Starting phenix.real_space_refine on Wed Aug 27 02:09:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nkj_12441/08_2025/7nkj_12441_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nkj_12441/08_2025/7nkj_12441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nkj_12441/08_2025/7nkj_12441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nkj_12441/08_2025/7nkj_12441.map" model { file = "/net/cci-nas-00/data/ceres_data/7nkj_12441/08_2025/7nkj_12441_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nkj_12441/08_2025/7nkj_12441_trim.cif" } resolution = 2.17 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= 0.002 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: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 71 5.16 5 C 14172 2.51 5 N 3928 2.21 5 O 4935 1.98 5 H 22478 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45605 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 7509 Classifications: {'peptide': 495} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain: "B" Number of atoms: 7250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 7250 Classifications: {'peptide': 476} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 454} Chain breaks: 1 Chain: "C" Number of atoms: 7403 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 486, 7382 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 464} Conformer: "B" Number of residues, atoms: 486, 7382 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 464} bond proxies already assigned to first conformer: 7418 Chain: "D" Number of atoms: 7144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 467, 7126 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Conformer: "B" Number of residues, atoms: 467, 7126 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} bond proxies already assigned to first conformer: 7172 Chain: "E" Number of atoms: 7087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 7087 Classifications: {'peptide': 464} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain: "F" Number of atoms: 7125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7125 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "G" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1388 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} Chain breaks: 2 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 9.83, per 1000 atoms: 0.22 Number of scatterers: 45605 At special positions: 0 Unit cell: (121.18, 125.33, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 71 16.00 P 16 15.00 Mg 5 11.99 O 4935 8.00 N 3928 7.00 C 14172 6.00 H 22478 1.00 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: 4.36 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5342 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 0 sheets defined 42.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 178 through 195 removed outlier: 4.171A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 243 through 263 Proline residue: A 250 - end of helix removed outlier: 3.630A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 393 through 406 removed outlier: 4.849A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 5.149A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 478 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 194 removed outlier: 3.665A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.663A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.592A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 384 through 405 removed outlier: 5.084A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 441 through 452 removed outlier: 3.655A pdb=" N GLY B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 477 removed outlier: 4.776A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 467 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 178 through 195 removed outlier: 3.672A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.682A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 301 through 311 removed outlier: 3.927A pdb=" N ARG C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 478 removed outlier: 5.115A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.782A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 243 removed outlier: 4.935A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 318 through 326 removed outlier: 4.442A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N HIS D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 363 through 389 removed outlier: 4.643A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 412 Processing helix chain 'D' and resid 420 through 423 No H-bonds generated for 'chain 'D' and resid 420 through 423' Processing helix chain 'D' and resid 432 through 443 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 194 through 206 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.870A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 276 through 278 No H-bonds generated for 'chain 'E' and resid 276 through 278' Processing helix chain 'E' and resid 283 through 293 removed outlier: 4.093A pdb=" N ARG E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 318 through 324 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 363 through 389 removed outlier: 4.321A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 396 through 411 Processing helix chain 'E' and resid 417 through 421 removed outlier: 3.857A pdb=" N GLN E 421 " --> pdb=" O ALA E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'F' and resid 194 through 207 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 244 removed outlier: 5.161A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 269 Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 283 through 293 Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.564A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 358 through 361 No H-bonds generated for 'chain 'F' and resid 358 through 361' Processing helix chain 'F' and resid 363 through 381 Processing helix chain 'F' and resid 383 through 389 removed outlier: 3.874A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 396 through 412 Processing helix chain 'F' and resid 417 through 423 removed outlier: 3.560A pdb=" N GLU F 420 " --> pdb=" O MET F 417 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 444 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'G' and resid 4 through 34 removed outlier: 3.530A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 303 735 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.86 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 22459 1.03 - 1.23: 112 1.23 - 1.42: 9196 1.42 - 1.62: 13573 1.62 - 1.81: 123 Bond restraints: 45463 Sorted by residual: bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.460 0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" O3B ATP F 600 " pdb=" PB ATP F 600 " ideal model delta sigma weight residual 1.592 1.550 0.042 3.00e-02 1.11e+03 1.97e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" CG PRO F 344 " pdb=" CD PRO F 344 " ideal model delta sigma weight residual 1.512 1.479 0.033 2.70e-02 1.37e+03 1.50e+00 bond pdb=" C GLU B 57 " pdb=" N PHE B 58 " ideal model delta sigma weight residual 1.339 1.273 0.066 5.57e-02 3.22e+02 1.41e+00 ... (remaining 45458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 81334 1.64 - 3.28: 893 3.28 - 4.91: 106 4.91 - 6.55: 25 6.55 - 8.19: 6 Bond angle restraints: 82364 Sorted by residual: angle pdb=" C ASP F 254 " pdb=" N ASN F 255 " pdb=" CA ASN F 255 " ideal model delta sigma weight residual 121.70 127.78 -6.08 1.80e+00 3.09e-01 1.14e+01 angle pdb=" C ASP E 254 " pdb=" N ASN E 255 " pdb=" CA ASN E 255 " ideal model delta sigma weight residual 121.70 127.66 -5.96 1.80e+00 3.09e-01 1.10e+01 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 127.25 -5.55 1.80e+00 3.09e-01 9.50e+00 angle pdb=" N THR F 8 " pdb=" CA THR F 8 " pdb=" CB THR F 8 " ideal model delta sigma weight residual 114.17 110.98 3.19 1.14e+00 7.69e-01 7.82e+00 angle pdb=" C2' ADP D 600 " pdb=" C3' ADP D 600 " pdb=" C4' ADP D 600 " ideal model delta sigma weight residual 111.00 102.81 8.19 3.00e+00 1.11e-01 7.45e+00 ... (remaining 82359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.98: 20042 27.98 - 55.97: 1080 55.97 - 83.95: 145 83.95 - 111.94: 17 111.94 - 139.92: 2 Dihedral angle restraints: 21286 sinusoidal: 11929 harmonic: 9357 Sorted by residual: dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 79.92 -139.92 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 71.43 -131.43 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O1B ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PB ADP E 600 " pdb=" PA ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -152.87 92.87 1 2.00e+01 2.50e-03 2.52e+01 ... (remaining 21283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3123 0.061 - 0.123: 394 0.123 - 0.184: 44 0.184 - 0.245: 4 0.245 - 0.306: 8 Chirality restraints: 3573 Sorted by residual: chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C3' ATP B 600 " pdb=" C2' ATP B 600 " pdb=" C4' ATP B 600 " pdb=" O3' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3570 not shown) Planarity restraints: 6893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 112 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO C 113 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 113 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 113 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 468 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C GLU A 468 " 0.025 2.00e-02 2.50e+03 pdb=" O GLU A 468 " -0.009 2.00e-02 2.50e+03 pdb=" N SER A 469 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 317 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO F 318 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO F 318 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 318 " -0.020 5.00e-02 4.00e+02 ... (remaining 6890 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 2629 2.17 - 2.78: 92595 2.78 - 3.38: 139633 3.38 - 3.99: 190494 3.99 - 4.60: 289756 Nonbonded interactions: 715107 Sorted by model distance: nonbonded pdb="HD22 ASN B 335 " pdb=" O HOH B 702 " model vdw 1.559 2.450 nonbonded pdb=" OE1 GLU E 239 " pdb="HH21 ARG E 293 " model vdw 1.576 2.450 nonbonded pdb=" O ALA C 192 " pdb=" HG1 THR C 195 " model vdw 1.595 2.450 nonbonded pdb=" OD1 ASP B 104 " pdb="HH12 ARG B 203 " model vdw 1.622 2.450 nonbonded pdb=" O PRO B 161 " pdb=" HG SER B 375 " model vdw 1.630 2.450 ... (remaining 715102 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 29 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 30 through 173 or resid 175 through 406 or ( \ resid 414 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 415 through 511 \ or resid 600 through 601)) selection = (chain 'B' and (resid 29 through 173 or resid 175 through 601)) selection = (chain 'C' and (resid 29 through 173 or resid 175 through 258 or (resid 259 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD2 or name HE1 or name HE2)) or resid 260 through 406 or (resid 414 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2 \ or name HA or name HB2 or name HB3)) or resid 415 through 511 or resid 600 throu \ gh 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 364 or (resid 365 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 366 through 452 or resid 455 through 471)) selection = (chain 'E' and (resid 8 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 452 or resid 455 t \ hrough 471)) selection = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 9 through 452 or resid 455 through 471)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.510 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: 0.250 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 42.640 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.060 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:5.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 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 0.066 22985 Z= 0.211 Angle : 0.588 8.189 31163 Z= 0.308 Chirality : 0.045 0.306 3573 Planarity : 0.004 0.040 4084 Dihedral : 17.265 139.921 8619 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.78 % Favored : 98.15 % Rotamer: Outliers : 1.05 % Allowed : 12.58 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.16), residues: 2929 helix: 1.12 (0.15), residues: 1226 sheet: 0.16 (0.23), residues: 453 loop : 0.68 (0.19), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 294 TYR 0.011 0.001 TYR A 251 PHE 0.018 0.002 PHE D 439 TRP 0.011 0.002 TRP E 201 HIS 0.005 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00465 (22985) covalent geometry : angle 0.58757 (31163) hydrogen bonds : bond 0.07217 ( 735) hydrogen bonds : angle 3.93439 ( 2049) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 1.271 Fit side-chains outliers start: 25 outliers final: 22 residues processed: 204 average time/residue: 1.5542 time to fit residues: 359.8115 Evaluate side-chains 196 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain C residue 240 SER Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain E residue 463 ASP Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 14 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 335 ASN E 198 ASN E 425 GLN F 180 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.092591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.075690 restraints weight = 96368.396| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.32 r_work: 0.2803 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.0345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 22985 Z= 0.271 Angle : 0.604 9.435 31163 Z= 0.318 Chirality : 0.045 0.164 3573 Planarity : 0.005 0.047 4084 Dihedral : 9.573 112.877 3343 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.64 % Favored : 98.26 % Rotamer: Outliers : 1.34 % Allowed : 12.49 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.15), residues: 2929 helix: 1.00 (0.14), residues: 1225 sheet: -0.03 (0.23), residues: 472 loop : 0.61 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 365 TYR 0.012 0.002 TYR A 251 PHE 0.020 0.002 PHE D 439 TRP 0.011 0.002 TRP E 201 HIS 0.007 0.002 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00602 (22985) covalent geometry : angle 0.60428 (31163) hydrogen bonds : bond 0.06634 ( 735) hydrogen bonds : angle 3.99129 ( 2049) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 1.312 Fit side-chains REVERT: B 488 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: G 26 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8212 (tm-30) outliers start: 32 outliers final: 17 residues processed: 200 average time/residue: 1.6217 time to fit residues: 369.3443 Evaluate side-chains 190 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 258 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 113 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 ASN E 425 GLN F 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.093267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.076330 restraints weight = 98599.620| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.34 r_work: 0.2814 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.0439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 22985 Z= 0.213 Angle : 0.564 9.101 31163 Z= 0.295 Chirality : 0.043 0.169 3573 Planarity : 0.004 0.048 4084 Dihedral : 9.362 114.596 3333 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 1.22 % Allowed : 12.49 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.16), residues: 2929 helix: 1.04 (0.15), residues: 1226 sheet: -0.25 (0.22), residues: 471 loop : 0.63 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 26 TYR 0.010 0.001 TYR A 251 PHE 0.017 0.002 PHE D 439 TRP 0.010 0.001 TRP E 201 HIS 0.006 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00467 (22985) covalent geometry : angle 0.56357 (31163) hydrogen bonds : bond 0.06162 ( 735) hydrogen bonds : angle 3.92295 ( 2049) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: B 488 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: E 298 ARG cc_start: 0.7536 (mtm-85) cc_final: 0.7308 (ttm110) REVERT: E 400 GLN cc_start: 0.7242 (tt0) cc_final: 0.6931 (tm-30) REVERT: G 26 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8245 (tm-30) outliers start: 29 outliers final: 17 residues processed: 203 average time/residue: 1.4629 time to fit residues: 338.8624 Evaluate side-chains 198 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 258 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 80 optimal weight: 0.9980 chunk 270 optimal weight: 0.0980 chunk 112 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 335 ASN E 425 GLN F 180 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.093606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.076815 restraints weight = 94514.288| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.31 r_work: 0.2826 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.0502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 22985 Z= 0.192 Angle : 0.549 9.068 31163 Z= 0.287 Chirality : 0.042 0.166 3573 Planarity : 0.004 0.047 4084 Dihedral : 9.171 113.018 3331 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 1.17 % Allowed : 12.49 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.16), residues: 2929 helix: 1.10 (0.15), residues: 1227 sheet: -0.38 (0.22), residues: 471 loop : 0.67 (0.19), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 11 TYR 0.009 0.001 TYR A 251 PHE 0.016 0.002 PHE D 439 TRP 0.010 0.001 TRP E 201 HIS 0.005 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00423 (22985) covalent geometry : angle 0.54943 (31163) hydrogen bonds : bond 0.05952 ( 735) hydrogen bonds : angle 3.87752 ( 2049) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: B 488 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: G 26 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8218 (tm-30) outliers start: 28 outliers final: 15 residues processed: 203 average time/residue: 1.5350 time to fit residues: 354.1548 Evaluate side-chains 196 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 258 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 12 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 250 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN E 425 GLN F 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.076795 restraints weight = 98446.839| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.36 r_work: 0.2822 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.0535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 22985 Z= 0.194 Angle : 0.549 9.051 31163 Z= 0.286 Chirality : 0.042 0.167 3573 Planarity : 0.004 0.046 4084 Dihedral : 9.118 113.704 3327 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.64 % Favored : 98.26 % Rotamer: Outliers : 1.09 % Allowed : 12.70 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.16), residues: 2929 helix: 1.10 (0.15), residues: 1228 sheet: -0.45 (0.22), residues: 471 loop : 0.69 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 11 TYR 0.009 0.001 TYR A 251 PHE 0.017 0.002 PHE D 439 TRP 0.010 0.001 TRP E 201 HIS 0.006 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00428 (22985) covalent geometry : angle 0.54921 (31163) hydrogen bonds : bond 0.05958 ( 735) hydrogen bonds : angle 3.85509 ( 2049) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7215 (p0) REVERT: B 488 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: D 136 MET cc_start: 0.9214 (ttt) cc_final: 0.8863 (ttt) REVERT: G 26 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8239 (tm-30) outliers start: 26 outliers final: 17 residues processed: 204 average time/residue: 1.5604 time to fit residues: 361.2101 Evaluate side-chains 197 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 258 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 61 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 335 ASN E 425 GLN F 180 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.093926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.077032 restraints weight = 96611.539| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.33 r_work: 0.2830 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.0570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 22985 Z= 0.180 Angle : 0.539 9.049 31163 Z= 0.281 Chirality : 0.042 0.165 3573 Planarity : 0.004 0.055 4084 Dihedral : 9.026 112.662 3327 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.61 % Favored : 98.29 % Rotamer: Outliers : 1.13 % Allowed : 12.75 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.16), residues: 2929 helix: 1.15 (0.15), residues: 1228 sheet: -0.50 (0.22), residues: 471 loop : 0.70 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 26 TYR 0.009 0.001 TYR E 315 PHE 0.016 0.002 PHE D 439 TRP 0.010 0.001 TRP E 201 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00395 (22985) covalent geometry : angle 0.53939 (31163) hydrogen bonds : bond 0.05801 ( 735) hydrogen bonds : angle 3.82327 ( 2049) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7201 (p0) REVERT: B 488 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: D 136 MET cc_start: 0.9232 (ttt) cc_final: 0.8894 (ttt) REVERT: G 26 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8233 (tm-30) outliers start: 27 outliers final: 16 residues processed: 202 average time/residue: 1.7790 time to fit residues: 407.8071 Evaluate side-chains 200 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 258 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 233 optimal weight: 3.9990 chunk 252 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 243 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 335 ASN E 425 GLN F 180 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.093541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.076543 restraints weight = 103260.507| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.41 r_work: 0.2818 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.0577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 22985 Z= 0.198 Angle : 0.551 9.080 31163 Z= 0.287 Chirality : 0.042 0.167 3573 Planarity : 0.004 0.075 4084 Dihedral : 9.072 113.615 3326 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.81 % Favored : 98.09 % Rotamer: Outliers : 1.01 % Allowed : 12.75 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.16), residues: 2929 helix: 1.13 (0.15), residues: 1227 sheet: -0.50 (0.22), residues: 471 loop : 0.70 (0.19), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 335 TYR 0.009 0.001 TYR E 315 PHE 0.017 0.002 PHE D 439 TRP 0.009 0.001 TRP E 201 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00438 (22985) covalent geometry : angle 0.55115 (31163) hydrogen bonds : bond 0.05961 ( 735) hydrogen bonds : angle 3.83707 ( 2049) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7228 (p0) REVERT: B 488 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: D 136 MET cc_start: 0.9248 (ttt) cc_final: 0.8867 (ttt) REVERT: E 403 ASN cc_start: 0.7793 (m-40) cc_final: 0.7517 (m-40) REVERT: G 26 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8243 (tm-30) outliers start: 24 outliers final: 17 residues processed: 200 average time/residue: 0.9977 time to fit residues: 227.8314 Evaluate side-chains 198 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 495 GLU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 258 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 176 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN E 425 GLN F 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.092901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.075991 restraints weight = 99610.828| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.37 r_work: 0.2809 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 22985 Z= 0.247 Angle : 0.585 9.367 31163 Z= 0.307 Chirality : 0.044 0.170 3573 Planarity : 0.005 0.056 4084 Dihedral : 9.198 115.065 3324 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.71 % Favored : 98.19 % Rotamer: Outliers : 1.13 % Allowed : 12.79 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.16), residues: 2929 helix: 1.00 (0.14), residues: 1228 sheet: -0.43 (0.22), residues: 471 loop : 0.65 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 294 TYR 0.012 0.002 TYR E 315 PHE 0.020 0.002 PHE D 439 TRP 0.009 0.002 TRP E 201 HIS 0.006 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00550 (22985) covalent geometry : angle 0.58492 (31163) hydrogen bonds : bond 0.06434 ( 735) hydrogen bonds : angle 3.91886 ( 2049) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7199 (p0) REVERT: B 488 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: D 136 MET cc_start: 0.9266 (ttt) cc_final: 0.8927 (ttt) REVERT: E 403 ASN cc_start: 0.7828 (m-40) cc_final: 0.7506 (m-40) REVERT: G 26 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8231 (tm-30) outliers start: 27 outliers final: 16 residues processed: 199 average time/residue: 1.0029 time to fit residues: 228.8722 Evaluate side-chains 195 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 258 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 288 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 228 optimal weight: 0.9980 chunk 237 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 335 ASN E 425 GLN F 180 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.077524 restraints weight = 97758.811| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.35 r_work: 0.2834 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 22985 Z= 0.158 Angle : 0.531 8.853 31163 Z= 0.276 Chirality : 0.042 0.172 3573 Planarity : 0.004 0.058 4084 Dihedral : 8.897 111.088 3324 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.71 % Favored : 98.19 % Rotamer: Outliers : 0.84 % Allowed : 12.87 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.16), residues: 2929 helix: 1.19 (0.15), residues: 1228 sheet: -0.57 (0.22), residues: 471 loop : 0.73 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 294 TYR 0.009 0.001 TYR E 315 PHE 0.014 0.001 PHE F 257 TRP 0.010 0.001 TRP E 201 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00344 (22985) covalent geometry : angle 0.53125 (31163) hydrogen bonds : bond 0.05611 ( 735) hydrogen bonds : angle 3.80628 ( 2049) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7182 (p0) REVERT: B 488 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: D 136 MET cc_start: 0.9251 (ttt) cc_final: 0.8868 (ttt) REVERT: E 403 ASN cc_start: 0.7765 (m-40) cc_final: 0.7485 (m-40) REVERT: G 26 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8225 (tm-30) outliers start: 20 outliers final: 15 residues processed: 198 average time/residue: 0.9285 time to fit residues: 211.1186 Evaluate side-chains 195 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 258 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 148 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 52 optimal weight: 0.0770 chunk 210 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 216 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 ASN C 188 ASN E 425 GLN F 180 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.094727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.077938 restraints weight = 100419.789| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.38 r_work: 0.2842 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22985 Z= 0.145 Angle : 0.518 8.876 31163 Z= 0.268 Chirality : 0.041 0.164 3573 Planarity : 0.004 0.062 4084 Dihedral : 8.672 110.134 3323 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.71 % Favored : 98.19 % Rotamer: Outliers : 0.84 % Allowed : 13.00 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.16), residues: 2929 helix: 1.32 (0.15), residues: 1225 sheet: -0.66 (0.22), residues: 471 loop : 0.76 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 294 TYR 0.008 0.001 TYR E 315 PHE 0.014 0.001 PHE F 257 TRP 0.010 0.001 TRP E 201 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00317 (22985) covalent geometry : angle 0.51761 (31163) hydrogen bonds : bond 0.05363 ( 735) hydrogen bonds : angle 3.72081 ( 2049) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7163 (p0) REVERT: B 488 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: D 136 MET cc_start: 0.9244 (ttt) cc_final: 0.8856 (ttt) REVERT: G 26 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8236 (tm-30) outliers start: 20 outliers final: 14 residues processed: 195 average time/residue: 0.9247 time to fit residues: 206.7673 Evaluate side-chains 191 residues out of total 2381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 398 SER Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 258 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 246 optimal weight: 0.9980 chunk 280 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 335 ASN C 150 GLN F 180 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.094567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.077787 restraints weight = 98662.718| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.37 r_work: 0.2838 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22985 Z= 0.155 Angle : 0.525 8.896 31163 Z= 0.271 Chirality : 0.041 0.171 3573 Planarity : 0.004 0.062 4084 Dihedral : 8.688 111.510 3321 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 0.80 % Allowed : 13.21 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.16), residues: 2929 helix: 1.32 (0.15), residues: 1227 sheet: -0.70 (0.22), residues: 473 loop : 0.79 (0.19), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 335 TYR 0.009 0.001 TYR E 315 PHE 0.015 0.001 PHE F 257 TRP 0.010 0.001 TRP E 201 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00340 (22985) covalent geometry : angle 0.52451 (31163) hydrogen bonds : bond 0.05462 ( 735) hydrogen bonds : angle 3.72653 ( 2049) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14235.52 seconds wall clock time: 240 minutes 57.57 seconds (14457.57 seconds total)