS 0.011 0.002 HIS a 151 Details of bonding type rmsd covalent geometry : bond 0.00518 (37700) covalent geometry : angle 0.85055 (51111) hydrogen bonds : bond 0.16291 ( 2319) hydrogen bonds : angle 6.93895 ( 6801) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 354 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9125 (mmm) cc_final: 0.8696 (mmm) REVERT: A 171 ASP cc_start: 0.9325 (p0) cc_final: 0.9103 (m-30) REVERT: A 179 MET cc_start: 0.9458 (mtp) cc_final: 0.9210 (mmm) REVERT: A 295 HIS cc_start: 0.9377 (m90) cc_final: 0.9047 (m90) REVERT: A 328 LEU cc_start: 0.9670 (mt) cc_final: 0.9427 (mt) REVERT: B 1 MET cc_start: 0.9209 (ppp) cc_final: 0.8936 (tpp) REVERT: B 53 MET cc_start: 0.8880 (mtm) cc_final: 0.8231 (mtm) REVERT: B 235 MET cc_start: 0.9650 (mmp) cc_final: 0.9383 (mmm) REVERT: B 238 LEU cc_start: 0.9817 (mt) cc_final: 0.9504 (pp) REVERT: B 246 MET cc_start: 0.9646 (mmp) cc_final: 0.9308 (mmm) REVERT: C 49 MET cc_start: 0.6567 (tpt) cc_final: 0.5808 (tpt) REVERT: C 63 MET cc_start: 0.9495 (tmm) cc_final: 0.9197 (tmm) REVERT: C 235 MET cc_start: 0.9438 (mpp) cc_final: 0.8898 (mpp) REVERT: C 237 TYR cc_start: 0.9708 (t80) cc_final: 0.9498 (t80) REVERT: C 484 MET cc_start: 0.9615 (mpp) cc_final: 0.9351 (mpp) REVERT: D 55 MET cc_start: 0.8857 (mmp) cc_final: 0.8345 (mmp) REVERT: D 159 MET cc_start: 0.9803 (mmp) cc_final: 0.9371 (mmm) REVERT: D 192 MET cc_start: 0.9775 (ptp) cc_final: 0.9420 (mtm) REVERT: D 225 MET cc_start: 0.9794 (mmp) cc_final: 0.9535 (mmm) REVERT: D 258 GLU cc_start: 0.9534 (mt-10) cc_final: 0.9319 (mt-10) REVERT: D 280 MET cc_start: 0.9649 (mmp) cc_final: 0.9228 (mmm) REVERT: D 450 MET cc_start: 0.9538 (mmp) cc_final: 0.9209 (mmm) REVERT: E 55 MET cc_start: 0.9569 (mpp) cc_final: 0.9348 (mpp) REVERT: E 192 MET cc_start: 0.9832 (mmm) cc_final: 0.9554 (tpp) REVERT: E 225 MET cc_start: 0.9860 (mmp) cc_final: 0.9537 (mmm) REVERT: E 319 HIS cc_start: 0.8715 (m90) cc_final: 0.8422 (m-70) REVERT: F 159 MET cc_start: 0.9784 (mtm) cc_final: 0.9527 (tpt) REVERT: F 203 MET cc_start: 0.8793 (tpt) cc_final: 0.8576 (tpt) REVERT: F 280 MET cc_start: 0.9693 (tpt) cc_final: 0.9343 (tpp) REVERT: F 285 GLU cc_start: 0.9314 (mm-30) cc_final: 0.7924 (tp30) REVERT: F 450 MET cc_start: 0.9012 (mmp) cc_final: 0.8810 (mmt) REVERT: G 34 PHE cc_start: 0.9531 (t80) cc_final: 0.9250 (t80) REVERT: J 60 ASP cc_start: 0.9163 (p0) cc_final: 0.8374 (t0) REVERT: J 64 MET cc_start: 0.9354 (mmp) cc_final: 0.8957 (mmp) REVERT: K 71 LEU cc_start: 0.9377 (mm) cc_final: 0.9174 (mm) REVERT: L 18 PHE cc_start: 0.8250 (t80) cc_final: 0.8044 (t80) REVERT: L 27 PHE cc_start: 0.9131 (m-10) cc_final: 0.8772 (m-10) REVERT: a 26 MET cc_start: 0.7242 (mpp) cc_final: 0.6003 (mpp) REVERT: a 125 MET cc_start: 0.8723 (ptt) cc_final: 0.8335 (ppp) REVERT: a 277 MET cc_start: 0.9345 (tmm) cc_final: 0.9109 (tmm) REVERT: b 148 MET cc_start: 0.8692 (pmm) cc_final: 0.8438 (pmm) REVERT: e 98 ARG cc_start: 0.8484 (ttm110) cc_final: 0.8177 (ttt180) REVERT: g 32 MET cc_start: 0.9337 (ttt) cc_final: 0.8754 (ttp) REVERT: g 39 MET cc_start: 0.9564 (mmp) cc_final: 0.9325 (mmm) REVERT: g 156 MET cc_start: 0.9619 (tpt) cc_final: 0.9007 (tpp) REVERT: g 229 MET cc_start: 0.8962 (mtm) cc_final: 0.8595 (mtp) REVERT: g 246 MET cc_start: 0.9198 (mtm) cc_final: 0.8831 (mtt) REVERT: p 110 ASP cc_start: 0.9450 (t0) cc_final: 0.9167 (p0) outliers start: 8 outliers final: 2 residues processed: 361 average time/residue: 0.2311 time to fit residues: 134.8617 Evaluate side-chains 257 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 255 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0470 chunk 470 optimal weight: 6.9990 overall best weight: 2.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN A 362 ASN B 2 GLN B 79 ASN B 84 GLN C 164 GLN C 203 GLN D 118 GLN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN E 118 GLN E 169 HIS ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN G 41 GLN J 41 GLN a 213 ASN ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 85 GLN b 137 ASN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 146 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.048240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.038904 restraints weight = 436334.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.040002 restraints weight = 229851.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.040739 restraints weight = 143405.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.041256 restraints weight = 99942.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.041579 restraints weight = 75345.238| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 37700 Z= 0.152 Angle : 0.651 8.563 51111 Z= 0.340 Chirality : 0.043 0.172 5988 Planarity : 0.005 0.053 6628 Dihedral : 6.951 133.962 5364 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.05 % Favored : 94.93 % Rotamer: Outliers : 0.23 % Allowed : 4.46 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.12), residues: 4851 helix: 0.72 (0.10), residues: 2671 sheet: -0.88 (0.22), residues: 514 loop : -1.64 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG g 167 TYR 0.022 0.002 TYR E 228 PHE 0.038 0.002 PHE J 18 TRP 0.024 0.002 TRP a 118 HIS 0.006 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00309 (37700) covalent geometry : angle 0.65059 (51111) hydrogen bonds : bond 0.04866 ( 2319) hydrogen bonds : angle 5.37597 ( 6801) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 343 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9404 (mmm) cc_final: 0.8999 (tpp) REVERT: A 171 ASP cc_start: 0.9474 (p0) cc_final: 0.9135 (m-30) REVERT: A 295 HIS cc_start: 0.9508 (m90) cc_final: 0.9199 (m90) REVERT: B 53 MET cc_start: 0.8827 (mtm) cc_final: 0.8380 (mtm) REVERT: B 235 MET cc_start: 0.9695 (mmp) cc_final: 0.9229 (mmm) REVERT: B 238 LEU cc_start: 0.9812 (mt) cc_final: 0.9472 (pp) REVERT: B 246 MET cc_start: 0.9615 (mmp) cc_final: 0.9414 (mmm) REVERT: B 299 LEU cc_start: 0.9656 (mt) cc_final: 0.9434 (pp) REVERT: B 484 MET cc_start: 0.8700 (ptp) cc_final: 0.8461 (ptp) REVERT: C 49 MET cc_start: 0.6952 (tpt) cc_final: 0.5549 (tpt) REVERT: C 63 MET cc_start: 0.9695 (tmm) cc_final: 0.9389 (tmm) REVERT: C 235 MET cc_start: 0.9336 (mpp) cc_final: 0.8826 (mpp) REVERT: C 237 TYR cc_start: 0.9673 (t80) cc_final: 0.9459 (t80) REVERT: C 356 LEU cc_start: 0.9295 (mm) cc_final: 0.9061 (mt) REVERT: C 432 MET cc_start: 0.9705 (mmp) cc_final: 0.9484 (mmp) REVERT: C 457 MET cc_start: 0.8971 (mmp) cc_final: 0.8765 (mmm) REVERT: C 484 MET cc_start: 0.9657 (mpp) cc_final: 0.9361 (mpp) REVERT: D 9 ILE cc_start: 0.9751 (pt) cc_final: 0.9396 (mp) REVERT: D 159 MET cc_start: 0.9772 (mmp) cc_final: 0.9516 (mmm) REVERT: D 192 MET cc_start: 0.9728 (ptp) cc_final: 0.9449 (ptt) REVERT: D 225 MET cc_start: 0.9769 (mmp) cc_final: 0.9389 (mmm) REVERT: D 280 MET cc_start: 0.9631 (mmp) cc_final: 0.9135 (mmm) REVERT: D 450 MET cc_start: 0.9549 (mmp) cc_final: 0.9156 (mmp) REVERT: E 158 MET cc_start: 0.9635 (tpt) cc_final: 0.9311 (tpp) REVERT: E 159 MET cc_start: 0.9724 (mmp) cc_final: 0.9412 (mmm) REVERT: E 192 MET cc_start: 0.9831 (mmm) cc_final: 0.9564 (tpp) REVERT: E 225 MET cc_start: 0.9867 (mmp) cc_final: 0.9574 (mmm) REVERT: E 262 LEU cc_start: 0.9515 (mp) cc_final: 0.9289 (pp) REVERT: E 319 HIS cc_start: 0.8777 (m90) cc_final: 0.8352 (m90) REVERT: E 366 GLN cc_start: 0.9742 (mp10) cc_final: 0.8981 (tm-30) REVERT: F 159 MET cc_start: 0.9736 (mtm) cc_final: 0.9495 (tpt) REVERT: F 280 MET cc_start: 0.9682 (tpt) cc_final: 0.9254 (tpp) REVERT: F 285 GLU cc_start: 0.9270 (mm-30) cc_final: 0.7913 (tp30) REVERT: F 415 PHE cc_start: 0.8822 (t80) cc_final: 0.7946 (m-80) REVERT: G 34 PHE cc_start: 0.9458 (t80) cc_final: 0.9108 (t80) REVERT: H 10 ILE cc_start: 0.8892 (mm) cc_final: 0.8650 (pt) REVERT: H 55 ILE cc_start: 0.9061 (mm) cc_final: 0.8644 (mm) REVERT: J 53 PHE cc_start: 0.9656 (m-80) cc_final: 0.9409 (m-80) REVERT: J 60 ASP cc_start: 0.9139 (p0) cc_final: 0.8404 (t0) REVERT: J 64 MET cc_start: 0.9306 (mmp) cc_final: 0.8941 (mmp) REVERT: L 27 PHE cc_start: 0.9100 (m-10) cc_final: 0.8711 (m-10) REVERT: S 64 MET cc_start: 0.9267 (mmp) cc_final: 0.9055 (mmm) REVERT: a 26 MET cc_start: 0.6384 (mpp) cc_final: 0.5424 (mpp) REVERT: a 118 TRP cc_start: 0.9074 (t60) cc_final: 0.8865 (t60) REVERT: a 125 MET cc_start: 0.8681 (ptt) cc_final: 0.8054 (ppp) REVERT: b 106 LYS cc_start: 0.8737 (tttt) cc_final: 0.8415 (tptm) REVERT: b 148 MET cc_start: 0.8565 (pmm) cc_final: 0.8298 (pmm) REVERT: g 24 MET cc_start: 0.9521 (mmt) cc_final: 0.9233 (mtt) REVERT: g 32 MET cc_start: 0.9336 (ttt) cc_final: 0.8722 (ttp) REVERT: g 39 MET cc_start: 0.9509 (mmp) cc_final: 0.9253 (mmm) REVERT: g 156 MET cc_start: 0.9642 (tpt) cc_final: 0.8819 (tpp) REVERT: g 229 MET cc_start: 0.8844 (mtm) cc_final: 0.8434 (mtp) REVERT: p 110 ASP cc_start: 0.9467 (t0) cc_final: 0.9074 (p0) outliers start: 9 outliers final: 1 residues processed: 350 average time/residue: 0.2235 time to fit residues: 127.9572 Evaluate side-chains 268 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 426 optimal weight: 9.9990 chunk 455 optimal weight: 0.0170 chunk 261 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 343 optimal weight: 10.0000 chunk 297 optimal weight: 6.9990 chunk 430 optimal weight: 5.9990 chunk 474 optimal weight: 5.9990 chunk 356 optimal weight: 9.9990 overall best weight: 3.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN A 362 ASN B 79 ASN C 173 GLN D 157 ASN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 GLN E 111 GLN E 358 HIS ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 265 HIS ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 GLN b 137 ASN ** b 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.047250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.037898 restraints weight = 443991.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.038992 restraints weight = 234843.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.039705 restraints weight = 147836.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.040213 restraints weight = 103852.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.040543 restraints weight = 78400.701| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37700 Z= 0.172 Angle : 0.630 8.119 51111 Z= 0.330 Chirality : 0.042 0.315 5988 Planarity : 0.005 0.064 6628 Dihedral : 6.681 119.983 5364 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.28 % Favored : 94.70 % Rotamer: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 4851 helix: 0.96 (0.10), residues: 2663 sheet: -0.95 (0.22), residues: 524 loop : -1.47 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 215 TYR 0.017 0.002 TYR C 475 PHE 0.040 0.002 PHE J 18 TRP 0.018 0.001 TRP a 118 HIS 0.006 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00349 (37700) covalent geometry : angle 0.62997 (51111) hydrogen bonds : bond 0.04569 ( 2319) hydrogen bonds : angle 5.19883 ( 6801) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9399 (mmm) cc_final: 0.9020 (tpp) REVERT: A 171 ASP cc_start: 0.9513 (p0) cc_final: 0.9215 (m-30) REVERT: A 295 HIS cc_start: 0.9469 (m90) cc_final: 0.9171 (m90) REVERT: B 53 MET cc_start: 0.8717 (mtm) cc_final: 0.8295 (mtm) REVERT: B 182 ASP cc_start: 0.9611 (t0) cc_final: 0.9370 (m-30) REVERT: B 235 MET cc_start: 0.9703 (mmp) cc_final: 0.9269 (mmm) REVERT: B 238 LEU cc_start: 0.9827 (mt) cc_final: 0.9501 (pp) REVERT: B 298 LEU cc_start: 0.9627 (tp) cc_final: 0.9387 (tp) REVERT: B 299 LEU cc_start: 0.9675 (mt) cc_final: 0.9453 (pp) REVERT: B 370 ASN cc_start: 0.9476 (t0) cc_final: 0.8820 (m-40) REVERT: C 49 MET cc_start: 0.7346 (tpt) cc_final: 0.5739 (tpt) REVERT: C 63 MET cc_start: 0.9692 (tmm) cc_final: 0.9400 (tmm) REVERT: C 182 ASP cc_start: 0.8779 (t0) cc_final: 0.8425 (t0) REVERT: C 235 MET cc_start: 0.9334 (mpp) cc_final: 0.8812 (mpp) REVERT: C 356 LEU cc_start: 0.9343 (mm) cc_final: 0.9139 (mt) REVERT: C 457 MET cc_start: 0.8956 (mmp) cc_final: 0.8751 (mmm) REVERT: C 484 MET cc_start: 0.9665 (mpp) cc_final: 0.9329 (mpp) REVERT: D 9 ILE cc_start: 0.9780 (pt) cc_final: 0.9444 (mp) REVERT: D 159 MET cc_start: 0.9803 (mmp) cc_final: 0.9484 (mmm) REVERT: D 192 MET cc_start: 0.9691 (ptp) cc_final: 0.9441 (ptt) REVERT: D 225 MET cc_start: 0.9760 (mmp) cc_final: 0.9460 (mmm) REVERT: D 280 MET cc_start: 0.9655 (mmp) cc_final: 0.9059 (mmm) REVERT: D 450 MET cc_start: 0.9523 (mmp) cc_final: 0.9167 (mmp) REVERT: E 158 MET cc_start: 0.9612 (tpt) cc_final: 0.9173 (tpp) REVERT: E 159 MET cc_start: 0.9713 (mmp) cc_final: 0.9332 (mmm) REVERT: E 192 MET cc_start: 0.9815 (mmm) cc_final: 0.9521 (tpp) REVERT: E 225 MET cc_start: 0.9836 (mmp) cc_final: 0.9565 (mmm) REVERT: E 262 LEU cc_start: 0.9554 (mp) cc_final: 0.9352 (pp) REVERT: E 319 HIS cc_start: 0.8724 (m90) cc_final: 0.8348 (m90) REVERT: E 372 TYR cc_start: 0.8899 (t80) cc_final: 0.8696 (t80) REVERT: F 159 MET cc_start: 0.9747 (mtm) cc_final: 0.9487 (tpt) REVERT: F 285 GLU cc_start: 0.9328 (mm-30) cc_final: 0.7981 (tp30) REVERT: F 415 PHE cc_start: 0.8834 (t80) cc_final: 0.7940 (m-80) REVERT: G 34 PHE cc_start: 0.9419 (t80) cc_final: 0.9085 (t80) REVERT: H 10 ILE cc_start: 0.8869 (mm) cc_final: 0.8626 (pt) REVERT: H 55 ILE cc_start: 0.9059 (mm) cc_final: 0.8828 (mm) REVERT: J 53 PHE cc_start: 0.9527 (m-80) cc_final: 0.9217 (m-80) REVERT: J 60 ASP cc_start: 0.9277 (p0) cc_final: 0.8575 (t0) REVERT: J 64 MET cc_start: 0.9310 (mmp) cc_final: 0.9095 (mmp) REVERT: K 53 PHE cc_start: 0.9275 (m-80) cc_final: 0.8966 (m-80) REVERT: L 27 PHE cc_start: 0.9073 (m-10) cc_final: 0.8686 (m-10) REVERT: Q 71 LEU cc_start: 0.9451 (mm) cc_final: 0.9151 (pp) REVERT: R 52 MET cc_start: 0.9039 (ppp) cc_final: 0.8831 (ppp) REVERT: S 64 MET cc_start: 0.9279 (mmp) cc_final: 0.9063 (mmm) REVERT: a 26 MET cc_start: 0.6651 (mpp) cc_final: 0.5588 (mpp) REVERT: a 125 MET cc_start: 0.8753 (ptt) cc_final: 0.8168 (ppp) REVERT: a 236 MET cc_start: 0.8869 (ttp) cc_final: 0.8634 (ttp) REVERT: a 278 MET cc_start: 0.9863 (mmp) cc_final: 0.9662 (mmm) REVERT: b 106 LYS cc_start: 0.8668 (tttt) cc_final: 0.8337 (tptm) REVERT: b 148 MET cc_start: 0.8574 (pmm) cc_final: 0.8310 (pmm) REVERT: g 32 MET cc_start: 0.9323 (ttt) cc_final: 0.8766 (ttp) REVERT: g 39 MET cc_start: 0.9542 (mmp) cc_final: 0.9326 (mmm) REVERT: g 156 MET cc_start: 0.9531 (tpp) cc_final: 0.8893 (tpp) REVERT: g 229 MET cc_start: 0.8874 (mtm) cc_final: 0.8432 (mtp) REVERT: p 110 ASP cc_start: 0.9442 (t0) cc_final: 0.9048 (p0) outliers start: 1 outliers final: 1 residues processed: 337 average time/residue: 0.2188 time to fit residues: 122.4089 Evaluate side-chains 274 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 254 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 412 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 410 optimal weight: 0.9990 chunk 405 optimal weight: 2.9990 chunk 290 optimal weight: 50.0000 chunk 392 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN B 79 ASN C 201 GLN C 362 ASN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 HIS E 111 GLN E 207 GLN E 358 HIS ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.046993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.038122 restraints weight = 441892.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.039111 restraints weight = 220391.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.039782 restraints weight = 124206.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.040119 restraints weight = 87304.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.040186 restraints weight = 75536.507| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37700 Z= 0.169 Angle : 0.619 8.277 51111 Z= 0.324 Chirality : 0.042 0.205 5988 Planarity : 0.004 0.060 6628 Dihedral : 6.495 126.499 5364 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.42 % Favored : 94.56 % Rotamer: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 4851 helix: 1.09 (0.10), residues: 2660 sheet: -0.95 (0.22), residues: 530 loop : -1.33 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 371 TYR 0.029 0.002 TYR a 283 PHE 0.046 0.002 PHE L 18 TRP 0.013 0.001 TRP a 118 HIS 0.006 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00343 (37700) covalent geometry : angle 0.61890 (51111) hydrogen bonds : bond 0.04260 ( 2319) hydrogen bonds : angle 5.02592 ( 6801) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 336 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9405 (mmm) cc_final: 0.8905 (tpp) REVERT: A 263 ASP cc_start: 0.8960 (m-30) cc_final: 0.8748 (m-30) REVERT: A 295 HIS cc_start: 0.9475 (m90) cc_final: 0.9115 (m90) REVERT: B 1 MET cc_start: 0.9188 (ppp) cc_final: 0.8889 (tpp) REVERT: B 53 MET cc_start: 0.8701 (mtm) cc_final: 0.8301 (mtm) REVERT: B 157 MET cc_start: 0.9426 (mmt) cc_final: 0.8997 (mmp) REVERT: B 182 ASP cc_start: 0.9608 (t0) cc_final: 0.9349 (m-30) REVERT: B 235 MET cc_start: 0.9707 (mmp) cc_final: 0.9297 (mmm) REVERT: B 238 LEU cc_start: 0.9833 (mt) cc_final: 0.9499 (pp) REVERT: B 246 MET cc_start: 0.9610 (mmp) cc_final: 0.9381 (mmm) REVERT: C 49 MET cc_start: 0.7612 (tpt) cc_final: 0.5954 (tpt) REVERT: C 63 MET cc_start: 0.9619 (tmm) cc_final: 0.9343 (tmm) REVERT: C 235 MET cc_start: 0.9335 (mpp) cc_final: 0.8825 (mpp) REVERT: C 457 MET cc_start: 0.8960 (mmp) cc_final: 0.8744 (mmm) REVERT: C 484 MET cc_start: 0.9683 (mpp) cc_final: 0.9449 (mpp) REVERT: D 9 ILE cc_start: 0.9793 (pt) cc_final: 0.9479 (mp) REVERT: D 159 MET cc_start: 0.9793 (mmp) cc_final: 0.9471 (mmm) REVERT: D 192 MET cc_start: 0.9677 (ptp) cc_final: 0.9455 (ptt) REVERT: D 225 MET cc_start: 0.9769 (mmp) cc_final: 0.9485 (mmm) REVERT: D 258 GLU cc_start: 0.9520 (mt-10) cc_final: 0.9310 (mt-10) REVERT: D 280 MET cc_start: 0.9659 (mmp) cc_final: 0.9035 (mmm) REVERT: D 450 MET cc_start: 0.9484 (mmp) cc_final: 0.9129 (mmp) REVERT: E 158 MET cc_start: 0.9635 (tpt) cc_final: 0.9106 (tpt) REVERT: E 159 MET cc_start: 0.9713 (mmp) cc_final: 0.9292 (mmm) REVERT: E 192 MET cc_start: 0.9817 (mmm) cc_final: 0.9512 (tpp) REVERT: E 225 MET cc_start: 0.9802 (mmp) cc_final: 0.9550 (mmm) REVERT: E 319 HIS cc_start: 0.8643 (m90) cc_final: 0.8181 (m90) REVERT: E 372 TYR cc_start: 0.8942 (t80) cc_final: 0.8587 (t80) REVERT: F 159 MET cc_start: 0.9762 (mtm) cc_final: 0.9496 (tpt) REVERT: F 285 GLU cc_start: 0.9268 (mm-30) cc_final: 0.7835 (tp30) REVERT: G 34 PHE cc_start: 0.9428 (t80) cc_final: 0.9120 (t80) REVERT: G 64 MET cc_start: 0.8311 (mmp) cc_final: 0.8062 (mmm) REVERT: G 65 ILE cc_start: 0.9017 (tt) cc_final: 0.8791 (pt) REVERT: H 10 ILE cc_start: 0.8883 (mm) cc_final: 0.8644 (pt) REVERT: H 55 ILE cc_start: 0.9002 (mm) cc_final: 0.8688 (mm) REVERT: J 53 PHE cc_start: 0.9479 (m-80) cc_final: 0.9184 (m-80) REVERT: K 53 PHE cc_start: 0.9238 (m-10) cc_final: 0.8942 (m-80) REVERT: L 18 PHE cc_start: 0.8225 (t80) cc_final: 0.7818 (t80) REVERT: L 27 PHE cc_start: 0.9102 (m-10) cc_final: 0.8726 (m-10) REVERT: Q 71 LEU cc_start: 0.9411 (mm) cc_final: 0.9105 (pp) REVERT: R 52 MET cc_start: 0.9063 (ppp) cc_final: 0.8831 (ppp) REVERT: S 27 PHE cc_start: 0.9336 (t80) cc_final: 0.8914 (t80) REVERT: S 64 MET cc_start: 0.9294 (mmp) cc_final: 0.9077 (mmm) REVERT: a 26 MET cc_start: 0.6588 (mpp) cc_final: 0.5646 (mpp) REVERT: a 125 MET cc_start: 0.8801 (ptt) cc_final: 0.8194 (ppp) REVERT: a 236 MET cc_start: 0.8910 (ttp) cc_final: 0.8561 (ttm) REVERT: a 277 MET cc_start: 0.9127 (ptt) cc_final: 0.8754 (ptt) REVERT: b 106 LYS cc_start: 0.8616 (tttt) cc_final: 0.8340 (tptm) REVERT: d 171 LYS cc_start: 0.9823 (pptt) cc_final: 0.9584 (tptt) REVERT: g 32 MET cc_start: 0.9277 (ttt) cc_final: 0.8909 (ttp) REVERT: g 156 MET cc_start: 0.9538 (tpp) cc_final: 0.8923 (tpp) REVERT: g 229 MET cc_start: 0.8911 (mtm) cc_final: 0.8452 (mtp) REVERT: p 110 ASP cc_start: 0.9440 (t0) cc_final: 0.9061 (p0) outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.2099 time to fit residues: 118.7783 Evaluate side-chains 272 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 309 optimal weight: 3.9990 chunk 416 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 251 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 330 optimal weight: 30.0000 chunk 146 optimal weight: 10.0000 chunk 405 optimal weight: 0.0070 chunk 169 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 135 optimal weight: 0.0010 overall best weight: 3.8010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 GLN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 GLN F 319 HIS F 366 GLN F 367 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.035648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.024968 restraints weight = 423306.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.025804 restraints weight = 288145.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.026410 restraints weight = 213075.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.026847 restraints weight = 171009.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.027155 restraints weight = 144609.849| |-----------------------------------------------------------------------------| r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37700 Z= 0.170 Angle : 0.618 11.517 51111 Z= 0.322 Chirality : 0.042 0.275 5988 Planarity : 0.004 0.058 6628 Dihedral : 6.478 132.602 5364 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.40 % Favored : 94.58 % Rotamer: Outliers : 0.08 % Allowed : 2.35 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.12), residues: 4851 helix: 1.14 (0.10), residues: 2664 sheet: -0.92 (0.22), residues: 541 loop : -1.30 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG g 71 TYR 0.022 0.002 TYR a 283 PHE 0.052 0.002 PHE L 18 TRP 0.010 0.001 TRP a 118 HIS 0.005 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00343 (37700) covalent geometry : angle 0.61826 (51111) hydrogen bonds : bond 0.04190 ( 2319) hydrogen bonds : angle 4.92709 ( 6801) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 329 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9351 (mmm) cc_final: 0.9035 (tpp) REVERT: A 49 MET cc_start: 0.8018 (tpt) cc_final: 0.7567 (tpt) REVERT: A 235 MET cc_start: 0.8835 (mpp) cc_final: 0.8568 (mpp) REVERT: A 238 LEU cc_start: 0.9700 (mt) cc_final: 0.9439 (pp) REVERT: A 263 ASP cc_start: 0.9039 (m-30) cc_final: 0.8838 (m-30) REVERT: A 295 HIS cc_start: 0.9467 (m90) cc_final: 0.9070 (m90) REVERT: B 1 MET cc_start: 0.9308 (ppp) cc_final: 0.9074 (tpp) REVERT: B 53 MET cc_start: 0.8585 (mtm) cc_final: 0.8263 (mtm) REVERT: B 157 MET cc_start: 0.9374 (mmt) cc_final: 0.9002 (mmp) REVERT: B 182 ASP cc_start: 0.9616 (t0) cc_final: 0.9343 (m-30) REVERT: B 235 MET cc_start: 0.9703 (mmp) cc_final: 0.9283 (mmm) REVERT: B 238 LEU cc_start: 0.9837 (mt) cc_final: 0.9540 (pp) REVERT: C 49 MET cc_start: 0.7764 (tpt) cc_final: 0.6084 (tpt) REVERT: C 63 MET cc_start: 0.9654 (tmm) cc_final: 0.9374 (tmm) REVERT: C 235 MET cc_start: 0.9311 (mpp) cc_final: 0.8778 (mpp) REVERT: C 457 MET cc_start: 0.9194 (mmp) cc_final: 0.8986 (mmm) REVERT: C 484 MET cc_start: 0.9708 (mpp) cc_final: 0.9453 (mpp) REVERT: D 9 ILE cc_start: 0.9782 (pt) cc_final: 0.9466 (mp) REVERT: D 159 MET cc_start: 0.9811 (mmp) cc_final: 0.9499 (mmm) REVERT: D 192 MET cc_start: 0.9702 (ptp) cc_final: 0.9501 (ptt) REVERT: D 225 MET cc_start: 0.9772 (mmp) cc_final: 0.9490 (mmm) REVERT: D 280 MET cc_start: 0.9689 (mmp) cc_final: 0.9118 (mmm) REVERT: D 450 MET cc_start: 0.9512 (mmp) cc_final: 0.9248 (mmm) REVERT: E 158 MET cc_start: 0.9637 (tpt) cc_final: 0.9093 (tpt) REVERT: E 159 MET cc_start: 0.9719 (mmp) cc_final: 0.9275 (mmm) REVERT: E 192 MET cc_start: 0.9837 (mmm) cc_final: 0.9577 (tpp) REVERT: E 225 MET cc_start: 0.9771 (mmp) cc_final: 0.9553 (mmm) REVERT: E 266 MET cc_start: 0.8194 (mmp) cc_final: 0.7854 (mmp) REVERT: E 319 HIS cc_start: 0.8666 (m90) cc_final: 0.8147 (m90) REVERT: F 159 MET cc_start: 0.9779 (mtm) cc_final: 0.9536 (tpt) REVERT: F 285 GLU cc_start: 0.9393 (mm-30) cc_final: 0.8017 (tp30) REVERT: F 415 PHE cc_start: 0.8957 (t80) cc_final: 0.8142 (m-80) REVERT: G 34 PHE cc_start: 0.9508 (t80) cc_final: 0.9044 (t80) REVERT: G 64 MET cc_start: 0.8345 (mmp) cc_final: 0.8116 (mmm) REVERT: G 65 ILE cc_start: 0.9076 (tt) cc_final: 0.8867 (pt) REVERT: J 53 PHE cc_start: 0.9276 (m-80) cc_final: 0.9060 (m-80) REVERT: J 59 LEU cc_start: 0.8668 (tt) cc_final: 0.8247 (tt) REVERT: J 60 ASP cc_start: 0.9242 (p0) cc_final: 0.8738 (t0) REVERT: K 53 PHE cc_start: 0.9219 (m-10) cc_final: 0.8907 (m-80) REVERT: L 18 PHE cc_start: 0.8046 (t80) cc_final: 0.7547 (t80) REVERT: L 27 PHE cc_start: 0.9010 (m-10) cc_final: 0.8671 (m-10) REVERT: Q 71 LEU cc_start: 0.9481 (mm) cc_final: 0.9176 (pp) REVERT: S 27 PHE cc_start: 0.9304 (t80) cc_final: 0.8845 (t80) REVERT: S 64 MET cc_start: 0.9292 (mmp) cc_final: 0.9080 (mmm) REVERT: a 26 MET cc_start: 0.7151 (mpp) cc_final: 0.5944 (mpp) REVERT: a 125 MET cc_start: 0.8756 (ptt) cc_final: 0.8364 (ppp) REVERT: a 236 MET cc_start: 0.8888 (ttp) cc_final: 0.8631 (ttm) REVERT: a 277 MET cc_start: 0.9112 (ptt) cc_final: 0.8777 (ptt) REVERT: d 171 LYS cc_start: 0.9815 (pptt) cc_final: 0.9543 (tptt) REVERT: g 32 MET cc_start: 0.9192 (ttt) cc_final: 0.8707 (ttp) REVERT: g 156 MET cc_start: 0.9554 (tpp) cc_final: 0.8944 (tpp) REVERT: g 229 MET cc_start: 0.8906 (mtm) cc_final: 0.8465 (mtp) REVERT: p 110 ASP cc_start: 0.9455 (t0) cc_final: 0.9134 (p0) outliers start: 3 outliers final: 1 residues processed: 331 average time/residue: 0.2048 time to fit residues: 114.9553 Evaluate side-chains 268 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 267 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 169 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 421 optimal weight: 10.0000 chunk 265 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 441 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.047102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.038483 restraints weight = 440379.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.039458 restraints weight = 205300.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.039750 restraints weight = 112205.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.039948 restraints weight = 99739.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.039994 restraints weight = 84674.036| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37700 Z= 0.156 Angle : 0.609 9.235 51111 Z= 0.318 Chirality : 0.042 0.329 5988 Planarity : 0.004 0.058 6628 Dihedral : 6.434 138.529 5364 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.07 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.12), residues: 4851 helix: 1.18 (0.10), residues: 2679 sheet: -0.92 (0.22), residues: 532 loop : -1.18 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 98 TYR 0.018 0.001 TYR C 475 PHE 0.028 0.001 PHE L 18 TRP 0.009 0.001 TRP p 26 HIS 0.005 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00317 (37700) covalent geometry : angle 0.60900 (51111) hydrogen bonds : bond 0.04090 ( 2319) hydrogen bonds : angle 4.87052 ( 6801) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9422 (mmm) cc_final: 0.9079 (tpp) REVERT: A 49 MET cc_start: 0.8096 (tpt) cc_final: 0.7582 (tpt) REVERT: A 246 MET cc_start: 0.9787 (mmp) cc_final: 0.9587 (mmm) REVERT: A 295 HIS cc_start: 0.9468 (m90) cc_final: 0.9072 (m90) REVERT: A 325 LEU cc_start: 0.9280 (mm) cc_final: 0.9004 (mm) REVERT: B 34 MET cc_start: 0.9610 (mmm) cc_final: 0.8981 (tpp) REVERT: B 53 MET cc_start: 0.8622 (mtm) cc_final: 0.8321 (mtm) REVERT: B 157 MET cc_start: 0.9389 (mmt) cc_final: 0.9037 (mmp) REVERT: B 182 ASP cc_start: 0.9592 (t0) cc_final: 0.9317 (m-30) REVERT: B 235 MET cc_start: 0.9711 (mmp) cc_final: 0.9343 (mmm) REVERT: B 238 LEU cc_start: 0.9842 (mt) cc_final: 0.9552 (pp) REVERT: B 246 MET cc_start: 0.9613 (mmp) cc_final: 0.9374 (mmm) REVERT: B 258 LEU cc_start: 0.9810 (tp) cc_final: 0.9259 (pp) REVERT: B 298 LEU cc_start: 0.9671 (tp) cc_final: 0.9389 (tp) REVERT: C 49 MET cc_start: 0.7776 (tpt) cc_final: 0.6158 (tpt) REVERT: C 63 MET cc_start: 0.9656 (tmm) cc_final: 0.9374 (tmm) REVERT: C 235 MET cc_start: 0.9286 (mpp) cc_final: 0.8656 (mpp) REVERT: C 457 MET cc_start: 0.9059 (mmp) cc_final: 0.8826 (mmm) REVERT: C 484 MET cc_start: 0.9718 (mpp) cc_final: 0.9438 (mpp) REVERT: D 9 ILE cc_start: 0.9811 (pt) cc_final: 0.9517 (mp) REVERT: D 159 MET cc_start: 0.9792 (mmp) cc_final: 0.9466 (mmm) REVERT: D 225 MET cc_start: 0.9770 (mmp) cc_final: 0.9486 (mmm) REVERT: D 280 MET cc_start: 0.9671 (mmp) cc_final: 0.9074 (mmm) REVERT: D 450 MET cc_start: 0.9480 (mmp) cc_final: 0.9235 (mmm) REVERT: E 158 MET cc_start: 0.9636 (tpt) cc_final: 0.9108 (tpt) REVERT: E 159 MET cc_start: 0.9707 (mmp) cc_final: 0.9269 (mmm) REVERT: E 192 MET cc_start: 0.9808 (mmm) cc_final: 0.9518 (tpp) REVERT: E 266 MET cc_start: 0.8533 (mmp) cc_final: 0.8193 (mmp) REVERT: E 319 HIS cc_start: 0.8664 (m90) cc_final: 0.8175 (m90) REVERT: F 159 MET cc_start: 0.9763 (mtm) cc_final: 0.9430 (tpt) REVERT: F 280 MET cc_start: 0.9646 (tpt) cc_final: 0.9430 (tpp) REVERT: F 285 GLU cc_start: 0.9253 (mm-30) cc_final: 0.7786 (tp30) REVERT: F 415 PHE cc_start: 0.8925 (t80) cc_final: 0.8099 (m-80) REVERT: G 34 PHE cc_start: 0.9456 (t80) cc_final: 0.9044 (t80) REVERT: G 64 MET cc_start: 0.8265 (mmp) cc_final: 0.8011 (mmm) REVERT: G 65 ILE cc_start: 0.9006 (tt) cc_final: 0.8772 (pt) REVERT: J 53 PHE cc_start: 0.9477 (m-80) cc_final: 0.9197 (m-80) REVERT: J 60 ASP cc_start: 0.9347 (p0) cc_final: 0.8623 (t0) REVERT: K 53 PHE cc_start: 0.9211 (m-10) cc_final: 0.8917 (m-80) REVERT: L 18 PHE cc_start: 0.8203 (t80) cc_final: 0.7855 (t80) REVERT: L 27 PHE cc_start: 0.9055 (m-10) cc_final: 0.8670 (m-10) REVERT: Q 71 LEU cc_start: 0.9443 (mm) cc_final: 0.9101 (pp) REVERT: R 52 MET cc_start: 0.9015 (ppp) cc_final: 0.8787 (ppp) REVERT: S 27 PHE cc_start: 0.9315 (t80) cc_final: 0.8816 (t80) REVERT: S 64 MET cc_start: 0.9314 (mmp) cc_final: 0.9099 (mmm) REVERT: a 26 MET cc_start: 0.6828 (mpp) cc_final: 0.5853 (mpp) REVERT: a 125 MET cc_start: 0.8857 (ptt) cc_final: 0.8235 (ppp) REVERT: a 236 MET cc_start: 0.8983 (ttp) cc_final: 0.8664 (ttm) REVERT: a 277 MET cc_start: 0.9136 (ptt) cc_final: 0.8553 (ptt) REVERT: b 148 MET cc_start: 0.8369 (pmm) cc_final: 0.8148 (pmm) REVERT: d 171 LYS cc_start: 0.9815 (pptt) cc_final: 0.9531 (tptm) REVERT: g 32 MET cc_start: 0.9303 (ttt) cc_final: 0.8856 (ttp) REVERT: g 39 MET cc_start: 0.9536 (mmp) cc_final: 0.9323 (mmm) REVERT: g 156 MET cc_start: 0.9548 (tpp) cc_final: 0.8930 (tpp) REVERT: g 229 MET cc_start: 0.8874 (mtm) cc_final: 0.8415 (mtp) REVERT: p 110 ASP cc_start: 0.9452 (t0) cc_final: 0.9040 (p0) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.2167 time to fit residues: 118.0447 Evaluate side-chains 264 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 478 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 442 optimal weight: 0.8980 chunk 454 optimal weight: 30.0000 chunk 100 optimal weight: 7.9990 chunk 315 optimal weight: 6.9990 chunk 406 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 354 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 455 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.035704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.024969 restraints weight = 418296.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.025800 restraints weight = 283816.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.026406 restraints weight = 211213.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.026868 restraints weight = 168585.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.027111 restraints weight = 141893.277| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37700 Z= 0.146 Angle : 0.603 8.433 51111 Z= 0.312 Chirality : 0.042 0.275 5988 Planarity : 0.004 0.049 6628 Dihedral : 6.394 143.845 5364 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.91 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.12), residues: 4851 helix: 1.26 (0.10), residues: 2680 sheet: -0.85 (0.22), residues: 534 loop : -1.11 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG p 100 TYR 0.018 0.001 TYR C 475 PHE 0.040 0.002 PHE p 17 TRP 0.010 0.001 TRP a 132 HIS 0.004 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00300 (37700) covalent geometry : angle 0.60279 (51111) hydrogen bonds : bond 0.04010 ( 2319) hydrogen bonds : angle 4.77361 ( 6801) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9456 (mmm) cc_final: 0.9098 (tpp) REVERT: A 49 MET cc_start: 0.8206 (tpt) cc_final: 0.7738 (tpt) REVERT: A 235 MET cc_start: 0.8822 (mpp) cc_final: 0.8550 (ptp) REVERT: A 263 ASP cc_start: 0.9132 (m-30) cc_final: 0.8899 (m-30) REVERT: A 295 HIS cc_start: 0.9471 (m90) cc_final: 0.9063 (m90) REVERT: A 325 LEU cc_start: 0.9346 (mm) cc_final: 0.9033 (mm) REVERT: B 34 MET cc_start: 0.9646 (mmm) cc_final: 0.9003 (tpp) REVERT: B 53 MET cc_start: 0.8572 (mtm) cc_final: 0.8288 (mtm) REVERT: B 157 MET cc_start: 0.9361 (mmt) cc_final: 0.9053 (mmp) REVERT: B 182 ASP cc_start: 0.9592 (t0) cc_final: 0.9308 (m-30) REVERT: B 235 MET cc_start: 0.9710 (mmp) cc_final: 0.9278 (mmm) REVERT: B 238 LEU cc_start: 0.9843 (mt) cc_final: 0.9541 (pp) REVERT: B 246 MET cc_start: 0.9610 (mmp) cc_final: 0.9390 (mmm) REVERT: B 298 LEU cc_start: 0.9698 (tp) cc_final: 0.9423 (tp) REVERT: C 49 MET cc_start: 0.7797 (tpt) cc_final: 0.6172 (tpt) REVERT: C 63 MET cc_start: 0.9687 (tmm) cc_final: 0.9413 (tmm) REVERT: C 235 MET cc_start: 0.9246 (mpp) cc_final: 0.8712 (mpp) REVERT: C 356 LEU cc_start: 0.9401 (mm) cc_final: 0.9189 (mt) REVERT: C 457 MET cc_start: 0.9215 (mmp) cc_final: 0.8998 (mmm) REVERT: D 9 ILE cc_start: 0.9806 (pt) cc_final: 0.9519 (mp) REVERT: D 159 MET cc_start: 0.9808 (mmp) cc_final: 0.9504 (mmm) REVERT: D 225 MET cc_start: 0.9790 (mmp) cc_final: 0.9515 (mmm) REVERT: D 280 MET cc_start: 0.9688 (mmp) cc_final: 0.9147 (mmm) REVERT: D 450 MET cc_start: 0.9451 (mmp) cc_final: 0.9236 (mmm) REVERT: E 87 MET cc_start: 0.9294 (mpp) cc_final: 0.9025 (mpp) REVERT: E 158 MET cc_start: 0.9715 (tpt) cc_final: 0.9327 (tpt) REVERT: E 159 MET cc_start: 0.9716 (mmp) cc_final: 0.9452 (mmm) REVERT: E 192 MET cc_start: 0.9826 (mmm) cc_final: 0.9553 (tpp) REVERT: E 225 MET cc_start: 0.9842 (mmp) cc_final: 0.9574 (mmm) REVERT: E 266 MET cc_start: 0.8319 (mmp) cc_final: 0.8010 (mmp) REVERT: E 319 HIS cc_start: 0.8636 (m90) cc_final: 0.8124 (m90) REVERT: F 159 MET cc_start: 0.9800 (mtm) cc_final: 0.9483 (tpt) REVERT: F 252 TYR cc_start: 0.9763 (t80) cc_final: 0.9212 (t80) REVERT: F 280 MET cc_start: 0.9700 (tpt) cc_final: 0.9437 (tpp) REVERT: F 285 GLU cc_start: 0.9395 (mm-30) cc_final: 0.7993 (tp30) REVERT: F 415 PHE cc_start: 0.8951 (t80) cc_final: 0.8156 (m-80) REVERT: G 34 PHE cc_start: 0.9544 (t80) cc_final: 0.9118 (t80) REVERT: G 64 MET cc_start: 0.8351 (mmp) cc_final: 0.8112 (mmm) REVERT: G 65 ILE cc_start: 0.9064 (tt) cc_final: 0.8864 (pt) REVERT: H 55 ILE cc_start: 0.8631 (mm) cc_final: 0.8324 (mm) REVERT: J 59 LEU cc_start: 0.8661 (tt) cc_final: 0.8428 (tt) REVERT: J 60 ASP cc_start: 0.9232 (p0) cc_final: 0.8739 (t0) REVERT: K 53 PHE cc_start: 0.9209 (m-10) cc_final: 0.8926 (m-80) REVERT: L 27 PHE cc_start: 0.8960 (m-10) cc_final: 0.8597 (m-10) REVERT: Q 71 LEU cc_start: 0.9511 (mm) cc_final: 0.9203 (pp) REVERT: S 27 PHE cc_start: 0.9252 (t80) cc_final: 0.8792 (t80) REVERT: S 64 MET cc_start: 0.9295 (mmp) cc_final: 0.9079 (mmm) REVERT: a 26 MET cc_start: 0.7186 (mpp) cc_final: 0.5959 (mpp) REVERT: a 236 MET cc_start: 0.8863 (ttp) cc_final: 0.8637 (ttm) REVERT: d 171 LYS cc_start: 0.9805 (pptt) cc_final: 0.9552 (tptt) REVERT: g 32 MET cc_start: 0.9185 (ttt) cc_final: 0.8738 (ttp) REVERT: g 156 MET cc_start: 0.9578 (tpp) cc_final: 0.9034 (tpp) REVERT: g 229 MET cc_start: 0.8899 (mtm) cc_final: 0.8449 (mtp) REVERT: p 110 ASP cc_start: 0.9407 (t0) cc_final: 0.8986 (p0) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.2107 time to fit residues: 115.4763 Evaluate side-chains 265 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 144 optimal weight: 9.9990 chunk 388 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 410 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 296 optimal weight: 8.9990 chunk 247 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.036233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.025386 restraints weight = 418316.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.026242 restraints weight = 279703.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.026800 restraints weight = 207305.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.027312 restraints weight = 166693.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.027655 restraints weight = 139765.725| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37700 Z= 0.122 Angle : 0.595 8.952 51111 Z= 0.306 Chirality : 0.042 0.239 5988 Planarity : 0.004 0.055 6628 Dihedral : 6.309 148.290 5364 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.12), residues: 4851 helix: 1.35 (0.10), residues: 2688 sheet: -0.82 (0.22), residues: 524 loop : -1.04 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 371 TYR 0.019 0.001 TYR C 475 PHE 0.053 0.001 PHE a 274 TRP 0.011 0.001 TRP a 132 HIS 0.003 0.001 HIS F 358 Details of bonding type rmsd covalent geometry : bond 0.00251 (37700) covalent geometry : angle 0.59520 (51111) hydrogen bonds : bond 0.03924 ( 2319) hydrogen bonds : angle 4.64961 ( 6801) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9474 (mmm) cc_final: 0.9122 (tpp) REVERT: A 49 MET cc_start: 0.8154 (tpt) cc_final: 0.7625 (tpt) REVERT: A 235 MET cc_start: 0.8812 (mpp) cc_final: 0.8504 (ptp) REVERT: A 246 MET cc_start: 0.9785 (mmp) cc_final: 0.9537 (mmm) REVERT: A 263 ASP cc_start: 0.9138 (m-30) cc_final: 0.8912 (m-30) REVERT: A 295 HIS cc_start: 0.9468 (m90) cc_final: 0.9042 (m90) REVERT: A 325 LEU cc_start: 0.9334 (mm) cc_final: 0.9026 (mm) REVERT: B 34 MET cc_start: 0.9668 (mmm) cc_final: 0.9018 (tpp) REVERT: B 49 MET cc_start: 0.8148 (mmm) cc_final: 0.7736 (tpt) REVERT: B 53 MET cc_start: 0.8616 (mtm) cc_final: 0.8378 (mtm) REVERT: B 157 MET cc_start: 0.9338 (mmt) cc_final: 0.9029 (mmm) REVERT: B 182 ASP cc_start: 0.9562 (t0) cc_final: 0.9271 (m-30) REVERT: B 235 MET cc_start: 0.9703 (mmp) cc_final: 0.9250 (mmm) REVERT: B 238 LEU cc_start: 0.9842 (mt) cc_final: 0.9527 (pp) REVERT: B 246 MET cc_start: 0.9599 (mmp) cc_final: 0.9393 (mmm) REVERT: B 298 LEU cc_start: 0.9712 (tp) cc_final: 0.9498 (tp) REVERT: C 34 MET cc_start: 0.9341 (mmm) cc_final: 0.9069 (mmm) REVERT: C 49 MET cc_start: 0.7618 (tpt) cc_final: 0.6072 (tpt) REVERT: C 63 MET cc_start: 0.9678 (tmm) cc_final: 0.9453 (tmm) REVERT: C 235 MET cc_start: 0.9216 (mpp) cc_final: 0.8606 (mpp) REVERT: C 246 MET cc_start: 0.9333 (mmp) cc_final: 0.9126 (mmm) REVERT: C 356 LEU cc_start: 0.9363 (mm) cc_final: 0.9145 (mt) REVERT: C 457 MET cc_start: 0.9176 (mmp) cc_final: 0.8956 (mmm) REVERT: D 9 ILE cc_start: 0.9799 (pt) cc_final: 0.9505 (mp) REVERT: D 55 MET cc_start: 0.8725 (mmp) cc_final: 0.8096 (mmp) REVERT: D 225 MET cc_start: 0.9788 (mmp) cc_final: 0.9500 (mmm) REVERT: D 258 GLU cc_start: 0.9530 (mt-10) cc_final: 0.9247 (mt-10) REVERT: D 280 MET cc_start: 0.9663 (mmp) cc_final: 0.9172 (mmm) REVERT: E 87 MET cc_start: 0.9289 (mpp) cc_final: 0.8963 (mpp) REVERT: E 158 MET cc_start: 0.9703 (tpt) cc_final: 0.9245 (tpt) REVERT: E 159 MET cc_start: 0.9717 (mmp) cc_final: 0.9421 (mmm) REVERT: E 192 MET cc_start: 0.9765 (mmm) cc_final: 0.9477 (tpp) REVERT: E 225 MET cc_start: 0.9832 (mmp) cc_final: 0.9580 (mmm) REVERT: E 266 MET cc_start: 0.8462 (mmp) cc_final: 0.8187 (mmp) REVERT: E 319 HIS cc_start: 0.8673 (m90) cc_final: 0.8138 (m90) REVERT: E 372 TYR cc_start: 0.8533 (t80) cc_final: 0.8249 (t80) REVERT: E 450 MET cc_start: 0.9060 (tpp) cc_final: 0.8796 (tpp) REVERT: F 159 MET cc_start: 0.9750 (mtm) cc_final: 0.9465 (tpt) REVERT: F 252 TYR cc_start: 0.9745 (t80) cc_final: 0.9193 (t80) REVERT: F 280 MET cc_start: 0.9677 (tpt) cc_final: 0.9396 (tpp) REVERT: F 285 GLU cc_start: 0.9370 (mm-30) cc_final: 0.7945 (tp30) REVERT: F 415 PHE cc_start: 0.8960 (t80) cc_final: 0.8185 (m-80) REVERT: G 30 LEU cc_start: 0.9330 (pp) cc_final: 0.9089 (mt) REVERT: G 34 PHE cc_start: 0.9497 (t80) cc_final: 0.9166 (t80) REVERT: G 64 MET cc_start: 0.8287 (mmp) cc_final: 0.8053 (mmm) REVERT: J 59 LEU cc_start: 0.8573 (tt) cc_final: 0.8154 (tt) REVERT: J 60 ASP cc_start: 0.9195 (p0) cc_final: 0.8705 (t0) REVERT: K 53 PHE cc_start: 0.9206 (m-10) cc_final: 0.8926 (m-80) REVERT: L 27 PHE cc_start: 0.9028 (m-10) cc_final: 0.8775 (m-10) REVERT: L 60 ASP cc_start: 0.9421 (t0) cc_final: 0.9030 (p0) REVERT: L 64 MET cc_start: 0.7997 (mtt) cc_final: 0.7727 (ttm) REVERT: Q 71 LEU cc_start: 0.9511 (mm) cc_final: 0.9208 (pp) REVERT: R 52 MET cc_start: 0.8925 (ppp) cc_final: 0.8635 (ppp) REVERT: S 27 PHE cc_start: 0.9236 (t80) cc_final: 0.8721 (t80) REVERT: S 64 MET cc_start: 0.9298 (mmp) cc_final: 0.9056 (mmp) REVERT: a 26 MET cc_start: 0.7134 (mpp) cc_final: 0.5885 (mpp) REVERT: a 236 MET cc_start: 0.8822 (ttp) cc_final: 0.8593 (ttm) REVERT: b 106 LYS cc_start: 0.8774 (tptm) cc_final: 0.8536 (mttt) REVERT: e 88 ASN cc_start: 0.9108 (t0) cc_final: 0.8838 (t0) REVERT: e 91 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6855 (pm20) REVERT: g 32 MET cc_start: 0.9255 (ttt) cc_final: 0.8790 (ttp) REVERT: g 156 MET cc_start: 0.9591 (tpp) cc_final: 0.9072 (tpp) REVERT: g 229 MET cc_start: 0.8883 (mtm) cc_final: 0.8426 (mtp) REVERT: p 110 ASP cc_start: 0.9382 (t0) cc_final: 0.8983 (p0) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.2089 time to fit residues: 117.2292 Evaluate side-chains 266 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 244 optimal weight: 10.0000 chunk 377 optimal weight: 20.0000 chunk 353 optimal weight: 7.9990 chunk 311 optimal weight: 5.9990 chunk 407 optimal weight: 6.9990 chunk 405 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 450 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN C 164 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 HIS F 366 GLN G 47 GLN ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.024552 restraints weight = 441750.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.025354 restraints weight = 302069.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.025936 restraints weight = 222950.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.026351 restraints weight = 178611.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.026649 restraints weight = 151966.561| |-----------------------------------------------------------------------------| r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 37700 Z= 0.226 Angle : 0.679 8.604 51111 Z= 0.355 Chirality : 0.043 0.311 5988 Planarity : 0.005 0.074 6628 Dihedral : 6.397 145.998 5364 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.30 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.12), residues: 4851 helix: 1.15 (0.10), residues: 2692 sheet: -0.94 (0.21), residues: 545 loop : -1.08 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG e 132 TYR 0.019 0.002 TYR C 475 PHE 0.041 0.002 PHE a 274 TRP 0.011 0.001 TRP a 132 HIS 0.007 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00450 (37700) covalent geometry : angle 0.67941 (51111) hydrogen bonds : bond 0.04143 ( 2319) hydrogen bonds : angle 4.91229 ( 6801) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9397 (mmm) cc_final: 0.9137 (mmm) REVERT: A 49 MET cc_start: 0.8641 (tpt) cc_final: 0.8416 (tpt) REVERT: A 235 MET cc_start: 0.8893 (mpp) cc_final: 0.8571 (mpp) REVERT: A 238 LEU cc_start: 0.9685 (mt) cc_final: 0.9425 (pp) REVERT: A 263 ASP cc_start: 0.9019 (m-30) cc_final: 0.8819 (m-30) REVERT: A 295 HIS cc_start: 0.9476 (m90) cc_final: 0.9060 (m90) REVERT: B 34 MET cc_start: 0.9708 (mmm) cc_final: 0.9040 (tpp) REVERT: B 53 MET cc_start: 0.8502 (mtm) cc_final: 0.8263 (mtm) REVERT: B 157 MET cc_start: 0.9353 (mmt) cc_final: 0.9040 (mmm) REVERT: B 182 ASP cc_start: 0.9579 (t0) cc_final: 0.9281 (m-30) REVERT: B 235 MET cc_start: 0.9714 (mmp) cc_final: 0.9313 (mmm) REVERT: B 238 LEU cc_start: 0.9847 (mt) cc_final: 0.9550 (pp) REVERT: B 298 LEU cc_start: 0.9725 (tp) cc_final: 0.9451 (tp) REVERT: B 484 MET cc_start: 0.8938 (ptp) cc_final: 0.8695 (mpp) REVERT: C 49 MET cc_start: 0.8078 (tpt) cc_final: 0.6341 (tpt) REVERT: C 63 MET cc_start: 0.9694 (tmm) cc_final: 0.9454 (tmm) REVERT: C 182 ASP cc_start: 0.8822 (t0) cc_final: 0.8474 (t0) REVERT: C 235 MET cc_start: 0.9316 (mpp) cc_final: 0.8922 (mpp) REVERT: C 457 MET cc_start: 0.9267 (mmp) cc_final: 0.9057 (mmm) REVERT: D 9 ILE cc_start: 0.9807 (pt) cc_final: 0.9525 (mp) REVERT: D 159 MET cc_start: 0.9654 (mmm) cc_final: 0.9394 (mmm) REVERT: D 225 MET cc_start: 0.9806 (mmp) cc_final: 0.9528 (mmm) REVERT: E 87 MET cc_start: 0.9180 (mpp) cc_final: 0.8922 (mpp) REVERT: E 158 MET cc_start: 0.9682 (tpt) cc_final: 0.9415 (mtt) REVERT: E 159 MET cc_start: 0.9714 (mmp) cc_final: 0.9510 (mmm) REVERT: E 192 MET cc_start: 0.9810 (mmm) cc_final: 0.9532 (tpp) REVERT: E 208 MET cc_start: 0.9360 (ptp) cc_final: 0.8705 (tmm) REVERT: E 225 MET cc_start: 0.9818 (mmp) cc_final: 0.9534 (mmm) REVERT: E 266 MET cc_start: 0.8463 (mmp) cc_final: 0.8171 (mmp) REVERT: E 319 HIS cc_start: 0.8653 (m90) cc_final: 0.8198 (m90) REVERT: F 159 MET cc_start: 0.9772 (mtm) cc_final: 0.9455 (tpt) REVERT: F 252 TYR cc_start: 0.9771 (t80) cc_final: 0.9237 (t80) REVERT: F 280 MET cc_start: 0.9689 (tpt) cc_final: 0.9413 (tpp) REVERT: F 285 GLU cc_start: 0.9398 (mm-30) cc_final: 0.8007 (tp30) REVERT: F 415 PHE cc_start: 0.8844 (t80) cc_final: 0.8043 (m-80) REVERT: G 30 LEU cc_start: 0.9388 (pp) cc_final: 0.9174 (mt) REVERT: G 34 PHE cc_start: 0.9526 (t80) cc_final: 0.9156 (t80) REVERT: J 59 LEU cc_start: 0.8642 (tt) cc_final: 0.8365 (tt) REVERT: J 60 ASP cc_start: 0.9192 (p0) cc_final: 0.8703 (t0) REVERT: K 53 PHE cc_start: 0.9220 (m-10) cc_final: 0.8941 (m-80) REVERT: L 18 PHE cc_start: 0.8169 (t80) cc_final: 0.7950 (t80) REVERT: L 27 PHE cc_start: 0.9001 (m-10) cc_final: 0.8719 (m-10) REVERT: L 60 ASP cc_start: 0.9456 (t0) cc_final: 0.9048 (p0) REVERT: R 52 MET cc_start: 0.8906 (ppp) cc_final: 0.8664 (ppp) REVERT: S 27 PHE cc_start: 0.9252 (t80) cc_final: 0.8767 (t80) REVERT: S 64 MET cc_start: 0.9320 (mmp) cc_final: 0.9105 (mmm) REVERT: a 26 MET cc_start: 0.7388 (mpp) cc_final: 0.5946 (mpp) REVERT: a 236 MET cc_start: 0.8919 (ttp) cc_final: 0.8661 (ttm) REVERT: a 278 MET cc_start: 0.9484 (mpp) cc_final: 0.9227 (mpp) REVERT: d 171 LYS cc_start: 0.9830 (pptt) cc_final: 0.9562 (tppt) REVERT: e 88 ASN cc_start: 0.9115 (t0) cc_final: 0.8845 (t0) REVERT: e 91 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6928 (pm20) REVERT: g 32 MET cc_start: 0.9269 (ttt) cc_final: 0.8746 (ttt) REVERT: g 156 MET cc_start: 0.9582 (tpp) cc_final: 0.9077 (tpp) REVERT: g 229 MET cc_start: 0.8950 (mtm) cc_final: 0.8494 (mtp) REVERT: p 110 ASP cc_start: 0.9436 (t0) cc_final: 0.9056 (p0) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.2088 time to fit residues: 111.6456 Evaluate side-chains 260 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 339 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 396 optimal weight: 4.9990 chunk 417 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 458 optimal weight: 20.0000 chunk 423 optimal weight: 0.9990 chunk 381 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 435 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN C 203 GLN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN a 272 GLN b 137 ASN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.035192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.024736 restraints weight = 436225.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.025540 restraints weight = 299584.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.026140 restraints weight = 223425.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.026590 restraints weight = 177567.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.026917 restraints weight = 149576.328| |-----------------------------------------------------------------------------| r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 37700 Z= 0.169 Angle : 0.642 10.596 51111 Z= 0.334 Chirality : 0.043 0.295 5988 Planarity : 0.004 0.054 6628 Dihedral : 6.373 148.580 5364 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.03 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 4851 helix: 1.18 (0.10), residues: 2688 sheet: -0.86 (0.21), residues: 540 loop : -1.07 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 347 TYR 0.018 0.002 TYR C 475 PHE 0.044 0.002 PHE a 274 TRP 0.011 0.001 TRP a 55 HIS 0.004 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00347 (37700) covalent geometry : angle 0.64234 (51111) hydrogen bonds : bond 0.04039 ( 2319) hydrogen bonds : angle 4.84108 ( 6801) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9445 (mmm) cc_final: 0.9115 (tpp) REVERT: A 235 MET cc_start: 0.8871 (mpp) cc_final: 0.8192 (ptp) REVERT: A 238 LEU cc_start: 0.9674 (mt) cc_final: 0.9409 (pp) REVERT: A 246 MET cc_start: 0.9773 (mmp) cc_final: 0.9530 (mmm) REVERT: A 263 ASP cc_start: 0.8968 (m-30) cc_final: 0.8762 (m-30) REVERT: A 295 HIS cc_start: 0.9463 (m90) cc_final: 0.9042 (m90) REVERT: A 325 LEU cc_start: 0.9248 (mm) cc_final: 0.9043 (mm) REVERT: B 34 MET cc_start: 0.9681 (mmm) cc_final: 0.9023 (tpp) REVERT: B 53 MET cc_start: 0.8543 (mtm) cc_final: 0.8314 (mtm) REVERT: B 157 MET cc_start: 0.9297 (mmt) cc_final: 0.8992 (mmm) REVERT: B 182 ASP cc_start: 0.9556 (t0) cc_final: 0.9254 (m-30) REVERT: B 235 MET cc_start: 0.9714 (mmp) cc_final: 0.9433 (mmm) REVERT: B 298 LEU cc_start: 0.9739 (tp) cc_final: 0.9475 (tp) REVERT: B 484 MET cc_start: 0.8962 (ptp) cc_final: 0.8716 (mpp) REVERT: C 49 MET cc_start: 0.7987 (tpt) cc_final: 0.6365 (tpt) REVERT: C 63 MET cc_start: 0.9682 (tmm) cc_final: 0.9419 (tmm) REVERT: C 182 ASP cc_start: 0.8817 (t0) cc_final: 0.8457 (t0) REVERT: C 235 MET cc_start: 0.9284 (mpp) cc_final: 0.8733 (mpp) REVERT: C 457 MET cc_start: 0.9210 (mmp) cc_final: 0.9003 (mmm) REVERT: C 484 MET cc_start: 0.9778 (mmp) cc_final: 0.9577 (mmm) REVERT: D 55 MET cc_start: 0.8756 (mmp) cc_final: 0.8056 (mmp) REVERT: D 159 MET cc_start: 0.9474 (mmm) cc_final: 0.9222 (mmm) REVERT: D 192 MET cc_start: 0.9751 (mtm) cc_final: 0.9482 (ptp) REVERT: D 225 MET cc_start: 0.9800 (mmp) cc_final: 0.9520 (mmm) REVERT: D 280 MET cc_start: 0.9691 (mmp) cc_final: 0.9158 (mmm) REVERT: E 87 MET cc_start: 0.9199 (mpp) cc_final: 0.8917 (mpp) REVERT: E 158 MET cc_start: 0.9677 (tpt) cc_final: 0.9352 (mtp) REVERT: E 159 MET cc_start: 0.9709 (mmp) cc_final: 0.9487 (mmm) REVERT: E 192 MET cc_start: 0.9783 (mmm) cc_final: 0.9523 (tpp) REVERT: E 225 MET cc_start: 0.9811 (mmp) cc_final: 0.9542 (mmm) REVERT: E 266 MET cc_start: 0.8484 (mmp) cc_final: 0.8280 (mmp) REVERT: E 319 HIS cc_start: 0.8641 (m90) cc_final: 0.8145 (m90) REVERT: F 159 MET cc_start: 0.9752 (mtm) cc_final: 0.9455 (tpt) REVERT: F 252 TYR cc_start: 0.9763 (t80) cc_final: 0.9224 (t80) REVERT: F 280 MET cc_start: 0.9683 (tpt) cc_final: 0.9394 (tpp) REVERT: F 285 GLU cc_start: 0.9392 (mm-30) cc_final: 0.7990 (tp30) REVERT: F 415 PHE cc_start: 0.8804 (t80) cc_final: 0.8010 (m-80) REVERT: G 30 LEU cc_start: 0.9351 (pp) cc_final: 0.9084 (mt) REVERT: G 34 PHE cc_start: 0.9508 (t80) cc_final: 0.9206 (t80) REVERT: J 59 LEU cc_start: 0.8592 (tt) cc_final: 0.8369 (tt) REVERT: J 60 ASP cc_start: 0.9190 (p0) cc_final: 0.8718 (t0) REVERT: K 53 PHE cc_start: 0.9230 (m-10) cc_final: 0.8955 (m-80) REVERT: L 27 PHE cc_start: 0.8984 (m-10) cc_final: 0.8710 (m-10) REVERT: L 60 ASP cc_start: 0.9474 (t0) cc_final: 0.9112 (p0) REVERT: L 64 MET cc_start: 0.8326 (mtt) cc_final: 0.8095 (ttm) REVERT: S 27 PHE cc_start: 0.9304 (t80) cc_final: 0.8795 (t80) REVERT: S 64 MET cc_start: 0.9321 (mmp) cc_final: 0.9112 (mmm) REVERT: a 26 MET cc_start: 0.7339 (mpp) cc_final: 0.6025 (mpp) REVERT: a 63 PHE cc_start: 0.9443 (t80) cc_final: 0.9228 (t80) REVERT: a 122 MET cc_start: 0.8677 (tmm) cc_final: 0.8475 (tmm) REVERT: a 278 MET cc_start: 0.9435 (mpp) cc_final: 0.9162 (mpp) REVERT: b 106 LYS cc_start: 0.8959 (tptm) cc_final: 0.8746 (tttt) REVERT: e 88 ASN cc_start: 0.9104 (t0) cc_final: 0.8822 (t0) REVERT: e 91 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6925 (pm20) REVERT: g 32 MET cc_start: 0.9273 (ttt) cc_final: 0.8984 (ttp) REVERT: g 156 MET cc_start: 0.9584 (tpp) cc_final: 0.9084 (tpp) REVERT: g 229 MET cc_start: 0.8909 (mtm) cc_final: 0.8451 (mtp) REVERT: g 246 MET cc_start: 0.9202 (ptp) cc_final: 0.8901 (mpp) REVERT: p 110 ASP cc_start: 0.9446 (t0) cc_final: 0.9099 (p0) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.2104 time to fit residues: 112.0353 Evaluate side-chains 262 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 300 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 309 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 371 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 377 optimal weight: 9.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN G 47 GLN b 137 ASN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 138 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.035716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.025093 restraints weight = 417707.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.025915 restraints weight = 283437.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.026520 restraints weight = 210023.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.026958 restraints weight = 168459.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.027266 restraints weight = 142195.733| |-----------------------------------------------------------------------------| r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37700 Z= 0.149 Angle : 0.637 16.627 51111 Z= 0.327 Chirality : 0.042 0.266 5988 Planarity : 0.004 0.052 6628 Dihedral : 6.352 150.305 5364 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.99 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.12), residues: 4851 helix: 1.22 (0.10), residues: 2690 sheet: -0.82 (0.22), residues: 542 loop : -1.00 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG p 100 TYR 0.020 0.001 TYR B 514 PHE 0.057 0.002 PHE L 18 TRP 0.016 0.001 TRP a 55 HIS 0.004 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00311 (37700) covalent geometry : angle 0.63667 (51111) hydrogen bonds : bond 0.03993 ( 2319) hydrogen bonds : angle 4.78141 ( 6801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5739.56 seconds wall clock time: 100 minutes 34.19 seconds (6034.19 seconds total)