Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 19 11:00:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkj_12441/07_2023/7nkj_12441_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkj_12441/07_2023/7nkj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkj_12441/07_2023/7nkj_12441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkj_12441/07_2023/7nkj_12441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkj_12441/07_2023/7nkj_12441_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkj_12441/07_2023/7nkj_12441_trim_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "E ASP 59": "OD1" <-> "OD2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F GLU 292": "OE1" <-> "OE2" Residue "G ASP 271": "OD1" <-> "OD2" Residue "G GLU 284": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/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: 23.45, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 43.98 Conformation dependent library (CDL) restraints added in 5.3 seconds 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... running ksdssp... Secondary structure from input PDB file: 126 helices and 21 sheets defined 42.7% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 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 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.443A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 102 Processing sheet with id= C, first strand: chain 'A' and resid 351 through 355 Processing sheet with id= D, first strand: chain 'A' and resid 232 through 237 removed outlier: 6.470A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 269 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 327 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 31 through 33 removed outlier: 4.051A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 99 through 102 Processing sheet with id= G, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.519A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 171 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 232 through 237 removed outlier: 6.510A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N SER B 323 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE B 269 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR B 325 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N PHE B 271 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 327 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.430A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLU C 45 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL C 34 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 99 through 102 Processing sheet with id= K, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.710A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 232 through 237 removed outlier: 8.599A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS C 266 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL C 205 " --> pdb=" O HIS C 266 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU C 268 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE C 209 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASP C 272 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU C 327 " --> pdb=" O PHE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.563A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 87 through 89 Processing sheet with id= O, first strand: chain 'D' and resid 329 through 332 removed outlier: 7.445A pdb=" N ILE D 156 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N SER D 304 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU D 158 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLN D 306 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY D 160 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL D 308 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR D 309 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ASP D 254 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA D 188 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.555A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL E 53 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 87 through 89 Processing sheet with id= R, first strand: chain 'E' and resid 329 through 332 removed outlier: 8.543A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ASP E 254 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA E 188 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 11 through 16 removed outlier: 6.579A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 87 through 89 Processing sheet with id= U, first strand: chain 'F' and resid 329 through 332 removed outlier: 7.552A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY F 160 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL F 308 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ASP F 254 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA F 188 " --> pdb=" O ASP F 254 " (cutoff:3.500A) 907 hydrogen bonds defined for protein. 2496 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: 19.40 Time building geometry restraints manager: 44.46 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: 98.71 - 107.05: 956 107.05 - 115.38: 58232 115.38 - 123.72: 19792 123.72 - 132.06: 3353 132.06 - 140.39: 31 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: 17066 27.98 - 55.97: 674 55.97 - 83.95: 102 83.95 - 111.94: 17 111.94 - 139.92: 2 Dihedral angle restraints: 17861 sinusoidal: 8504 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 17858 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: 2481 2.17 - 2.78: 92571 2.78 - 3.38: 139459 3.38 - 3.99: 190148 3.99 - 4.60: 289588 Nonbonded interactions: 714247 Sorted by model distance: nonbonded pdb="HD22 ASN B 335 " pdb=" O HOH B 702 " model vdw 1.559 1.850 nonbonded pdb=" OE1 GLU E 239 " pdb="HH21 ARG E 293 " model vdw 1.576 1.850 nonbonded pdb=" O ALA C 192 " pdb=" HG1 THR C 195 " model vdw 1.595 1.850 nonbonded pdb=" OD1 ASP B 104 " pdb="HH12 ARG B 203 " model vdw 1.622 1.850 nonbonded pdb=" O PRO B 161 " pdb=" HG SER B 375 " model vdw 1.630 1.850 ... (remaining 714242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 511 or resid 600 throu \ gh 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: 9.450 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: 0.800 Extract box with map and model: 29.310 Check model and map are aligned: 0.730 Set scattering table: 0.390 Process input model: 156.650 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 213.600 ------------------------------------------------------------------------------- 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= 0.307 Angle : 0.588 8.189 31163 Z= 0.308 Chirality : 0.045 0.306 3573 Planarity : 0.004 0.040 4084 Dihedral : 16.782 139.921 8495 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.78 % Favored : 98.15 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (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 *********************** 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 fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 3.800 Fit side-chains outliers start: 25 outliers final: 22 residues processed: 204 average time/residue: 3.3397 time to fit residues: 779.1215 Evaluate side-chains 196 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 3.617 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 0 time to fit residues: 4.5289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 22985 Z= 0.327 Angle : 0.571 8.918 31163 Z= 0.299 Chirality : 0.043 0.161 3573 Planarity : 0.004 0.042 4084 Dihedral : 6.523 113.702 3191 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.61 % Favored : 98.32 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 2929 helix: 1.08 (0.14), residues: 1229 sheet: 0.16 (0.23), residues: 453 loop : 0.64 (0.18), residues: 1247 *********************** 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 212 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 176 time to evaluate : 4.174 Fit side-chains outliers start: 36 outliers final: 25 residues processed: 205 average time/residue: 3.2427 time to fit residues: 762.6195 Evaluate side-chains 201 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 3.781 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 3 average time/residue: 1.8025 time to fit residues: 11.1270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN F 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 22985 Z= 0.321 Angle : 0.568 8.854 31163 Z= 0.298 Chirality : 0.043 0.168 3573 Planarity : 0.004 0.042 4084 Dihedral : 6.497 116.255 3191 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.78 % Favored : 98.15 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 2929 helix: 1.09 (0.14), residues: 1228 sheet: 0.16 (0.23), residues: 453 loop : 0.64 (0.18), residues: 1248 *********************** 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 218 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 181 time to evaluate : 3.661 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 26 residues processed: 213 average time/residue: 3.2298 time to fit residues: 792.6493 Evaluate side-chains 204 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 3.691 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 2.4446 time to fit residues: 10.3456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 265 optimal weight: 2.9990 chunk 281 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 75 optimal weight: 0.0060 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.0307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 22985 Z= 0.190 Angle : 0.513 8.412 31163 Z= 0.264 Chirality : 0.041 0.169 3573 Planarity : 0.003 0.033 4084 Dihedral : 6.178 111.692 3191 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.40 % Favored : 98.53 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.16), residues: 2929 helix: 1.36 (0.15), residues: 1226 sheet: 0.19 (0.23), residues: 463 loop : 0.76 (0.19), residues: 1240 *********************** 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 213 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 3.416 Fit side-chains outliers start: 30 outliers final: 23 residues processed: 208 average time/residue: 3.2723 time to fit residues: 781.1865 Evaluate side-chains 197 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 4.126 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 4.8346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 252 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.0204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 22985 Z= 0.329 Angle : 0.566 9.010 31163 Z= 0.296 Chirality : 0.043 0.167 3573 Planarity : 0.004 0.049 4084 Dihedral : 6.403 115.958 3191 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.78 % Favored : 98.15 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2929 helix: 1.19 (0.15), residues: 1228 sheet: 0.18 (0.23), residues: 453 loop : 0.68 (0.19), residues: 1248 *********************** 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 208 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 175 time to evaluate : 4.140 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 25 residues processed: 203 average time/residue: 3.2944 time to fit residues: 769.1639 Evaluate side-chains 198 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 3.768 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 2.4964 time to fit residues: 10.6630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 281 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN F 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 22985 Z= 0.249 Angle : 0.537 8.704 31163 Z= 0.279 Chirality : 0.041 0.170 3573 Planarity : 0.004 0.080 4084 Dihedral : 6.305 114.374 3191 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.64 % Favored : 98.29 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.16), residues: 2929 helix: 1.26 (0.15), residues: 1227 sheet: 0.18 (0.23), residues: 463 loop : 0.70 (0.19), residues: 1239 *********************** 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 205 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 177 time to evaluate : 3.638 Fit side-chains outliers start: 28 outliers final: 23 residues processed: 204 average time/residue: 3.2057 time to fit residues: 753.1394 Evaluate side-chains 202 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 3.511 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 4.2078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 280 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 F 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.0292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 22985 Z= 0.232 Angle : 0.529 8.682 31163 Z= 0.274 Chirality : 0.041 0.167 3573 Planarity : 0.004 0.068 4084 Dihedral : 6.224 113.334 3191 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.81 % Favored : 98.12 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.16), residues: 2929 helix: 1.33 (0.15), residues: 1225 sheet: 0.21 (0.23), residues: 463 loop : 0.72 (0.19), residues: 1241 *********************** 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 208 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 3.550 Fit side-chains outliers start: 27 outliers final: 23 residues processed: 206 average time/residue: 3.2591 time to fit residues: 775.7554 Evaluate side-chains 197 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 3.515 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 4.4262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN F 180 ASN F 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.0232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 22985 Z= 0.379 Angle : 0.592 9.143 31163 Z= 0.311 Chirality : 0.044 0.174 3573 Planarity : 0.004 0.060 4084 Dihedral : 6.487 116.504 3191 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.68 % Favored : 98.26 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.15), residues: 2929 helix: 1.08 (0.14), residues: 1226 sheet: 0.19 (0.23), residues: 463 loop : 0.62 (0.19), residues: 1240 *********************** 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 203 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 3.728 Fit side-chains outliers start: 30 outliers final: 25 residues processed: 198 average time/residue: 3.2621 time to fit residues: 743.5216 Evaluate side-chains 199 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 3.727 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 2.3277 time to fit residues: 10.4317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 260 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN F 180 ASN F 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 22985 Z= 0.243 Angle : 0.539 8.700 31163 Z= 0.280 Chirality : 0.041 0.174 3573 Planarity : 0.004 0.061 4084 Dihedral : 6.313 114.268 3191 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.71 % Favored : 98.22 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.16), residues: 2929 helix: 1.23 (0.15), residues: 1229 sheet: 0.18 (0.23), residues: 463 loop : 0.71 (0.19), residues: 1237 *********************** 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 204 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 177 time to evaluate : 3.625 Fit side-chains outliers start: 27 outliers final: 23 residues processed: 203 average time/residue: 3.3342 time to fit residues: 779.5873 Evaluate side-chains 200 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 3.632 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 4.5251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 0.0270 chunk 276 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- 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 F 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.0210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 22985 Z= 0.305 Angle : 0.563 8.916 31163 Z= 0.294 Chirality : 0.042 0.172 3573 Planarity : 0.004 0.060 4084 Dihedral : 6.382 115.453 3191 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.71 % Favored : 98.22 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.16), residues: 2929 helix: 1.17 (0.15), residues: 1227 sheet: 0.17 (0.23), residues: 463 loop : 0.66 (0.19), residues: 1239 ********************** 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 fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 3.694 Fit side-chains outliers start: 24 outliers final: 23 residues processed: 199 average time/residue: 3.3960 time to fit residues: 776.2930 Evaluate side-chains 197 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 3.941 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 4.2574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 231 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 237 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 F 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.077877 restraints weight = 96053.685| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.32 r_work: 0.2840 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.0327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 22985 Z= 0.189 Angle : 0.519 8.401 31163 Z= 0.268 Chirality : 0.041 0.172 3573 Planarity : 0.004 0.082 4084 Dihedral : 6.173 112.304 3191 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.54 % Favored : 98.39 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.16), residues: 2929 helix: 1.37 (0.15), residues: 1225 sheet: 0.19 (0.23), residues: 463 loop : 0.76 (0.19), residues: 1241 =============================================================================== Job complete usr+sys time: 14296.52 seconds wall clock time: 252 minutes 1.16 seconds (15121.16 seconds total)