Starting phenix.real_space_refine on Sun Jul 28 12:22:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkj_12441/07_2024/7nkj_12441_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkj_12441/07_2024/7nkj_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_2024/7nkj_12441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkj_12441/07_2024/7nkj_12441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkj_12441/07_2024/7nkj_12441_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nkj_12441/07_2024/7nkj_12441_neut_trim.cif" } resolution = 2.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 27.69, per 1000 atoms: 0.61 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: 42.21 Conformation dependent library (CDL) restraints added in 6.0 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... 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: 3.12 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: 15.17 Time building geometry restraints manager: 43.84 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: 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 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 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 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: 6.730 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: 0.780 Extract box with map and model: 1.840 Check model and map are aligned: 0.330 Set scattering table: 0.390 Process input model: 155.240 Find NCS groups from input model: 2.480 Set up NCS constraints: 0.180 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.080 ------------------------------------------------------------------------------- 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= 0.308 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 : 2.88 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 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 201 HIS 0.005 0.001 HIS A 266 PHE 0.018 0.002 PHE D 439 TYR 0.011 0.001 TYR A 251 ARG 0.005 0.000 ARG C 294 *********************** 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 : 3.671 Fit side-chains outliers start: 25 outliers final: 22 residues processed: 204 average time/residue: 3.2791 time to fit residues: 760.9168 Evaluate side-chains 196 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 3.621 ------------------------------------------------------------------------------- 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 245 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 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: 1.5186 ------------------------------------------------------------------------------- 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: 0.8752 moved from start: 0.0148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 22985 Z= 0.329 Angle : 0.565 8.902 31163 Z= 0.295 Chirality : 0.042 0.164 3573 Planarity : 0.004 0.042 4084 Dihedral : 9.412 114.228 3343 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.57 % Favored : 98.36 % Rotamer: Outliers : 1.17 % Allowed : 12.37 % Favored : 86.46 % 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: 1.08 (0.14), residues: 1229 sheet: 0.28 (0.23), residues: 473 loop : 0.67 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 201 HIS 0.006 0.001 HIS A 266 PHE 0.019 0.002 PHE D 439 TYR 0.011 0.001 TYR A 251 ARG 0.004 0.000 ARG F 122 *********************** 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 203 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 3.771 Fit side-chains REVERT: B 488 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: G 26 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7906 (tm-30) outliers start: 28 outliers final: 16 residues processed: 196 average time/residue: 3.2769 time to fit residues: 732.3352 Evaluate side-chains 192 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 3.809 ------------------------------------------------------------------------------- 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 495 GLU 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 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 146 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 264 optimal weight: 0.9980 chunk 285 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 262 optimal weight: 0.0370 chunk 90 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- 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: 0.8741 moved from start: 0.0241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22985 Z= 0.235 Angle : 0.526 8.592 31163 Z= 0.272 Chirality : 0.041 0.167 3573 Planarity : 0.004 0.042 4084 Dihedral : 9.148 114.285 3332 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.61 % Favored : 98.32 % Rotamer: Outliers : 0.96 % Allowed : 12.66 % 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 (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: 1.19 (0.16), residues: 2929 helix: 1.23 (0.15), residues: 1228 sheet: 0.34 (0.23), residues: 473 loop : 0.74 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 201 HIS 0.005 0.001 HIS B 479 PHE 0.015 0.001 PHE D 439 TYR 0.009 0.001 TYR A 251 ARG 0.005 0.000 ARG E 298 *********************** 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 202 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 3.650 Fit side-chains revert: symmetry clash REVERT: B 488 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: E 400 GLN cc_start: 0.7284 (tt0) cc_final: 0.7019 (tm-30) REVERT: G 26 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7904 (tm-30) outliers start: 23 outliers final: 15 residues processed: 195 average time/residue: 3.2339 time to fit residues: 719.8833 Evaluate side-chains 191 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 3.741 ------------------------------------------------------------------------------- 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 488 GLU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 495 GLU 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 179 ARG 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 258 SER 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: 1.9990 chunk 29 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 281 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.8745 moved from start: 0.0256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22985 Z= 0.277 Angle : 0.539 8.781 31163 Z= 0.280 Chirality : 0.041 0.169 3573 Planarity : 0.004 0.091 4084 Dihedral : 9.120 114.715 3328 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.64 % Favored : 98.29 % Rotamer: Outliers : 1.13 % Allowed : 12.45 % Favored : 86.42 % 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: 1.18 (0.16), residues: 2929 helix: 1.20 (0.15), residues: 1229 sheet: 0.35 (0.23), residues: 473 loop : 0.73 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 201 HIS 0.005 0.001 HIS C 43 PHE 0.017 0.002 PHE D 439 TYR 0.009 0.001 TYR A 251 ARG 0.010 0.000 ARG C 294 *********************** 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 202 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 3.907 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.6946 (p0) REVERT: B 488 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: E 400 GLN cc_start: 0.7285 (tt0) cc_final: 0.7016 (tm-30) REVERT: G 26 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7887 (tm-30) outliers start: 27 outliers final: 18 residues processed: 195 average time/residue: 3.2320 time to fit residues: 720.6165 Evaluate side-chains 195 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 3.587 ------------------------------------------------------------------------------- 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 C residue 480 SER Chi-restraints excluded: chain C residue 495 GLU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 0.9990 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: 1.9990 chunk 194 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 70 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: E 425 GLN F 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 22985 Z= 0.386 Angle : 0.589 9.129 31163 Z= 0.309 Chirality : 0.044 0.172 3573 Planarity : 0.005 0.080 4084 Dihedral : 9.347 116.605 3328 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.74 % Favored : 98.19 % Rotamer: Outliers : 1.30 % Allowed : 12.37 % 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 (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 (0.16), residues: 2929 helix: 1.04 (0.14), residues: 1226 sheet: 0.32 (0.23), residues: 472 loop : 0.64 (0.19), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 201 HIS 0.007 0.002 HIS A 43 PHE 0.021 0.002 PHE D 439 TYR 0.012 0.002 TYR A 251 ARG 0.011 0.001 ARG C 294 *********************** 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 207 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 3.583 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.6993 (p0) REVERT: B 488 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: D 136 MET cc_start: 0.9042 (ttt) cc_final: 0.8700 (ttt) REVERT: E 400 GLN cc_start: 0.7254 (tt0) cc_final: 0.6978 (tm-30) REVERT: G 26 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7877 (tm-30) outliers start: 31 outliers final: 21 residues processed: 199 average time/residue: 3.2991 time to fit residues: 749.9760 Evaluate side-chains 201 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 3.588 ------------------------------------------------------------------------------- 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 B residue 491 LYS Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 495 GLU 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 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 228 MET 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=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: 1.9990 chunk 281 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8740 moved from start: 0.0289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22985 Z= 0.228 Angle : 0.526 8.593 31163 Z= 0.273 Chirality : 0.041 0.172 3573 Planarity : 0.004 0.073 4084 Dihedral : 9.032 113.886 3328 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.64 % Favored : 98.26 % Rotamer: Outliers : 0.92 % Allowed : 12.70 % 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 (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: 1.23 (0.15), residues: 1227 sheet: 0.34 (0.23), residues: 473 loop : 0.77 (0.19), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 201 HIS 0.005 0.001 HIS C 43 PHE 0.015 0.001 PHE D 439 TYR 0.009 0.001 TYR A 251 ARG 0.010 0.000 ARG C 294 *********************** 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 203 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 3.982 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.6929 (p0) REVERT: B 488 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: G 26 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7880 (tm-30) outliers start: 22 outliers final: 15 residues processed: 197 average time/residue: 3.3139 time to fit residues: 744.0063 Evaluate side-chains 195 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 3.634 ------------------------------------------------------------------------------- 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 488 GLU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 495 GLU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 175 optimal weight: 0.0980 chunk 170 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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: 0.8740 moved from start: 0.0314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22985 Z= 0.246 Angle : 0.528 8.736 31163 Z= 0.273 Chirality : 0.041 0.169 3573 Planarity : 0.004 0.067 4084 Dihedral : 8.956 113.686 3326 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.78 % Favored : 98.12 % Rotamer: Outliers : 1.01 % Allowed : 12.66 % 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 (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: 1.27 (0.15), residues: 1229 sheet: 0.36 (0.23), residues: 473 loop : 0.79 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 201 HIS 0.005 0.001 HIS C 43 PHE 0.016 0.001 PHE D 439 TYR 0.009 0.001 TYR E 315 ARG 0.010 0.000 ARG C 294 *********************** 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 204 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 3.802 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.6946 (p0) REVERT: B 488 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: D 136 MET cc_start: 0.9035 (ttt) cc_final: 0.8657 (ttt) REVERT: G 26 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7905 (tm-30) outliers start: 24 outliers final: 15 residues processed: 198 average time/residue: 3.2850 time to fit residues: 748.7473 Evaluate side-chains 197 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 3.529 ------------------------------------------------------------------------------- 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 488 GLU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 495 GLU 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 178 optimal weight: 0.4980 chunk 191 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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: 0.0279 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= 0.319 Angle : 0.559 8.928 31163 Z= 0.292 Chirality : 0.042 0.172 3573 Planarity : 0.004 0.060 4084 Dihedral : 9.147 115.853 3326 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.71 % Favored : 98.19 % Rotamer: Outliers : 1.05 % Allowed : 12.54 % Favored : 86.42 % 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: 1.13 (0.16), residues: 2929 helix: 1.16 (0.15), residues: 1227 sheet: 0.35 (0.23), residues: 472 loop : 0.70 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 201 HIS 0.006 0.001 HIS A 266 PHE 0.019 0.002 PHE D 439 TYR 0.010 0.001 TYR E 315 ARG 0.009 0.001 ARG C 294 *********************** 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 204 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 4.203 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.6977 (p0) REVERT: B 488 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: D 136 MET cc_start: 0.9052 (ttt) cc_final: 0.8671 (ttt) REVERT: G 26 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7892 (tm-30) outliers start: 25 outliers final: 16 residues processed: 198 average time/residue: 3.1227 time to fit residues: 706.2929 Evaluate side-chains 198 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 3.286 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 80 optimal weight: 0.0060 chunk 236 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 260 optimal weight: 0.5980 overall best weight: 0.8798 ------------------------------------------------------------------------------- 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: 0.8736 moved from start: 0.0354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22985 Z= 0.218 Angle : 0.519 8.524 31163 Z= 0.268 Chirality : 0.041 0.171 3573 Planarity : 0.004 0.062 4084 Dihedral : 8.888 113.293 3326 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.61 % Favored : 98.29 % Rotamer: Outliers : 0.75 % Allowed : 12.79 % Favored : 86.46 % 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: 1.31 (0.16), residues: 2929 helix: 1.32 (0.15), residues: 1228 sheet: 0.41 (0.23), residues: 470 loop : 0.80 (0.19), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 201 HIS 0.005 0.001 HIS C 43 PHE 0.014 0.001 PHE D 439 TYR 0.008 0.001 TYR A 251 ARG 0.009 0.000 ARG C 294 *********************** 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 202 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 4.091 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.6927 (p0) REVERT: B 159 MET cc_start: 0.8099 (mtm) cc_final: 0.7665 (mtm) REVERT: B 488 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: D 136 MET cc_start: 0.9046 (ttt) cc_final: 0.8645 (ttt) REVERT: G 26 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7892 (tm-30) outliers start: 18 outliers final: 14 residues processed: 196 average time/residue: 3.2036 time to fit residues: 719.7988 Evaluate side-chains 196 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 3.704 ------------------------------------------------------------------------------- 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 67 LEU 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 C residue 495 GLU 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 179 ARG 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 G residue 7 GLU Chi-restraints excluded: chain G residue 26 GLU 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 171 optimal weight: 0.0070 chunk 276 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 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: 0.5980 chunk 141 optimal weight: 0.4980 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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: 0.8732 moved from start: 0.0394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22985 Z= 0.211 Angle : 0.513 8.619 31163 Z= 0.264 Chirality : 0.040 0.166 3573 Planarity : 0.004 0.060 4084 Dihedral : 8.708 112.186 3323 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.64 % Favored : 98.26 % Rotamer: Outliers : 0.75 % Allowed : 12.83 % Favored : 86.42 % 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: 1.38 (0.16), residues: 2929 helix: 1.40 (0.15), residues: 1226 sheet: 0.40 (0.23), residues: 473 loop : 0.83 (0.19), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 201 HIS 0.004 0.001 HIS C 43 PHE 0.014 0.001 PHE D 439 TYR 0.008 0.001 TYR A 251 ARG 0.009 0.000 ARG C 294 ********************** 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 199 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 3.657 Fit side-chains revert: symmetry clash REVERT: B 488 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: D 136 MET cc_start: 0.9049 (ttt) cc_final: 0.8641 (ttt) REVERT: E 442 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8178 (mt) REVERT: G 26 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7895 (tm-30) outliers start: 18 outliers final: 14 residues processed: 194 average time/residue: 2.9793 time to fit residues: 657.5859 Evaluate side-chains 196 residues out of total 2381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU 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 C residue 495 GLU 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 179 ARG Chi-restraints excluded: chain E residue 442 LEU 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 G residue 7 GLU Chi-restraints excluded: chain G residue 26 GLU 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 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: 1.9990 chunk 64 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 237 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.076587 restraints weight = 96192.388| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.32 r_work: 0.2817 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 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 = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.0323 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= 0.309 Angle : 0.553 8.911 31163 Z= 0.288 Chirality : 0.042 0.171 3573 Planarity : 0.004 0.056 4084 Dihedral : 8.977 115.667 3321 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.81 % Favored : 98.12 % Rotamer: Outliers : 0.88 % Allowed : 12.70 % Favored : 86.42 % 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: 1.21 (0.16), residues: 2929 helix: 1.24 (0.15), residues: 1228 sheet: 0.36 (0.23), residues: 472 loop : 0.75 (0.19), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 201 HIS 0.006 0.001 HIS A 266 PHE 0.018 0.002 PHE D 439 TYR 0.010 0.001 TYR A 251 ARG 0.009 0.001 ARG E 298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13867.09 seconds wall clock time: 239 minutes 55.03 seconds (14395.03 seconds total)