Starting phenix.real_space_refine on Mon Jul 6 17:10:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7p3n_13181/07_2026/7p3n_13181.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p3n_13181/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7p3n_13181/07_2026/7p3n_13181.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7p3n_13181/07_2026/7p3n_13181.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p3n_13181/07_2026/7p3n_13181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p3n_13181/07_2026/7p3n_13181.map" model { file = "/net/cci-nas-00/data/ceres_data/7p3n_13181/07_2026/7p3n_13181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p3n_13181/07_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): 0.07s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 8.16, 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: 3.60 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: 1.06 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: 8.55 Time building geometry restraints manager: 4.64 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: 21804 25.20 - 50.41: 779 50.41 - 75.61: 105 75.61 - 100.82: 35 100.82 - 126.02: 1 Dihedral angle restraints: 22724 sinusoidal: 8805 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 22721 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 35.190 Find NCS groups from input model: 0.960 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: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 13.736 126.024 13810 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/Z covalent geometry : bond 0.00518 / 0.29 (37700) covalent geometry : angle 0.85055 / 0.50 (51111) hydrogen bonds : bond 0.16291 / 11.21 ( 2319) hydrogen bonds : angle 6.93895 / 4.85 ( 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 : 1.467 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: 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: 0.2457 time to fit residues: 143.5535 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 : 1.554 ------------------------------------------------------------------------------- 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... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 2 GLN B 79 ASN B 84 GLN C 164 GLN C 203 GLN D 118 GLN D 157 ASN ** 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 63 GLN ** 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.048006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.038671 restraints weight = 438045.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.039774 restraints weight = 231419.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.040509 restraints weight = 144295.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.041018 restraints weight = 100252.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.041356 restraints weight = 75853.913| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 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 = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37700 Z= 0.156 Angle : 0.649 8.506 51111 Z= 0.340 Chirality : 0.043 0.182 5988 Planarity : 0.005 0.052 6628 Dihedral : 6.294 133.274 5271 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.11 % Favored : 94.87 % Rotamer: Outliers : 0.18 % Allowed : 3.94 % Favored : 95.88 % 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: 0.70 (0.10), residues: 2667 sheet: -0.89 (0.22), residues: 519 loop : -1.66 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 279 TYR 0.021 0.002 TYR E 228 PHE 0.039 0.002 PHE J 18 TRP 0.023 0.002 TRP a 118 HIS 0.006 0.001 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (37700) covalent geometry : angle 0.64900 / 0.34 (51111) hydrogen bonds : bond 0.05119 / 3.48 ( 2319) hydrogen bonds : angle 5.45430 / 3.80 ( 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 345 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 338 time to evaluate : 1.548 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: 0.9011 (tpp) REVERT: A 171 ASP cc_start: 0.9468 (p0) cc_final: 0.9169 (m-30) REVERT: A 295 HIS cc_start: 0.9491 (m90) cc_final: 0.9190 (m90) REVERT: B 53 MET cc_start: 0.8805 (mtm) cc_final: 0.8364 (mtm) REVERT: B 235 MET cc_start: 0.9691 (mmp) cc_final: 0.9236 (mmm) REVERT: B 238 LEU cc_start: 0.9813 (mt) cc_final: 0.9476 (pp) REVERT: B 246 MET cc_start: 0.9619 (mmp) cc_final: 0.9411 (mmm) REVERT: C 49 MET cc_start: 0.6914 (tpt) cc_final: 0.5539 (tpt) REVERT: C 63 MET cc_start: 0.9692 (tmm) cc_final: 0.9395 (tmm) REVERT: C 235 MET cc_start: 0.9344 (mpp) cc_final: 0.8817 (mpp) REVERT: C 237 TYR cc_start: 0.9676 (t80) cc_final: 0.9459 (t80) REVERT: C 356 LEU cc_start: 0.9282 (mm) cc_final: 0.9046 (mt) REVERT: C 432 MET cc_start: 0.9710 (mmp) cc_final: 0.9487 (mmp) REVERT: C 457 MET cc_start: 0.8991 (mmp) cc_final: 0.8787 (mmm) REVERT: C 484 MET cc_start: 0.9651 (mpp) cc_final: 0.9361 (mpp) REVERT: D 9 ILE cc_start: 0.9748 (pt) cc_final: 0.9385 (mp) REVERT: D 159 MET cc_start: 0.9775 (mmp) cc_final: 0.9525 (mmm) REVERT: D 192 MET cc_start: 0.9730 (ptp) cc_final: 0.9439 (ptt) REVERT: D 225 MET cc_start: 0.9770 (mmp) cc_final: 0.9393 (mmm) REVERT: D 280 MET cc_start: 0.9629 (mmp) cc_final: 0.9137 (mmm) REVERT: D 450 MET cc_start: 0.9548 (mmp) cc_final: 0.9154 (mmp) REVERT: E 158 MET cc_start: 0.9625 (tpt) cc_final: 0.9264 (tpp) REVERT: E 159 MET cc_start: 0.9726 (mmp) cc_final: 0.9402 (mmm) REVERT: E 192 MET cc_start: 0.9831 (mmm) cc_final: 0.9559 (tpp) REVERT: E 225 MET cc_start: 0.9862 (mmp) cc_final: 0.9565 (mmm) REVERT: E 262 LEU cc_start: 0.9520 (mp) cc_final: 0.9224 (pp) REVERT: E 319 HIS cc_start: 0.8765 (m90) cc_final: 0.8349 (m-70) REVERT: E 366 GLN cc_start: 0.9738 (mp10) cc_final: 0.8984 (tm-30) REVERT: F 159 MET cc_start: 0.9736 (mtm) cc_final: 0.9493 (tpt) REVERT: F 280 MET cc_start: 0.9682 (tpt) cc_final: 0.9252 (tpp) REVERT: F 285 GLU cc_start: 0.9255 (mm-30) cc_final: 0.7887 (tp30) REVERT: F 415 PHE cc_start: 0.8819 (t80) cc_final: 0.7938 (m-80) REVERT: G 34 PHE cc_start: 0.9463 (t80) cc_final: 0.9111 (t80) REVERT: H 10 ILE cc_start: 0.8892 (mm) cc_final: 0.8652 (pt) REVERT: H 55 ILE cc_start: 0.9077 (mm) cc_final: 0.8796 (mm) REVERT: J 53 PHE cc_start: 0.9660 (m-80) cc_final: 0.9409 (m-80) REVERT: J 60 ASP cc_start: 0.9150 (p0) cc_final: 0.8434 (t0) REVERT: J 64 MET cc_start: 0.9317 (mmp) cc_final: 0.8971 (mmp) REVERT: L 27 PHE cc_start: 0.9094 (m-10) cc_final: 0.8712 (m-10) REVERT: L 64 MET cc_start: 0.7911 (mtt) cc_final: 0.7368 (ttm) REVERT: S 64 MET cc_start: 0.9268 (mmp) cc_final: 0.9057 (mmm) REVERT: a 26 MET cc_start: 0.6327 (mpp) cc_final: 0.5343 (mpp) REVERT: a 125 MET cc_start: 0.8681 (ptt) cc_final: 0.8053 (ppp) REVERT: a 278 MET cc_start: 0.9805 (mmp) cc_final: 0.9474 (mmm) REVERT: b 106 LYS cc_start: 0.8715 (tttt) cc_final: 0.8390 (tptm) REVERT: b 148 MET cc_start: 0.8581 (pmm) cc_final: 0.8310 (pmm) REVERT: g 24 MET cc_start: 0.9514 (mmt) cc_final: 0.9181 (mtt) REVERT: g 32 MET cc_start: 0.9336 (ttt) cc_final: 0.8727 (ttp) REVERT: g 39 MET cc_start: 0.9518 (mmp) cc_final: 0.9270 (mmm) REVERT: g 156 MET cc_start: 0.9644 (tpt) cc_final: 0.8827 (tpp) REVERT: g 229 MET cc_start: 0.8841 (mtm) cc_final: 0.8431 (mtp) REVERT: p 110 ASP cc_start: 0.9468 (t0) cc_final: 0.9075 (p0) outliers start: 7 outliers final: 0 residues processed: 343 average time/residue: 0.2452 time to fit residues: 138.0566 Evaluate side-chains 268 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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: 8.9990 chunk 455 optimal weight: 0.0970 chunk 261 optimal weight: 0.1980 chunk 208 optimal weight: 7.9990 chunk 182 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 343 optimal weight: 20.0000 chunk 297 optimal weight: 6.9990 chunk 430 optimal weight: 1.9990 chunk 474 optimal weight: 6.9990 chunk 356 optimal weight: 10.0000 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN C 173 GLN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN E 207 GLN ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 63 GLN b 93 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.048798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.039312 restraints weight = 434860.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.040440 restraints weight = 228054.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.041188 restraints weight = 142533.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.041682 restraints weight = 99133.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.042031 restraints weight = 74738.770| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37700 Z= 0.135 Angle : 0.603 9.444 51111 Z= 0.313 Chirality : 0.042 0.269 5988 Planarity : 0.004 0.053 6628 Dihedral : 5.978 119.885 5271 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.76 % Favored : 95.22 % Rotamer: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.35 % 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: 1.05 (0.10), residues: 2664 sheet: -0.84 (0.22), residues: 513 loop : -1.48 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 215 TYR 0.025 0.001 TYR E 205 PHE 0.039 0.001 PHE J 18 TRP 0.016 0.001 TRP a 118 HIS 0.004 0.001 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (37700) covalent geometry : angle 0.60277 / 0.31 (51111) hydrogen bonds : bond 0.04479 / 3.04 ( 2319) hydrogen bonds : angle 5.07907 / 3.53 ( 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 350 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 349 time to evaluate : 1.603 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: 0.9440 (mmm) cc_final: 0.8984 (tpp) REVERT: A 49 MET cc_start: 0.7357 (tpt) cc_final: 0.7114 (tpt) REVERT: A 171 ASP cc_start: 0.9464 (p0) cc_final: 0.9229 (m-30) REVERT: A 263 ASP cc_start: 0.9016 (m-30) cc_final: 0.8799 (m-30) REVERT: A 295 HIS cc_start: 0.9471 (m90) cc_final: 0.9170 (m90) REVERT: B 49 MET cc_start: 0.7340 (mmm) cc_final: 0.6852 (tpt) REVERT: B 53 MET cc_start: 0.8754 (mtm) cc_final: 0.8332 (mtm) REVERT: B 182 ASP cc_start: 0.9633 (t0) cc_final: 0.9378 (m-30) REVERT: B 235 MET cc_start: 0.9707 (mmp) cc_final: 0.9238 (mmm) REVERT: B 238 LEU cc_start: 0.9823 (mt) cc_final: 0.9484 (pp) REVERT: B 298 LEU cc_start: 0.9586 (tp) cc_final: 0.9133 (tp) REVERT: B 299 LEU cc_start: 0.9667 (mt) cc_final: 0.9465 (pp) REVERT: C 49 MET cc_start: 0.7118 (tpt) cc_final: 0.5604 (tpt) REVERT: C 63 MET cc_start: 0.9730 (tmm) cc_final: 0.9521 (tmm) REVERT: C 182 ASP cc_start: 0.8756 (t0) cc_final: 0.8396 (t0) REVERT: C 235 MET cc_start: 0.9290 (mpp) cc_final: 0.8785 (mpp) REVERT: C 356 LEU cc_start: 0.9277 (mm) cc_final: 0.9016 (mt) REVERT: C 457 MET cc_start: 0.8958 (mmp) cc_final: 0.8740 (mmm) REVERT: C 484 MET cc_start: 0.9676 (mpp) cc_final: 0.9340 (mpp) REVERT: D 9 ILE cc_start: 0.9777 (pt) cc_final: 0.9435 (mp) REVERT: D 159 MET cc_start: 0.9807 (mmp) cc_final: 0.9479 (mmm) REVERT: D 192 MET cc_start: 0.9690 (ptp) cc_final: 0.9450 (ptt) REVERT: D 225 MET cc_start: 0.9737 (mmp) cc_final: 0.9451 (mmm) REVERT: D 450 MET cc_start: 0.9535 (mmp) cc_final: 0.9144 (mmp) REVERT: E 158 MET cc_start: 0.9645 (tpt) cc_final: 0.9219 (tpp) REVERT: E 159 MET cc_start: 0.9732 (mmp) cc_final: 0.9353 (mmm) REVERT: E 192 MET cc_start: 0.9811 (mmm) cc_final: 0.9516 (tpp) REVERT: E 225 MET cc_start: 0.9845 (mmp) cc_final: 0.9582 (mmm) REVERT: E 262 LEU cc_start: 0.9489 (mp) cc_final: 0.9254 (pp) REVERT: E 319 HIS cc_start: 0.8747 (m90) cc_final: 0.8339 (m90) REVERT: E 366 GLN cc_start: 0.9775 (mp10) cc_final: 0.9129 (tm-30) REVERT: E 372 TYR cc_start: 0.8871 (t80) cc_final: 0.8655 (t80) REVERT: F 159 MET cc_start: 0.9749 (mtm) cc_final: 0.9503 (tpt) REVERT: F 280 MET cc_start: 0.9672 (tpt) cc_final: 0.9251 (tpp) REVERT: F 285 GLU cc_start: 0.9330 (mm-30) cc_final: 0.7967 (tp30) REVERT: F 415 PHE cc_start: 0.8870 (t80) cc_final: 0.7976 (m-80) REVERT: G 34 PHE cc_start: 0.9410 (t80) cc_final: 0.9072 (t80) REVERT: H 10 ILE cc_start: 0.8857 (mm) cc_final: 0.8612 (pt) REVERT: H 55 ILE cc_start: 0.9022 (mm) cc_final: 0.8672 (mm) REVERT: J 53 PHE cc_start: 0.9508 (m-80) cc_final: 0.9228 (m-80) REVERT: J 60 ASP cc_start: 0.9185 (p0) cc_final: 0.8499 (t0) REVERT: J 64 MET cc_start: 0.9282 (mmp) cc_final: 0.9072 (mmp) REVERT: K 53 PHE cc_start: 0.9270 (m-80) cc_final: 0.8968 (m-80) REVERT: L 27 PHE cc_start: 0.9047 (m-10) cc_final: 0.8661 (m-10) REVERT: Q 71 LEU cc_start: 0.9486 (mm) cc_final: 0.9206 (pp) REVERT: R 52 MET cc_start: 0.8990 (ppp) cc_final: 0.8783 (ppp) REVERT: S 27 PHE cc_start: 0.9396 (t80) cc_final: 0.9039 (t80) REVERT: S 64 MET cc_start: 0.9265 (mmp) cc_final: 0.9042 (mmm) REVERT: a 26 MET cc_start: 0.6391 (mpp) cc_final: 0.5339 (mpp) REVERT: a 125 MET cc_start: 0.8675 (ptt) cc_final: 0.8084 (ppp) REVERT: a 278 MET cc_start: 0.9841 (mmp) cc_final: 0.9571 (mmm) REVERT: b 106 LYS cc_start: 0.8720 (tttt) cc_final: 0.8493 (tptt) REVERT: b 148 MET cc_start: 0.8479 (pmm) cc_final: 0.8223 (pmm) REVERT: d 168 LYS cc_start: 0.9712 (ptpp) cc_final: 0.9483 (ptpp) REVERT: d 171 LYS cc_start: 0.9844 (pptt) cc_final: 0.9493 (tptt) REVERT: g 32 MET cc_start: 0.9307 (ttt) cc_final: 0.8746 (ttp) REVERT: g 39 MET cc_start: 0.9539 (mmp) cc_final: 0.9317 (mmm) REVERT: g 156 MET cc_start: 0.9546 (tpp) cc_final: 0.8927 (tpp) REVERT: g 229 MET cc_start: 0.8862 (mtm) cc_final: 0.8410 (mtp) REVERT: p 110 ASP cc_start: 0.9440 (t0) cc_final: 0.9075 (p0) outliers start: 1 outliers final: 0 residues processed: 349 average time/residue: 0.2411 time to fit residues: 138.6939 Evaluate side-chains 282 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 2.235 ------------------------------------------------------------------------------- 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: 7.9990 chunk 235 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 412 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 410 optimal weight: 3.9990 chunk 405 optimal weight: 6.9990 chunk 290 optimal weight: 40.0000 chunk 392 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN A 362 ASN C 201 GLN ** C 434 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** D 366 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.047953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.038623 restraints weight = 436422.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.039706 restraints weight = 229507.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.040443 restraints weight = 143375.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.040947 restraints weight = 100458.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.041288 restraints weight = 75790.879| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2252 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= 0.150 Angle : 0.600 8.367 51111 Z= 0.312 Chirality : 0.042 0.209 5988 Planarity : 0.004 0.062 6628 Dihedral : 5.841 124.965 5271 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.82 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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: 0.16 (0.12), residues: 4851 helix: 1.20 (0.10), residues: 2665 sheet: -0.87 (0.22), residues: 531 loop : -1.31 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 371 TYR 0.030 0.001 TYR a 283 PHE 0.048 0.001 PHE L 18 TRP 0.011 0.001 TRP a 118 HIS 0.005 0.001 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (37700) covalent geometry : angle 0.59987 / 0.31 (51111) hydrogen bonds : bond 0.04202 / 2.85 ( 2319) hydrogen bonds : angle 4.93577 / 3.43 ( 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 340 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.581 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: 0.9401 (mmm) cc_final: 0.9085 (tpp) REVERT: A 171 ASP cc_start: 0.9486 (p0) cc_final: 0.9208 (m-30) REVERT: A 295 HIS cc_start: 0.9485 (m90) cc_final: 0.9205 (m90) REVERT: A 325 LEU cc_start: 0.9340 (mm) cc_final: 0.9044 (mm) REVERT: B 49 MET cc_start: 0.7866 (mmm) cc_final: 0.7305 (tpt) REVERT: B 53 MET cc_start: 0.8702 (mtm) cc_final: 0.8308 (mtm) REVERT: B 157 MET cc_start: 0.9418 (mmt) cc_final: 0.8983 (mmp) REVERT: B 182 ASP cc_start: 0.9616 (t0) cc_final: 0.9354 (m-30) REVERT: B 235 MET cc_start: 0.9709 (mmp) cc_final: 0.9250 (mmm) REVERT: B 238 LEU cc_start: 0.9827 (mt) cc_final: 0.9499 (pp) REVERT: B 246 MET cc_start: 0.9594 (mmp) cc_final: 0.9377 (mmm) REVERT: B 298 LEU cc_start: 0.9614 (tp) cc_final: 0.9157 (tp) REVERT: B 299 LEU cc_start: 0.9677 (mt) cc_final: 0.9455 (pp) REVERT: B 370 ASN cc_start: 0.9481 (t0) cc_final: 0.8836 (m-40) REVERT: C 49 MET cc_start: 0.7347 (tpt) cc_final: 0.5800 (tpt) REVERT: C 63 MET cc_start: 0.9688 (tmm) cc_final: 0.9463 (tmm) REVERT: C 182 ASP cc_start: 0.8712 (t0) cc_final: 0.8340 (t0) REVERT: C 235 MET cc_start: 0.9314 (mpp) cc_final: 0.8808 (mpp) REVERT: C 356 LEU cc_start: 0.9337 (mm) cc_final: 0.9126 (mt) REVERT: C 457 MET cc_start: 0.8946 (mmp) cc_final: 0.8729 (mmm) REVERT: C 484 MET cc_start: 0.9687 (mpp) cc_final: 0.9452 (mpp) REVERT: D 9 ILE cc_start: 0.9781 (pt) cc_final: 0.9464 (mp) REVERT: D 159 MET cc_start: 0.9805 (mmp) cc_final: 0.9503 (mmm) REVERT: D 192 MET cc_start: 0.9669 (ptp) cc_final: 0.9455 (ptt) REVERT: D 225 MET cc_start: 0.9763 (mmp) cc_final: 0.9473 (mmm) REVERT: D 258 GLU cc_start: 0.9518 (mt-10) cc_final: 0.9288 (mt-10) REVERT: D 280 MET cc_start: 0.9646 (mmp) cc_final: 0.9032 (mmm) REVERT: D 450 MET cc_start: 0.9519 (mmp) cc_final: 0.9150 (mmp) REVERT: E 158 MET cc_start: 0.9629 (tpt) cc_final: 0.9112 (tpt) REVERT: E 159 MET cc_start: 0.9717 (mmp) cc_final: 0.9309 (mmm) REVERT: E 192 MET cc_start: 0.9801 (mmm) cc_final: 0.9517 (tpp) REVERT: E 225 MET cc_start: 0.9809 (mmp) cc_final: 0.9550 (mmm) REVERT: E 262 LEU cc_start: 0.9527 (mp) cc_final: 0.9321 (pp) REVERT: E 266 MET cc_start: 0.8705 (mmt) cc_final: 0.8311 (mmp) REVERT: E 319 HIS cc_start: 0.8730 (m90) cc_final: 0.8251 (m90) REVERT: F 159 MET cc_start: 0.9741 (mtm) cc_final: 0.9482 (tpt) REVERT: F 280 MET cc_start: 0.9660 (tpt) cc_final: 0.9229 (tpp) REVERT: F 285 GLU cc_start: 0.9278 (mm-30) cc_final: 0.7935 (tp30) REVERT: F 415 PHE cc_start: 0.8874 (t80) cc_final: 0.7949 (m-80) REVERT: G 34 PHE cc_start: 0.9400 (t80) cc_final: 0.9098 (t80) REVERT: G 64 MET cc_start: 0.8290 (mmp) cc_final: 0.8042 (mmm) REVERT: G 65 ILE cc_start: 0.9010 (tt) cc_final: 0.8777 (pt) REVERT: H 10 ILE cc_start: 0.8889 (mm) cc_final: 0.8653 (pt) REVERT: K 53 PHE cc_start: 0.9264 (m-10) cc_final: 0.8960 (m-80) REVERT: L 18 PHE cc_start: 0.8167 (t80) cc_final: 0.7749 (t80) REVERT: L 27 PHE cc_start: 0.9081 (m-10) cc_final: 0.8706 (m-10) REVERT: Q 71 LEU cc_start: 0.9449 (mm) cc_final: 0.9154 (pp) REVERT: R 52 MET cc_start: 0.9028 (ppp) cc_final: 0.8807 (ppp) REVERT: S 27 PHE cc_start: 0.9337 (t80) cc_final: 0.8926 (t80) REVERT: S 64 MET cc_start: 0.9289 (mmp) cc_final: 0.9065 (mmm) REVERT: a 26 MET cc_start: 0.6611 (mpp) cc_final: 0.5562 (mpp) REVERT: a 125 MET cc_start: 0.8731 (ptt) cc_final: 0.8192 (ppp) REVERT: a 278 MET cc_start: 0.9828 (mmp) cc_final: 0.9562 (mmm) REVERT: b 106 LYS cc_start: 0.8634 (tttt) cc_final: 0.8349 (tptm) REVERT: d 168 LYS cc_start: 0.9670 (ptpp) cc_final: 0.9469 (ptpp) REVERT: d 171 LYS cc_start: 0.9822 (pptt) cc_final: 0.9572 (tptt) REVERT: e 137 ARG cc_start: 0.8047 (ptp-110) cc_final: 0.7781 (ttm110) REVERT: g 32 MET cc_start: 0.9270 (ttt) cc_final: 0.8745 (ttp) REVERT: g 156 MET cc_start: 0.9540 (tpp) cc_final: 0.8916 (tpp) REVERT: g 229 MET cc_start: 0.8909 (mtm) cc_final: 0.8447 (mtp) REVERT: p 110 ASP cc_start: 0.9431 (t0) cc_final: 0.9056 (p0) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.2346 time to fit residues: 132.8686 Evaluate side-chains 273 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.851 ------------------------------------------------------------------------------- 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: 0.0570 chunk 416 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 330 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 405 optimal weight: 0.0970 chunk 169 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 135 optimal weight: 0.0980 overall best weight: 1.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 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** D 442 HIS ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN F 367 ASN J 49 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN ** d 58 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.049109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.040048 restraints weight = 430115.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.041077 restraints weight = 213854.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.041897 restraints weight = 121291.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.042125 restraints weight = 78462.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.042187 restraints weight = 71178.969| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37700 Z= 0.123 Angle : 0.581 12.317 51111 Z= 0.299 Chirality : 0.041 0.185 5988 Planarity : 0.004 0.055 6628 Dihedral : 5.700 129.794 5271 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.29 % Favored : 95.69 % Rotamer: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.83 % 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: 0.38 (0.12), residues: 4851 helix: 1.36 (0.10), residues: 2665 sheet: -0.77 (0.22), residues: 523 loop : -1.20 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 371 TYR 0.021 0.001 TYR a 283 PHE 0.051 0.001 PHE L 18 TRP 0.008 0.001 TRP a 132 HIS 0.004 0.001 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (37700) covalent geometry : angle 0.58132 / 0.30 (51111) hydrogen bonds : bond 0.04045 / 2.74 ( 2319) hydrogen bonds : angle 4.73756 / 3.28 ( 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 344 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 1.478 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: 0.9476 (mmm) cc_final: 0.9104 (tpp) REVERT: A 49 MET cc_start: 0.7424 (tpt) cc_final: 0.6953 (tpt) REVERT: A 171 ASP cc_start: 0.9529 (p0) cc_final: 0.9269 (m-30) REVERT: A 235 MET cc_start: 0.8720 (mpp) cc_final: 0.8462 (ptp) REVERT: A 263 ASP cc_start: 0.9067 (m-30) cc_final: 0.8797 (m-30) REVERT: A 295 HIS cc_start: 0.9495 (m90) cc_final: 0.9113 (m90) REVERT: A 325 LEU cc_start: 0.9346 (mm) cc_final: 0.9005 (mm) REVERT: B 34 MET cc_start: 0.9595 (mmm) cc_final: 0.8938 (tpp) REVERT: B 53 MET cc_start: 0.8711 (mtm) cc_final: 0.8419 (mtm) REVERT: B 157 MET cc_start: 0.9384 (mmt) cc_final: 0.8992 (mmp) REVERT: B 182 ASP cc_start: 0.9596 (t0) cc_final: 0.9327 (m-30) REVERT: B 235 MET cc_start: 0.9713 (mmp) cc_final: 0.9255 (mmm) REVERT: B 238 LEU cc_start: 0.9838 (mt) cc_final: 0.9522 (pp) REVERT: B 258 LEU cc_start: 0.9797 (tp) cc_final: 0.9243 (pp) REVERT: B 298 LEU cc_start: 0.9626 (tp) cc_final: 0.9217 (tp) REVERT: C 49 MET cc_start: 0.7286 (tpt) cc_final: 0.5860 (tpt) REVERT: C 55 GLU cc_start: 0.9466 (tt0) cc_final: 0.9027 (tp30) REVERT: C 63 MET cc_start: 0.9725 (tmm) cc_final: 0.9400 (tmm) REVERT: C 182 ASP cc_start: 0.8758 (t0) cc_final: 0.8366 (t0) REVERT: C 235 MET cc_start: 0.9262 (mpp) cc_final: 0.8781 (mpp) REVERT: C 457 MET cc_start: 0.8911 (mmp) cc_final: 0.8705 (mmm) REVERT: C 484 MET cc_start: 0.9715 (mpp) cc_final: 0.9467 (mpp) REVERT: D 9 ILE cc_start: 0.9783 (pt) cc_final: 0.9472 (mp) REVERT: D 159 MET cc_start: 0.9805 (mmp) cc_final: 0.9489 (mmm) REVERT: D 225 MET cc_start: 0.9754 (mmp) cc_final: 0.9478 (mmm) REVERT: D 280 MET cc_start: 0.9647 (mmp) cc_final: 0.9046 (mmm) REVERT: D 450 MET cc_start: 0.9555 (mmp) cc_final: 0.9166 (mmp) REVERT: E 158 MET cc_start: 0.9658 (tpt) cc_final: 0.9109 (tpt) REVERT: E 159 MET cc_start: 0.9714 (mmp) cc_final: 0.9291 (mmm) REVERT: E 192 MET cc_start: 0.9780 (mmm) cc_final: 0.9496 (tpp) REVERT: E 225 MET cc_start: 0.9779 (mmp) cc_final: 0.9565 (mmm) REVERT: E 262 LEU cc_start: 0.9505 (mp) cc_final: 0.9291 (pp) REVERT: E 266 MET cc_start: 0.8774 (mmt) cc_final: 0.8417 (mmp) REVERT: E 319 HIS cc_start: 0.8753 (m90) cc_final: 0.8243 (m90) REVERT: E 372 TYR cc_start: 0.8800 (t80) cc_final: 0.8490 (t80) REVERT: F 39 LEU cc_start: 0.9817 (mp) cc_final: 0.9491 (mp) REVERT: F 159 MET cc_start: 0.9752 (mtm) cc_final: 0.9501 (tpt) REVERT: F 280 MET cc_start: 0.9665 (tpt) cc_final: 0.9235 (tpp) REVERT: F 285 GLU cc_start: 0.9260 (mm-30) cc_final: 0.7892 (tp30) REVERT: G 34 PHE cc_start: 0.9426 (t80) cc_final: 0.9029 (t80) REVERT: G 64 MET cc_start: 0.8175 (mmp) cc_final: 0.7973 (mmp) REVERT: G 65 ILE cc_start: 0.8963 (tt) cc_final: 0.8734 (pt) REVERT: H 10 ILE cc_start: 0.8891 (mm) cc_final: 0.8653 (pt) REVERT: H 55 ILE cc_start: 0.8937 (mm) cc_final: 0.8725 (mm) REVERT: J 53 PHE cc_start: 0.9619 (m-80) cc_final: 0.9294 (m-80) REVERT: J 60 ASP cc_start: 0.9333 (p0) cc_final: 0.8698 (t0) REVERT: K 53 PHE cc_start: 0.9235 (m-10) cc_final: 0.8934 (m-80) REVERT: L 18 PHE cc_start: 0.8196 (t80) cc_final: 0.7659 (t80) REVERT: L 27 PHE cc_start: 0.9086 (m-10) cc_final: 0.8714 (m-10) REVERT: Q 71 LEU cc_start: 0.9452 (mm) cc_final: 0.9166 (pp) REVERT: S 27 PHE cc_start: 0.9313 (t80) cc_final: 0.8852 (t80) REVERT: S 64 MET cc_start: 0.9303 (mmp) cc_final: 0.9080 (mmm) REVERT: a 26 MET cc_start: 0.6472 (mpp) cc_final: 0.5500 (mpp) REVERT: a 125 MET cc_start: 0.8748 (ptt) cc_final: 0.8159 (ppp) REVERT: a 236 MET cc_start: 0.8695 (ttp) cc_final: 0.8457 (ttm) REVERT: a 278 MET cc_start: 0.9818 (mmp) cc_final: 0.9548 (mmm) REVERT: b 106 LYS cc_start: 0.8612 (tttt) cc_final: 0.8311 (tptt) REVERT: d 171 LYS cc_start: 0.9814 (pptt) cc_final: 0.9591 (tptt) REVERT: g 32 MET cc_start: 0.9268 (ttt) cc_final: 0.8790 (ttp) REVERT: g 39 MET cc_start: 0.9542 (mmp) cc_final: 0.9313 (mmm) REVERT: g 156 MET cc_start: 0.9552 (tpp) cc_final: 0.8927 (tpp) REVERT: g 229 MET cc_start: 0.8901 (mtm) cc_final: 0.8435 (mtp) REVERT: p 110 ASP cc_start: 0.9420 (t0) cc_final: 0.9017 (p0) outliers start: 1 outliers final: 1 residues processed: 344 average time/residue: 0.2313 time to fit residues: 133.0337 Evaluate side-chains 277 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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: 9.9990 chunk 7 optimal weight: 0.5980 chunk 421 optimal weight: 20.0000 chunk 265 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 441 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 250 optimal weight: 8.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 436 GLN D 186 ASN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 63 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.036496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.025574 restraints weight = 411291.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.026415 restraints weight = 277456.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.027029 restraints weight = 206560.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.027488 restraints weight = 165400.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.027810 restraints weight = 139598.078| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2751 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= 0.138 Angle : 0.588 9.664 51111 Z= 0.303 Chirality : 0.042 0.327 5988 Planarity : 0.004 0.069 6628 Dihedral : 5.643 136.394 5271 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.45 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: 0.48 (0.12), residues: 4851 helix: 1.42 (0.10), residues: 2676 sheet: -0.80 (0.22), residues: 539 loop : -1.08 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 371 TYR 0.035 0.001 TYR E 372 PHE 0.035 0.001 PHE J 53 TRP 0.010 0.001 TRP a 132 HIS 0.004 0.001 HIS F 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (37700) covalent geometry : angle 0.58765 / 0.30 (51111) hydrogen bonds : bond 0.03945 / 2.68 ( 2319) hydrogen bonds : angle 4.70048 / 3.26 ( 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 323 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 1.537 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: 0.9419 (mmm) cc_final: 0.9064 (tpp) REVERT: A 49 MET cc_start: 0.7783 (tpt) cc_final: 0.7325 (tpt) REVERT: A 171 ASP cc_start: 0.9592 (p0) cc_final: 0.9241 (m-30) REVERT: A 246 MET cc_start: 0.9785 (mmp) cc_final: 0.9578 (mmm) REVERT: A 263 ASP cc_start: 0.9153 (m-30) cc_final: 0.8913 (m-30) REVERT: A 295 HIS cc_start: 0.9494 (m90) cc_final: 0.9080 (m90) REVERT: A 325 LEU cc_start: 0.9331 (mm) cc_final: 0.9046 (mm) REVERT: B 1 MET cc_start: 0.9307 (ppp) cc_final: 0.9096 (tpp) REVERT: B 34 MET cc_start: 0.9647 (mmm) cc_final: 0.8983 (tpp) REVERT: B 49 MET cc_start: 0.8066 (mmm) cc_final: 0.7414 (tpt) REVERT: B 53 MET cc_start: 0.8576 (mtm) cc_final: 0.8299 (mtm) REVERT: B 157 MET cc_start: 0.9379 (mmt) cc_final: 0.9026 (mmp) REVERT: B 182 ASP cc_start: 0.9590 (t0) cc_final: 0.9308 (m-30) REVERT: B 235 MET cc_start: 0.9721 (mmp) cc_final: 0.9262 (mmm) REVERT: B 238 LEU cc_start: 0.9837 (mt) cc_final: 0.9530 (pp) REVERT: B 246 MET cc_start: 0.9640 (mmp) cc_final: 0.9383 (mmm) REVERT: B 258 LEU cc_start: 0.9771 (tp) cc_final: 0.9153 (pp) REVERT: B 298 LEU cc_start: 0.9584 (tp) cc_final: 0.9218 (tp) REVERT: C 49 MET cc_start: 0.7531 (tpt) cc_final: 0.5887 (tpt) REVERT: C 63 MET cc_start: 0.9735 (tmm) cc_final: 0.9508 (tmm) REVERT: C 182 ASP cc_start: 0.8876 (t0) cc_final: 0.8506 (t0) REVERT: C 235 MET cc_start: 0.9276 (mpp) cc_final: 0.8666 (mpp) REVERT: C 457 MET cc_start: 0.9155 (mmp) cc_final: 0.8952 (mmm) REVERT: C 484 MET cc_start: 0.9734 (mpp) cc_final: 0.9456 (mpp) REVERT: D 9 ILE cc_start: 0.9773 (pt) cc_final: 0.9455 (mp) REVERT: D 159 MET cc_start: 0.9816 (mmp) cc_final: 0.9515 (mmm) REVERT: D 225 MET cc_start: 0.9755 (mmp) cc_final: 0.9468 (mmm) REVERT: D 245 PHE cc_start: 0.9535 (m-10) cc_final: 0.9316 (m-10) REVERT: D 280 MET cc_start: 0.9674 (mmp) cc_final: 0.9098 (mmm) REVERT: D 450 MET cc_start: 0.9513 (mmp) cc_final: 0.9120 (mmp) REVERT: E 158 MET cc_start: 0.9637 (tpt) cc_final: 0.9116 (tpt) REVERT: E 159 MET cc_start: 0.9713 (mmp) cc_final: 0.9279 (mmm) REVERT: E 192 MET cc_start: 0.9807 (mmm) cc_final: 0.9540 (tpp) REVERT: E 225 MET cc_start: 0.9750 (mmp) cc_final: 0.9544 (mmm) REVERT: E 262 LEU cc_start: 0.9522 (mp) cc_final: 0.9313 (pp) REVERT: E 266 MET cc_start: 0.8676 (mmt) cc_final: 0.8308 (mmm) REVERT: E 319 HIS cc_start: 0.8709 (m90) cc_final: 0.8187 (m90) REVERT: E 366 GLN cc_start: 0.9774 (mp-120) cc_final: 0.9184 (tm-30) REVERT: E 372 TYR cc_start: 0.8546 (t80) cc_final: 0.8273 (t80) REVERT: F 159 MET cc_start: 0.9788 (mtm) cc_final: 0.9542 (tpt) REVERT: F 280 MET cc_start: 0.9696 (tpt) cc_final: 0.9427 (ptt) REVERT: F 285 GLU cc_start: 0.9398 (mm-30) cc_final: 0.8079 (tp30) REVERT: F 415 PHE cc_start: 0.9009 (t80) cc_final: 0.8267 (m-80) REVERT: G 30 LEU cc_start: 0.9290 (pp) cc_final: 0.9023 (mt) REVERT: G 34 PHE cc_start: 0.9435 (t80) cc_final: 0.9135 (t80) REVERT: G 64 MET cc_start: 0.8254 (mmp) cc_final: 0.8042 (mmp) REVERT: J 53 PHE cc_start: 0.9505 (m-80) cc_final: 0.9226 (m-80) REVERT: J 59 LEU cc_start: 0.8632 (tt) cc_final: 0.8169 (tt) REVERT: J 60 ASP cc_start: 0.9225 (p0) cc_final: 0.8757 (t0) REVERT: K 53 PHE cc_start: 0.9213 (m-10) cc_final: 0.8918 (m-80) REVERT: L 18 PHE cc_start: 0.8135 (t80) cc_final: 0.7858 (t80) REVERT: L 27 PHE cc_start: 0.9057 (m-10) cc_final: 0.8728 (m-10) REVERT: Q 71 LEU cc_start: 0.9479 (mm) cc_final: 0.9168 (pp) REVERT: R 52 MET cc_start: 0.8920 (ppp) cc_final: 0.8719 (ppp) REVERT: S 27 PHE cc_start: 0.9264 (t80) cc_final: 0.8794 (t80) REVERT: S 64 MET cc_start: 0.9306 (mmp) cc_final: 0.9067 (mmp) REVERT: a 26 MET cc_start: 0.6870 (mpp) cc_final: 0.5615 (mpp) REVERT: a 125 MET cc_start: 0.8754 (ptt) cc_final: 0.8367 (ppp) REVERT: a 236 MET cc_start: 0.8694 (ttp) cc_final: 0.8318 (ttm) REVERT: b 106 LYS cc_start: 0.8547 (tttt) cc_final: 0.8301 (tptm) REVERT: d 172 MET cc_start: 0.9762 (ppp) cc_final: 0.9561 (ppp) REVERT: g 32 MET cc_start: 0.9214 (ttt) cc_final: 0.8757 (ttp) REVERT: g 156 MET cc_start: 0.9567 (tpp) cc_final: 0.8987 (tpp) REVERT: g 229 MET cc_start: 0.8903 (mtm) cc_final: 0.8446 (mtp) REVERT: p 110 ASP cc_start: 0.9407 (t0) cc_final: 0.9060 (p0) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.2270 time to fit residues: 123.8363 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 : 1.422 ------------------------------------------------------------------------------- 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: 10.0000 chunk 70 optimal weight: 10.0000 chunk 442 optimal weight: 3.9990 chunk 454 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 315 optimal weight: 20.0000 chunk 406 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 chunk 142 optimal weight: 30.0000 chunk 455 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 ASN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 366 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 HIS F 358 HIS F 366 GLN G 47 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.039119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.028629 restraints weight = 444606.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.029574 restraints weight = 277577.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.030245 restraints weight = 196961.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.030681 restraints weight = 153279.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.031052 restraints weight = 128738.965| |-----------------------------------------------------------------------------| r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 37700 Z= 0.233 Angle : 0.682 8.724 51111 Z= 0.356 Chirality : 0.043 0.266 5988 Planarity : 0.005 0.060 6628 Dihedral : 5.835 140.521 5271 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.55 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: 0.13 (0.12), residues: 4851 helix: 1.09 (0.10), residues: 2685 sheet: -0.96 (0.21), residues: 552 loop : -1.16 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG d 175 TYR 0.031 0.002 TYR E 372 PHE 0.038 0.002 PHE p 17 TRP 0.011 0.001 TRP a 132 HIS 0.007 0.001 HIS E 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.23 (37700) covalent geometry : angle 0.68154 / 0.36 (51111) hydrogen bonds : bond 0.04222 / 2.86 ( 2319) hydrogen bonds : angle 4.99639 / 3.46 ( 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 306 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.656 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: 0.9346 (mmm) cc_final: 0.9004 (mmm) REVERT: A 171 ASP cc_start: 0.9602 (p0) cc_final: 0.9350 (t70) REVERT: A 235 MET cc_start: 0.8870 (mpp) cc_final: 0.8168 (ptp) REVERT: A 238 LEU cc_start: 0.9695 (mt) cc_final: 0.9460 (pp) REVERT: A 295 HIS cc_start: 0.9461 (m90) cc_final: 0.9051 (m90) REVERT: A 328 LEU cc_start: 0.9762 (mt) cc_final: 0.9552 (mt) REVERT: B 34 MET cc_start: 0.9712 (mmm) cc_final: 0.9060 (tpp) REVERT: B 53 MET cc_start: 0.8564 (mtm) cc_final: 0.8288 (mtm) REVERT: B 157 MET cc_start: 0.9355 (mmt) cc_final: 0.9021 (mmm) REVERT: B 182 ASP cc_start: 0.9630 (t0) cc_final: 0.9338 (m-30) REVERT: B 235 MET cc_start: 0.9731 (mmp) cc_final: 0.9339 (mmm) REVERT: B 238 LEU cc_start: 0.9852 (mt) cc_final: 0.9557 (pp) REVERT: B 246 MET cc_start: 0.9605 (mmp) cc_final: 0.9360 (mmm) REVERT: B 298 LEU cc_start: 0.9636 (tp) cc_final: 0.9285 (tp) REVERT: C 49 MET cc_start: 0.8031 (tpt) cc_final: 0.6069 (tpt) REVERT: C 63 MET cc_start: 0.9735 (tmm) cc_final: 0.9532 (tmm) REVERT: C 235 MET cc_start: 0.9335 (mpp) cc_final: 0.8941 (mpp) REVERT: C 457 MET cc_start: 0.9300 (mmp) cc_final: 0.9098 (mmm) REVERT: C 484 MET cc_start: 0.9622 (mpp) cc_final: 0.9364 (mpp) REVERT: D 9 ILE cc_start: 0.9799 (pt) cc_final: 0.9511 (mp) REVERT: D 159 MET cc_start: 0.9823 (mmp) cc_final: 0.9499 (mmm) REVERT: D 225 MET cc_start: 0.9796 (mmp) cc_final: 0.9512 (mmm) REVERT: D 258 GLU cc_start: 0.9534 (mt-10) cc_final: 0.9275 (mt-10) REVERT: D 450 MET cc_start: 0.9315 (mmp) cc_final: 0.8983 (mmp) REVERT: E 158 MET cc_start: 0.9613 (tpt) cc_final: 0.9071 (tpt) REVERT: E 159 MET cc_start: 0.9729 (mmp) cc_final: 0.9279 (mmm) REVERT: E 192 MET cc_start: 0.9810 (mmm) cc_final: 0.9532 (tpp) REVERT: E 225 MET cc_start: 0.9720 (mmp) cc_final: 0.9511 (mmm) REVERT: E 266 MET cc_start: 0.8981 (mmt) cc_final: 0.8571 (mmm) REVERT: E 319 HIS cc_start: 0.8721 (m90) cc_final: 0.8257 (m90) REVERT: E 372 TYR cc_start: 0.8709 (t80) cc_final: 0.8381 (t80) REVERT: F 159 MET cc_start: 0.9791 (mtm) cc_final: 0.9470 (tpt) REVERT: F 280 MET cc_start: 0.9721 (tpt) cc_final: 0.9371 (tpp) REVERT: F 285 GLU cc_start: 0.9407 (mm-30) cc_final: 0.8083 (tp30) REVERT: F 415 PHE cc_start: 0.8958 (t80) cc_final: 0.8199 (m-80) REVERT: G 34 PHE cc_start: 0.9517 (t80) cc_final: 0.9131 (t80) REVERT: J 53 PHE cc_start: 0.9581 (m-80) cc_final: 0.9326 (m-80) REVERT: J 60 ASP cc_start: 0.9323 (p0) cc_final: 0.8754 (t0) REVERT: K 53 PHE cc_start: 0.9196 (m-10) cc_final: 0.8907 (m-80) REVERT: L 27 PHE cc_start: 0.9049 (m-10) cc_final: 0.8693 (m-10) REVERT: R 52 MET cc_start: 0.8985 (ppp) cc_final: 0.8773 (ppp) REVERT: S 27 PHE cc_start: 0.9235 (t80) cc_final: 0.8772 (t80) REVERT: S 64 MET cc_start: 0.9309 (mmp) cc_final: 0.9091 (mmm) REVERT: a 26 MET cc_start: 0.7508 (mpp) cc_final: 0.6045 (mpp) REVERT: a 125 MET cc_start: 0.8781 (ptt) cc_final: 0.8479 (ppp) REVERT: b 106 LYS cc_start: 0.8623 (tttt) cc_final: 0.8291 (tptt) REVERT: e 88 ASN cc_start: 0.9113 (t0) cc_final: 0.8820 (t0) REVERT: e 91 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6967 (pm20) REVERT: g 32 MET cc_start: 0.9241 (ttt) cc_final: 0.8795 (ttp) REVERT: g 156 MET cc_start: 0.9570 (tpp) cc_final: 0.9078 (tpp) REVERT: g 229 MET cc_start: 0.8931 (mtm) cc_final: 0.8484 (mtp) REVERT: p 110 ASP cc_start: 0.9460 (t0) cc_final: 0.9119 (p0) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2313 time to fit residues: 118.7496 Evaluate side-chains 261 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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: 6.9990 chunk 388 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 410 optimal weight: 9.9990 chunk 109 optimal weight: 0.0770 chunk 54 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 296 optimal weight: 9.9990 chunk 247 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN G 47 GLN ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.036024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.025174 restraints weight = 413690.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.026029 restraints weight = 280120.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.026651 restraints weight = 206694.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.027098 restraints weight = 164979.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.027439 restraints weight = 138846.253| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3051 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= 0.132 Angle : 0.606 15.757 51111 Z= 0.311 Chirality : 0.042 0.248 5988 Planarity : 0.004 0.052 6628 Dihedral : 5.686 145.843 5271 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: 0.39 (0.12), residues: 4851 helix: 1.32 (0.10), residues: 2679 sheet: -0.85 (0.21), residues: 544 loop : -1.08 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 371 TYR 0.025 0.001 TYR E 372 PHE 0.032 0.001 PHE p 17 TRP 0.014 0.001 TRP a 55 HIS 0.004 0.001 HIS D 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (37700) covalent geometry : angle 0.60643 / 0.31 (51111) hydrogen bonds : bond 0.03949 / 2.67 ( 2319) hydrogen bonds : angle 4.74594 / 3.28 ( 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 322 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.517 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: 0.9431 (mmm) cc_final: 0.9094 (tpp) REVERT: A 49 MET cc_start: 0.8167 (tpt) cc_final: 0.7644 (tpt) REVERT: A 171 ASP cc_start: 0.9591 (p0) cc_final: 0.9370 (t70) REVERT: A 235 MET cc_start: 0.8792 (mpp) cc_final: 0.8526 (ptp) REVERT: A 246 MET cc_start: 0.9795 (mmp) cc_final: 0.9543 (mmm) REVERT: A 263 ASP cc_start: 0.9140 (m-30) cc_final: 0.8903 (m-30) REVERT: A 295 HIS cc_start: 0.9472 (m90) cc_final: 0.9063 (m90) REVERT: A 325 LEU cc_start: 0.9346 (mm) cc_final: 0.9055 (mm) REVERT: B 34 MET cc_start: 0.9688 (mmm) cc_final: 0.9008 (tpp) REVERT: B 49 MET cc_start: 0.8172 (tpt) cc_final: 0.7635 (tpt) REVERT: B 53 MET cc_start: 0.8612 (mtm) cc_final: 0.8354 (mtm) REVERT: B 157 MET cc_start: 0.9341 (mmt) cc_final: 0.9030 (mmm) REVERT: B 182 ASP cc_start: 0.9587 (t0) cc_final: 0.9299 (m-30) REVERT: B 235 MET cc_start: 0.9710 (mmp) cc_final: 0.9266 (mmm) REVERT: B 238 LEU cc_start: 0.9837 (mt) cc_final: 0.9529 (pp) REVERT: B 246 MET cc_start: 0.9611 (mmp) cc_final: 0.9394 (mmm) REVERT: B 298 LEU cc_start: 0.9615 (tp) cc_final: 0.9253 (tp) REVERT: C 49 MET cc_start: 0.7750 (tpt) cc_final: 0.6123 (tpt) REVERT: C 63 MET cc_start: 0.9708 (tmm) cc_final: 0.9461 (tmm) REVERT: C 235 MET cc_start: 0.9269 (mpp) cc_final: 0.8730 (mpp) REVERT: C 457 MET cc_start: 0.9217 (mmp) cc_final: 0.8994 (mmm) REVERT: C 484 MET cc_start: 0.9652 (mpp) cc_final: 0.9343 (mpp) REVERT: D 9 ILE cc_start: 0.9794 (pt) cc_final: 0.9495 (mp) REVERT: D 55 MET cc_start: 0.8718 (mmp) cc_final: 0.8140 (mmp) REVERT: D 159 MET cc_start: 0.9800 (mmp) cc_final: 0.9487 (mmm) REVERT: D 225 MET cc_start: 0.9781 (mmp) cc_final: 0.9495 (mmm) REVERT: D 258 GLU cc_start: 0.9536 (mt-10) cc_final: 0.9258 (mt-10) REVERT: D 280 MET cc_start: 0.9670 (mmp) cc_final: 0.9121 (mmm) REVERT: D 450 MET cc_start: 0.9440 (mmp) cc_final: 0.9231 (mmm) REVERT: E 158 MET cc_start: 0.9695 (tpt) cc_final: 0.9237 (tpt) REVERT: E 159 MET cc_start: 0.9709 (mmp) cc_final: 0.9413 (mmm) REVERT: E 192 MET cc_start: 0.9805 (mmm) cc_final: 0.9524 (tpp) REVERT: E 266 MET cc_start: 0.8856 (mmt) cc_final: 0.8480 (mmm) REVERT: E 319 HIS cc_start: 0.8682 (m90) cc_final: 0.8125 (m90) REVERT: E 450 MET cc_start: 0.9092 (tpp) cc_final: 0.8825 (tpp) REVERT: F 252 TYR cc_start: 0.9751 (t80) cc_final: 0.9203 (t80) REVERT: F 280 MET cc_start: 0.9646 (tpt) cc_final: 0.9325 (tpp) REVERT: F 285 GLU cc_start: 0.9410 (mm-30) cc_final: 0.8022 (tp30) REVERT: F 415 PHE cc_start: 0.8961 (t80) cc_final: 0.8207 (m-80) REVERT: G 34 PHE cc_start: 0.9542 (t80) cc_final: 0.9220 (t80) REVERT: H 55 ILE cc_start: 0.8593 (mm) cc_final: 0.8282 (mm) REVERT: J 53 PHE cc_start: 0.9541 (m-80) cc_final: 0.9338 (m-80) REVERT: J 59 LEU cc_start: 0.8572 (tt) cc_final: 0.8329 (tt) REVERT: J 60 ASP cc_start: 0.9225 (p0) cc_final: 0.8740 (t0) REVERT: K 53 PHE cc_start: 0.9200 (m-10) cc_final: 0.8914 (m-80) REVERT: L 27 PHE cc_start: 0.9065 (m-10) cc_final: 0.8721 (m-10) REVERT: R 52 MET cc_start: 0.8971 (ppp) cc_final: 0.8675 (ppp) REVERT: S 27 PHE cc_start: 0.9251 (t80) cc_final: 0.8757 (t80) REVERT: S 64 MET cc_start: 0.9315 (mmp) cc_final: 0.9078 (mmp) REVERT: a 26 MET cc_start: 0.7068 (mpp) cc_final: 0.5726 (mpp) REVERT: a 236 MET cc_start: 0.8830 (ttt) cc_final: 0.7729 (ppp) REVERT: b 106 LYS cc_start: 0.8610 (tttt) cc_final: 0.8347 (tptm) REVERT: e 88 ASN cc_start: 0.9125 (t0) cc_final: 0.8852 (t0) REVERT: e 91 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6848 (pm20) REVERT: g 32 MET cc_start: 0.9284 (ttt) cc_final: 0.8996 (ttp) REVERT: g 156 MET cc_start: 0.9574 (tpp) cc_final: 0.9033 (tpp) REVERT: g 229 MET cc_start: 0.8885 (mtm) cc_final: 0.8434 (mtp) REVERT: g 246 MET cc_start: 0.9083 (ptp) cc_final: 0.8815 (ptp) REVERT: p 110 ASP cc_start: 0.9435 (t0) cc_final: 0.9094 (p0) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2313 time to fit residues: 124.5416 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 : 1.493 ------------------------------------------------------------------------------- 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: 4.9990 chunk 377 optimal weight: 0.7980 chunk 353 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 chunk 407 optimal weight: 1.9990 chunk 405 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 450 optimal weight: 0.7980 chunk 322 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 GLN B 486 GLN ** 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 63 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.036085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.025382 restraints weight = 421528.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.026228 restraints weight = 284890.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.026854 restraints weight = 210133.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.027284 restraints weight = 166954.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.027625 restraints weight = 141701.683| |-----------------------------------------------------------------------------| r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3209 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= 0.141 Angle : 0.607 12.820 51111 Z= 0.311 Chirality : 0.042 0.306 5988 Planarity : 0.004 0.063 6628 Dihedral : 5.614 148.286 5271 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.82 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 0.46 (0.12), residues: 4851 helix: 1.38 (0.10), residues: 2676 sheet: -0.82 (0.21), residues: 545 loop : -1.04 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 371 TYR 0.045 0.001 TYR E 372 PHE 0.029 0.001 PHE p 17 TRP 0.009 0.001 TRP p 26 HIS 0.004 0.001 HIS E 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (37700) covalent geometry : angle 0.60651 / 0.31 (51111) hydrogen bonds : bond 0.03871 / 2.62 ( 2319) hydrogen bonds : angle 4.71620 / 3.26 ( 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 317 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.534 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: A 34 MET cc_start: 0.9447 (mmm) cc_final: 0.9096 (tpp) REVERT: A 49 MET cc_start: 0.8303 (tpt) cc_final: 0.7741 (tpt) REVERT: A 171 ASP cc_start: 0.9581 (p0) cc_final: 0.9349 (t70) REVERT: A 235 MET cc_start: 0.8824 (mpp) cc_final: 0.8154 (ptp) REVERT: A 238 LEU cc_start: 0.9681 (mt) cc_final: 0.9409 (pp) REVERT: A 263 ASP cc_start: 0.9155 (m-30) cc_final: 0.8909 (m-30) REVERT: A 295 HIS cc_start: 0.9469 (m90) cc_final: 0.9052 (m90) REVERT: B 34 MET cc_start: 0.9722 (mmm) cc_final: 0.8998 (tpp) REVERT: B 53 MET cc_start: 0.8623 (mtm) cc_final: 0.8387 (mtm) REVERT: B 157 MET cc_start: 0.9358 (mmt) cc_final: 0.9048 (mmm) REVERT: B 182 ASP cc_start: 0.9564 (t0) cc_final: 0.9264 (m-30) REVERT: B 235 MET cc_start: 0.9713 (mmp) cc_final: 0.9278 (mmm) REVERT: B 238 LEU cc_start: 0.9843 (mt) cc_final: 0.9542 (pp) REVERT: B 246 MET cc_start: 0.9604 (mmp) cc_final: 0.9396 (mmm) REVERT: B 298 LEU cc_start: 0.9644 (tp) cc_final: 0.9289 (tp) REVERT: C 49 MET cc_start: 0.7757 (tpt) cc_final: 0.6056 (tpt) REVERT: C 63 MET cc_start: 0.9731 (tmm) cc_final: 0.9481 (tmm) REVERT: C 235 MET cc_start: 0.9280 (mpp) cc_final: 0.8915 (mpp) REVERT: C 356 LEU cc_start: 0.9418 (mm) cc_final: 0.9205 (mt) REVERT: C 457 MET cc_start: 0.9217 (mmp) cc_final: 0.8992 (mmm) REVERT: C 484 MET cc_start: 0.9657 (mpp) cc_final: 0.9349 (mpp) REVERT: D 9 ILE cc_start: 0.9800 (pt) cc_final: 0.9511 (mp) REVERT: D 115 TYR cc_start: 0.9362 (t80) cc_final: 0.9138 (t80) REVERT: D 225 MET cc_start: 0.9797 (mmp) cc_final: 0.9506 (mmm) REVERT: D 258 GLU cc_start: 0.9530 (mt-10) cc_final: 0.9249 (mt-10) REVERT: D 280 MET cc_start: 0.9673 (mmp) cc_final: 0.9136 (mmm) REVERT: D 450 MET cc_start: 0.9436 (mmp) cc_final: 0.9216 (mmm) REVERT: E 87 MET cc_start: 0.9173 (mpp) cc_final: 0.8883 (mpp) REVERT: E 158 MET cc_start: 0.9681 (tpt) cc_final: 0.9046 (tpp) REVERT: E 159 MET cc_start: 0.9699 (mmp) cc_final: 0.9242 (mmm) REVERT: E 192 MET cc_start: 0.9769 (mmm) cc_final: 0.9456 (tpp) REVERT: E 225 MET cc_start: 0.9841 (mmp) cc_final: 0.9569 (mmm) REVERT: E 266 MET cc_start: 0.8873 (mmt) cc_final: 0.8492 (mmm) REVERT: E 319 HIS cc_start: 0.8692 (m90) cc_final: 0.8149 (m90) REVERT: E 450 MET cc_start: 0.9084 (tpp) cc_final: 0.8823 (tpp) REVERT: F 252 TYR cc_start: 0.9747 (t80) cc_final: 0.9188 (t80) REVERT: F 280 MET cc_start: 0.9646 (tpt) cc_final: 0.9317 (tpp) REVERT: F 285 GLU cc_start: 0.9397 (mm-30) cc_final: 0.8033 (tp30) REVERT: F 415 PHE cc_start: 0.8954 (t80) cc_final: 0.8185 (m-80) REVERT: G 30 LEU cc_start: 0.9355 (pp) cc_final: 0.9154 (mt) REVERT: G 34 PHE cc_start: 0.9488 (t80) cc_final: 0.9197 (t80) REVERT: J 59 LEU cc_start: 0.8618 (tt) cc_final: 0.8229 (tt) REVERT: J 60 ASP cc_start: 0.9226 (p0) cc_final: 0.8715 (t0) REVERT: K 53 PHE cc_start: 0.9193 (m-10) cc_final: 0.8913 (m-80) REVERT: L 18 PHE cc_start: 0.8210 (t80) cc_final: 0.7983 (t80) REVERT: L 27 PHE cc_start: 0.9052 (m-10) cc_final: 0.8799 (m-10) REVERT: L 60 ASP cc_start: 0.9257 (t0) cc_final: 0.8993 (p0) REVERT: O 52 MET cc_start: 0.9255 (ppp) cc_final: 0.9051 (ppp) REVERT: R 52 MET cc_start: 0.8885 (ppp) cc_final: 0.8667 (ppp) REVERT: S 27 PHE cc_start: 0.9252 (t80) cc_final: 0.8739 (t80) REVERT: S 64 MET cc_start: 0.9315 (mmp) cc_final: 0.9077 (mmp) REVERT: a 26 MET cc_start: 0.7137 (mpp) cc_final: 0.5743 (mpp) REVERT: a 236 MET cc_start: 0.8970 (ttt) cc_final: 0.8569 (ttt) REVERT: b 106 LYS cc_start: 0.8581 (tttt) cc_final: 0.8241 (tptt) REVERT: e 88 ASN cc_start: 0.9165 (t0) cc_final: 0.8912 (t0) REVERT: e 91 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6921 (pm20) REVERT: g 32 MET cc_start: 0.9290 (ttt) cc_final: 0.8977 (ttp) REVERT: g 156 MET cc_start: 0.9585 (tpp) cc_final: 0.9059 (tpp) REVERT: g 229 MET cc_start: 0.8910 (mtm) cc_final: 0.8448 (mtp) REVERT: g 246 MET cc_start: 0.9024 (ptp) cc_final: 0.8812 (ptp) REVERT: p 110 ASP cc_start: 0.9418 (t0) cc_final: 0.9084 (p0) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2265 time to fit residues: 121.4031 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 : 1.512 ------------------------------------------------------------------------------- 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: 8.9990 chunk 120 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 396 optimal weight: 9.9990 chunk 417 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 chunk 458 optimal weight: 10.0000 chunk 423 optimal weight: 4.9990 chunk 381 optimal weight: 0.6980 chunk 123 optimal weight: 8.9990 chunk 435 optimal weight: 9.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 122 GLN b 137 ASN ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 272 GLN p 138 GLN ** p 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 146 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.044923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.036355 restraints weight = 450141.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.037354 restraints weight = 225916.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.038109 restraints weight = 127981.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.038166 restraints weight = 91554.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.038342 restraints weight = 82260.319| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 37700 Z= 0.236 Angle : 0.704 12.986 51111 Z= 0.366 Chirality : 0.043 0.269 5988 Planarity : 0.005 0.063 6628 Dihedral : 5.903 145.222 5271 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.59 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 0.08 (0.12), residues: 4851 helix: 1.04 (0.10), residues: 2692 sheet: -0.99 (0.21), residues: 561 loop : -1.15 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG e 132 TYR 0.043 0.002 TYR E 372 PHE 0.033 0.002 PHE J 18 TRP 0.021 0.002 TRP a 55 HIS 0.008 0.001 HIS D 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.24 (37700) covalent geometry : angle 0.70396 / 0.37 (51111) hydrogen bonds : bond 0.04204 / 2.85 ( 2319) hydrogen bonds : angle 5.02118 / 3.48 ( 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 300 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.518 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: 0.9433 (mmm) cc_final: 0.9144 (mmm) REVERT: A 235 MET cc_start: 0.8771 (mpp) cc_final: 0.8509 (mpp) REVERT: A 238 LEU cc_start: 0.9681 (mt) cc_final: 0.9427 (pp) REVERT: A 246 MET cc_start: 0.9781 (mmp) cc_final: 0.9530 (mmm) REVERT: A 295 HIS cc_start: 0.9457 (m90) cc_final: 0.9074 (m90) REVERT: B 34 MET cc_start: 0.9725 (mmm) cc_final: 0.8898 (tpp) REVERT: B 53 MET cc_start: 0.8538 (mtm) cc_final: 0.8291 (mtm) REVERT: B 157 MET cc_start: 0.9361 (mmt) cc_final: 0.9056 (mmm) REVERT: B 182 ASP cc_start: 0.9581 (t0) cc_final: 0.9264 (m-30) REVERT: B 235 MET cc_start: 0.9700 (mmp) cc_final: 0.9307 (mmm) REVERT: B 238 LEU cc_start: 0.9854 (mt) cc_final: 0.9570 (pp) REVERT: B 298 LEU cc_start: 0.9621 (tp) cc_final: 0.9272 (tp) REVERT: B 484 MET cc_start: 0.8904 (ptp) cc_final: 0.8653 (mpp) REVERT: C 49 MET cc_start: 0.8081 (tpt) cc_final: 0.6450 (tpt) REVERT: C 63 MET cc_start: 0.9698 (tmm) cc_final: 0.9425 (tmm) REVERT: C 182 ASP cc_start: 0.8751 (t0) cc_final: 0.8389 (t0) REVERT: C 235 MET cc_start: 0.9368 (mpp) cc_final: 0.9000 (mpp) REVERT: C 457 MET cc_start: 0.9123 (mmp) cc_final: 0.8903 (mmm) REVERT: C 484 MET cc_start: 0.9653 (mpp) cc_final: 0.9326 (mpp) REVERT: D 55 MET cc_start: 0.8808 (mmp) cc_final: 0.8174 (mmp) REVERT: D 159 MET cc_start: 0.9649 (mmm) cc_final: 0.9342 (mmm) REVERT: D 225 MET cc_start: 0.9806 (mmp) cc_final: 0.9523 (mmm) REVERT: D 258 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9191 (mt-10) REVERT: E 158 MET cc_start: 0.9677 (tpt) cc_final: 0.9395 (mtt) REVERT: E 159 MET cc_start: 0.9692 (mmp) cc_final: 0.9479 (mmm) REVERT: E 192 MET cc_start: 0.9790 (mmm) cc_final: 0.9504 (tpp) REVERT: E 225 MET cc_start: 0.9821 (mmp) cc_final: 0.9546 (mmm) REVERT: E 266 MET cc_start: 0.9146 (mmt) cc_final: 0.8684 (mmm) REVERT: E 319 HIS cc_start: 0.8651 (m90) cc_final: 0.8185 (m90) REVERT: F 252 TYR cc_start: 0.9761 (t80) cc_final: 0.9390 (t80) REVERT: F 280 MET cc_start: 0.9634 (tpt) cc_final: 0.9290 (tpp) REVERT: F 285 GLU cc_start: 0.9303 (mm-30) cc_final: 0.7868 (tp30) REVERT: F 415 PHE cc_start: 0.8813 (t80) cc_final: 0.8010 (m-80) REVERT: G 34 PHE cc_start: 0.9521 (t80) cc_final: 0.8962 (t80) REVERT: J 53 PHE cc_start: 0.9707 (m-80) cc_final: 0.9469 (m-80) REVERT: J 60 ASP cc_start: 0.9363 (p0) cc_final: 0.8730 (t0) REVERT: L 18 PHE cc_start: 0.8340 (t80) cc_final: 0.8072 (t80) REVERT: L 27 PHE cc_start: 0.9061 (m-10) cc_final: 0.8729 (m-80) REVERT: L 60 ASP cc_start: 0.9305 (t0) cc_final: 0.9036 (p0) REVERT: R 52 MET cc_start: 0.8978 (ppp) cc_final: 0.8747 (ppp) REVERT: S 27 PHE cc_start: 0.9279 (t80) cc_final: 0.8763 (t80) REVERT: S 64 MET cc_start: 0.9336 (mmp) cc_final: 0.9119 (mmm) REVERT: a 26 MET cc_start: 0.7047 (mpp) cc_final: 0.5774 (mpp) REVERT: a 63 PHE cc_start: 0.9520 (t80) cc_final: 0.9319 (t80) REVERT: a 122 MET cc_start: 0.8759 (tmm) cc_final: 0.8457 (tmm) REVERT: a 236 MET cc_start: 0.9180 (ttt) cc_final: 0.8688 (ptm) REVERT: a 278 MET cc_start: 0.9826 (mmp) cc_final: 0.9587 (mmm) REVERT: b 106 LYS cc_start: 0.8623 (tttt) cc_final: 0.8300 (tptm) REVERT: e 88 ASN cc_start: 0.9259 (t0) cc_final: 0.8972 (t0) REVERT: e 91 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7218 (pm20) REVERT: g 32 MET cc_start: 0.9371 (ttt) cc_final: 0.8971 (ttt) REVERT: g 156 MET cc_start: 0.9569 (tpp) cc_final: 0.9054 (tpp) REVERT: g 229 MET cc_start: 0.8898 (mtm) cc_final: 0.8429 (mtp) REVERT: g 246 MET cc_start: 0.8911 (ptp) cc_final: 0.8601 (ptp) REVERT: p 110 ASP cc_start: 0.9467 (t0) cc_final: 0.9072 (p0) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2297 time to fit residues: 115.9306 Evaluate side-chains 254 residues out of total 3851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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: 20.0000 chunk 263 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 309 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 0.0370 chunk 371 optimal weight: 7.9990 chunk 337 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 45 optimal weight: 0.0050 chunk 377 optimal weight: 9.9990 overall best weight: 2.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 273 GLN ** 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 63 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** p 146 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.035357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.024830 restraints weight = 421680.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.025655 restraints weight = 281199.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.026183 restraints weight = 209331.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.026621 restraints weight = 169967.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.026957 restraints weight = 143760.984| |-----------------------------------------------------------------------------| r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3427 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= 0.148 Angle : 0.623 12.490 51111 Z= 0.320 Chirality : 0.042 0.262 5988 Planarity : 0.004 0.052 6628 Dihedral : 5.838 150.297 5271 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.76 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 1.24 (0.10), residues: 2691 sheet: -0.83 (0.21), residues: 551 loop : -1.03 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 371 TYR 0.041 0.001 TYR E 372 PHE 0.068 0.002 PHE L 18 TRP 0.013 0.001 TRP a 55 HIS 0.004 0.001 HIS E 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (37700) covalent geometry : angle 0.62307 / 0.32 (51111) hydrogen bonds : bond 0.03959 / 2.69 ( 2319) hydrogen bonds : angle 4.78047 / 3.32 ( 6801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6235.74 seconds wall clock time: 109 minutes 44.34 seconds (6584.34 seconds total)