Starting phenix.real_space_refine on Sun Sep 29 13:50:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njs_12417/09_2024/7njs_12417_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njs_12417/09_2024/7njs_12417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njs_12417/09_2024/7njs_12417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njs_12417/09_2024/7njs_12417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njs_12417/09_2024/7njs_12417_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njs_12417/09_2024/7njs_12417_trim.cif" } resolution = 2.46 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= 0.001 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 107 5.16 5 C 23583 2.51 5 N 6405 2.21 5 O 7180 1.98 5 H 37346 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74642 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 7808 Classifications: {'peptide': 517} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 495} Chain: "B" Number of atoms: 7623 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 503, 7602 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 503, 7602 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 bond proxies already assigned to first conformer: 7635 Chain: "C" Number of atoms: 7942 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 521, 7900 Classifications: {'peptide': 521} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 496} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 521, 7900 Classifications: {'peptide': 521} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 496} Chain breaks: 2 bond proxies already assigned to first conformer: 7916 Chain: "D" Number of atoms: 7162 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Conformer: "B" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} bond proxies already assigned to first conformer: 7190 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: 7144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "G" Number of atoms: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 4567 Classifications: {'peptide': 297} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 287} Chain breaks: 1 Chain: "H" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1802 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2161 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "d" Number of atoms: 6640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 6640 Classifications: {'peptide': 437} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 424} Chain breaks: 1 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N APHE B 354 " occ=0.80 ... (38 atoms not shown) pdb=" HZ BPHE B 354 " occ=0.20 residue: pdb=" N APHE C 354 " occ=0.70 ... (38 atoms not shown) pdb=" HZ BPHE C 354 " occ=0.30 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 35.56, per 1000 atoms: 0.48 Number of scatterers: 74642 At special positions: 0 Unit cell: (139.44, 126.16, 250.66, 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 107 16.00 P 16 15.00 Mg 5 11.99 O 7180 8.00 N 6405 7.00 C 23583 6.00 H 37346 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.71 Conformation dependent library (CDL) restraints added in 6.3 seconds 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8886 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 0 sheets defined 55.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 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: 4.134A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.665A 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 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 243 through 263 Proline residue: A 250 - end of helix removed outlier: 3.612A pdb=" N ASN A 263 " --> pdb=" O HIS A 259 " (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 311 removed outlier: 4.004A pdb=" N ARG A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) 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: 4.861A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 5.549A 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: 5.154A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 475 " --> pdb=" O LEU A 472 " (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 9 through 19 removed outlier: 3.533A pdb=" N VAL B 19 " --> pdb=" O GLU B 16 " (cutoff:3.500A) 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 195 removed outlier: 3.852A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 5.017A 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 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.727A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.651A 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 309 removed outlier: 3.574A 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 406 removed outlier: 4.912A 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: 4.130A 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 Processing helix chain 'B' and resid 461 through 477 removed outlier: 4.863A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.685A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 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 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 178 through 195 removed outlier: 3.787A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.932A 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 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.703A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.538A 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 309 removed outlier: 3.522A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (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: 4.898A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.990A 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 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: 4.865A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 267 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: 4.319A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.593A 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: 4.689A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.895A 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 417 through 423 removed outlier: 3.674A pdb=" N GLU D 420 " --> pdb=" O MET D 417 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) 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 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 207 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: 4.899A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.679A 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: 4.030A 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 339 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: 4.302A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.700A 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 418 through 421 removed outlier: 3.592A pdb=" N GLN E 421 " --> pdb=" O ALA E 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 418 through 421' Processing helix chain 'E' and resid 432 through 443 Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 461 through 469 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 206 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 243 removed outlier: 4.848A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.861A 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: 4.427A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 removed outlier: 3.603A pdb=" N LYS F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) 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 389 removed outlier: 4.552A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.762A 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 411 Processing helix chain 'F' and resid 420 through 423 No H-bonds generated for 'chain 'F' and resid 420 through 423' 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 471 Processing helix chain 'G' and resid 4 through 59 Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 121 through 130 Processing helix chain 'G' and resid 147 through 163 Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 228 through 303 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 92 through 98 Processing helix chain 'H' and resid 104 through 117 Processing helix chain 'L' and resid 5 through 45 Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 51 through 79 removed outlier: 4.045A pdb=" N THR L 55 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.307A pdb=" N ALA L 66 " --> pdb=" O LEU L 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 45 Processing helix chain 'M' and resid 47 through 80 removed outlier: 3.822A pdb=" N GLN M 50 " --> pdb=" O PRO M 47 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLY M 51 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE M 54 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR M 55 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.756A pdb=" N ALA M 67 " --> pdb=" O VAL M 64 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE M 80 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 45 Processing helix chain 'N' and resid 47 through 79 removed outlier: 3.935A pdb=" N GLY N 51 " --> pdb=" O GLU N 48 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE N 54 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR N 55 " --> pdb=" O ARG N 52 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.586A pdb=" N GLU N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 45 Processing helix chain 'O' and resid 47 through 80 removed outlier: 4.033A pdb=" N GLY O 51 " --> pdb=" O GLU O 48 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE O 54 " --> pdb=" O GLY O 51 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR O 55 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.963A pdb=" N ALA O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL O 79 " --> pdb=" O ALA O 76 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE O 80 " --> pdb=" O LEU O 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 45 Processing helix chain 'P' and resid 50 through 80 removed outlier: 3.950A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix Processing helix chain 'Q' and resid 5 through 45 Processing helix chain 'Q' and resid 47 through 80 removed outlier: 3.842A pdb=" N GLN Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY Q 51 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU Q 53 " --> pdb=" O GLN Q 50 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE Q 54 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR Q 55 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) Proline residue: Q 56 - end of helix removed outlier: 3.514A pdb=" N GLU Q 65 " --> pdb=" O GLY Q 62 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE Q 80 " --> pdb=" O LEU Q 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 45 Processing helix chain 'R' and resid 47 through 80 removed outlier: 4.124A pdb=" N GLY R 51 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU R 53 " --> pdb=" O GLN R 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE R 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 4.167A pdb=" N ALA R 66 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE R 80 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 45 Processing helix chain 'S' and resid 50 through 80 Proline residue: S 56 - end of helix removed outlier: 3.539A pdb=" N ALA S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 45 Processing helix chain 'T' and resid 47 through 79 removed outlier: 4.702A pdb=" N GLY T 51 " --> pdb=" O GLU T 48 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR T 55 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.883A pdb=" N ALA T 66 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 51 Processing helix chain 'a' and resid 61 through 80 Processing helix chain 'a' and resid 88 through 108 removed outlier: 3.921A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL a 108 " --> pdb=" O ASN a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 129 No H-bonds generated for 'chain 'a' and resid 127 through 129' Processing helix chain 'a' and resid 131 through 153 Processing helix chain 'a' and resid 157 through 164 Processing helix chain 'a' and resid 168 through 205 Proline residue: a 172 - end of helix removed outlier: 4.535A pdb=" N LYS a 181 " --> pdb=" O GLU a 178 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 4.128A pdb=" N LEU a 187 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG a 188 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA a 195 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL a 200 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 244 removed outlier: 5.824A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.860A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 47 Processing helix chain 'b' and resid 50 through 146 removed outlier: 3.890A pdb=" N GLN b 82 " --> pdb=" O VAL b 78 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU b 145 " --> pdb=" O ARG b 141 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 160 Processing helix chain 'd' and resid 2 through 21 Processing helix chain 'd' and resid 23 through 136 Processing helix chain 'd' and resid 140 through 156 Processing helix chain 'd' and resid 174 through 190 Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 217 through 224 Processing helix chain 'd' and resid 231 through 241 Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 286 removed outlier: 3.944A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 304 Processing helix chain 'd' and resid 307 through 314 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 350 Processing helix chain 'd' and resid 357 through 372 removed outlier: 4.033A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 401 Processing helix chain 'd' and resid 413 through 415 No H-bonds generated for 'chain 'd' and resid 413 through 415' Processing helix chain 'd' and resid 432 through 442 1898 hydrogen bonds defined for protein. 4920 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: 23.38 Time building geometry restraints manager: 19.14 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: 37326 1.03 - 1.23: 558 1.23 - 1.43: 14817 1.43 - 1.62: 22347 1.62 - 1.82: 194 Bond restraints: 75242 Sorted by residual: bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C LEU C 47 " pdb=" O LEU C 47 " ideal model delta sigma weight residual 1.235 1.240 -0.005 4.70e-03 4.53e+04 1.20e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.20e+00 bond pdb=" CG PRO F 344 " pdb=" CD PRO F 344 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.70e-02 1.37e+03 9.65e-01 bond pdb=" CB MET d 109 " pdb=" CG MET d 109 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.27e-01 ... (remaining 75237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 135692 2.00 - 3.99: 554 3.99 - 5.99: 66 5.99 - 7.98: 11 7.98 - 9.98: 2 Bond angle restraints: 136325 Sorted by residual: angle pdb=" CB MET d 109 " pdb=" CG MET d 109 " pdb=" SD MET d 109 " ideal model delta sigma weight residual 112.70 122.68 -9.98 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 126.99 -5.29 1.80e+00 3.09e-01 8.63e+00 angle pdb=" C ASP E 254 " pdb=" N ASN E 255 " pdb=" CA ASN E 255 " ideal model delta sigma weight residual 121.70 126.97 -5.27 1.80e+00 3.09e-01 8.56e+00 angle pdb=" C ASP F 254 " pdb=" N ASN F 255 " pdb=" CA ASN F 255 " ideal model delta sigma weight residual 121.70 126.91 -5.21 1.80e+00 3.09e-01 8.37e+00 angle pdb=" CB MET R 21 " pdb=" CG MET R 21 " pdb=" SD MET R 21 " ideal model delta sigma weight residual 112.70 120.95 -8.25 3.00e+00 1.11e-01 7.56e+00 ... (remaining 136320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 32460 24.33 - 48.65: 1958 48.65 - 72.98: 706 72.98 - 97.30: 63 97.30 - 121.63: 1 Dihedral angle restraints: 35188 sinusoidal: 19492 harmonic: 15696 Sorted by residual: dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 178.37 121.63 1 2.00e+01 2.50e-03 3.66e+01 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 -134.69 74.69 1 2.00e+01 2.50e-03 1.77e+01 dihedral pdb=" CA GLY F 218 " pdb=" C GLY F 218 " pdb=" N GLN F 219 " pdb=" CA GLN F 219 " ideal model delta harmonic sigma weight residual -180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 35185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5189 0.058 - 0.116: 689 0.116 - 0.175: 74 0.175 - 0.233: 3 0.233 - 0.291: 9 Chirality restraints: 5964 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 -2.97 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C2' ATP F 600 " pdb=" C1' ATP F 600 " pdb=" C3' ATP F 600 " pdb=" O2' ATP F 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.11e+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 2.07e+00 ... (remaining 5961 not shown) Planarity restraints: 11437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 35 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO H 36 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO H 36 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 36 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL d 23 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO d 24 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO d 24 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO d 24 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE b 37 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C ILE b 37 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE b 37 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE b 38 " 0.009 2.00e-02 2.50e+03 ... (remaining 11434 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 3594 2.16 - 2.77: 148414 2.77 - 3.38: 227220 3.38 - 3.99: 296714 3.99 - 4.60: 462772 Nonbonded interactions: 1138714 Sorted by model distance: nonbonded pdb=" O ALA B 339 " pdb=" HG1 THR B 343 " model vdw 1.550 2.450 nonbonded pdb=" OE1 GLU Q 48 " pdb=" H GLU Q 48 " model vdw 1.587 2.450 nonbonded pdb=" O PRO a 207 " pdb=" H GLN a 211 " model vdw 1.590 2.450 nonbonded pdb=" O ALA B 192 " pdb=" HG1 THR B 195 " model vdw 1.597 2.450 nonbonded pdb=" O LEU a 187 " pdb=" H GLY a 191 " model vdw 1.599 2.450 ... (remaining 1138709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or resid 8 through 21 \ or (resid 30 and (name N or name CA or name C or name O or name CB or name CG o \ r 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 31 through 173 or resid 175 through 353 or resid 356 thr \ ough 407 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 41 \ 5 through 515 or resid 518 through 519 or resid 600 through 601)) selection = (chain 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or resid 8 through 21 \ or (resid 30 and (name N or name CA or name C or name O or name CB or name CG o \ r 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 31 through 173 or resid 175 through 353 or resid 356 thr \ ough 515 or resid 518 through 519 or resid 600 through 601)) selection = (chain 'C' and (resid 7 through 21 or resid 30 through 173 or resid 175 through \ 353 or resid 356 through 407 or (resid 414 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name OD2 or name HA or name HB2 or na \ me HB3)) or resid 415 through 514 or resid 532 or resid 537 through 538 or resid \ 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 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 through 452 or resid 455 through 471)) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = (chain 'T' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) } 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=0.20 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: 141.150 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: 1.080 Extract box with map and model: 2.440 Check model and map are aligned: 0.440 Set scattering table: 0.580 Process input model: 129.510 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.340 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: 0.020 Load rotamer database and sin/cos tables:10.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 288.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.002 0.029 37896 Z= 0.164 Angle : 0.496 9.975 51405 Z= 0.258 Chirality : 0.041 0.291 5964 Planarity : 0.003 0.045 6729 Dihedral : 16.979 121.626 13873 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.68 % Favored : 98.30 % Rotamer: Outliers : 1.22 % Allowed : 16.34 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 2.22 (0.12), residues: 4890 helix: 2.36 (0.10), residues: 2659 sheet: -0.12 (0.21), residues: 536 loop : 0.70 (0.16), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS E 97 PHE 0.014 0.001 PHE a 142 TYR 0.019 0.001 TYR a 145 ARG 0.010 0.000 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 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 305 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 258 time to evaluate : 4.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 400 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: F 173 MET cc_start: 0.8932 (mmt) cc_final: 0.8554 (mmt) REVERT: a 72 GLN cc_start: 0.8356 (tp-100) cc_final: 0.7987 (tp40) REVERT: b 70 ASP cc_start: 0.7753 (m-30) cc_final: 0.7486 (t0) outliers start: 47 outliers final: 39 residues processed: 302 average time/residue: 2.8123 time to fit residues: 1038.0429 Evaluate side-chains 262 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 222 time to evaluate : 4.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain F residue 64 CYS Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 93 SER Chi-restraints excluded: chain a residue 150 ILE Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain d residue 64 ASP Chi-restraints excluded: chain d residue 161 SER Chi-restraints excluded: chain d residue 265 SER Chi-restraints excluded: chain d residue 310 SER Chi-restraints excluded: chain d residue 428 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 2.9990 chunk 366 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 246 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 378 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 230 optimal weight: 0.8980 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 GLN C 335 ASN F 425 GLN G 25 GLN ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN R 86 GLN a 174 ASN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 131 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 37896 Z= 0.296 Angle : 0.521 7.278 51405 Z= 0.278 Chirality : 0.041 0.147 5964 Planarity : 0.004 0.052 6729 Dihedral : 7.932 117.463 5478 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.25 % Favored : 97.73 % Rotamer: Outliers : 1.85 % Allowed : 16.29 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.85 (0.12), residues: 4890 helix: 2.05 (0.10), residues: 2660 sheet: -0.37 (0.21), residues: 545 loop : 0.61 (0.16), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.004 0.001 HIS A 266 PHE 0.017 0.001 PHE a 142 TYR 0.019 0.001 TYR a 145 ARG 0.005 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 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 301 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 230 time to evaluate : 4.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 39 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6864 (m-30) REVERT: E 26 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6887 (tmt-80) REVERT: E 400 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: G 250 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: S 30 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7922 (mm) REVERT: T 48 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: a 72 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8224 (tp40) REVERT: a 199 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8643 (mm) REVERT: b 70 ASP cc_start: 0.7782 (m-30) cc_final: 0.7514 (t0) outliers start: 71 outliers final: 28 residues processed: 283 average time/residue: 2.9252 time to fit residues: 1016.8468 Evaluate side-chains 248 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 213 time to evaluate : 5.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 150 ILE Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 234 SER Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 161 SER Chi-restraints excluded: chain d residue 265 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 365 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 439 optimal weight: 5.9990 chunk 474 optimal weight: 6.9990 chunk 391 optimal weight: 3.9990 chunk 435 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 352 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 37896 Z= 0.339 Angle : 0.531 9.126 51405 Z= 0.282 Chirality : 0.041 0.159 5964 Planarity : 0.004 0.047 6729 Dihedral : 7.771 115.343 5446 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.56 % Favored : 97.42 % Rotamer: Outliers : 1.95 % Allowed : 15.85 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.59 (0.12), residues: 4890 helix: 1.83 (0.10), residues: 2654 sheet: -0.53 (0.21), residues: 543 loop : 0.50 (0.16), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.005 0.001 HIS A 266 PHE 0.017 0.001 PHE a 142 TYR 0.018 0.001 TYR a 145 ARG 0.005 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 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 298 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 223 time to evaluate : 4.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 26 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7377 (tmt-80) REVERT: E 219 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8046 (mt0) REVERT: F 173 MET cc_start: 0.8972 (mmt) cc_final: 0.8597 (mmt) REVERT: G 250 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: S 30 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.8017 (mm) REVERT: T 48 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: a 199 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8658 (mm) REVERT: b 70 ASP cc_start: 0.7778 (m-30) cc_final: 0.7503 (t0) outliers start: 75 outliers final: 32 residues processed: 281 average time/residue: 2.8141 time to fit residues: 965.7423 Evaluate side-chains 249 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 211 time to evaluate : 3.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 409 GLU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain d residue 64 ASP Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 265 SER Chi-restraints excluded: chain d residue 310 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 5.9990 chunk 330 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 295 optimal weight: 0.9980 chunk 440 optimal weight: 0.6980 chunk 466 optimal weight: 4.9990 chunk 230 optimal weight: 0.4980 chunk 417 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN F 425 GLN N 50 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37896 Z= 0.240 Angle : 0.503 7.993 51405 Z= 0.265 Chirality : 0.040 0.152 5964 Planarity : 0.004 0.046 6729 Dihedral : 7.428 114.655 5436 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 1.54 % Allowed : 16.37 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.60 (0.12), residues: 4890 helix: 1.87 (0.10), residues: 2653 sheet: -0.67 (0.21), residues: 540 loop : 0.52 (0.16), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS A 259 PHE 0.017 0.001 PHE a 142 TYR 0.018 0.001 TYR a 145 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 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 278 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 219 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6893 (m-30) REVERT: E 26 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6999 (tmt-80) REVERT: E 219 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8012 (mt0) REVERT: E 400 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: F 173 MET cc_start: 0.8944 (mmt) cc_final: 0.8492 (mmt) REVERT: G 250 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: S 30 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7966 (mm) REVERT: T 48 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: a 72 GLN cc_start: 0.8500 (tp-100) cc_final: 0.8235 (tp40) REVERT: a 199 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8665 (mm) REVERT: b 70 ASP cc_start: 0.7787 (m-30) cc_final: 0.7478 (t0) outliers start: 59 outliers final: 29 residues processed: 266 average time/residue: 2.7021 time to fit residues: 882.6621 Evaluate side-chains 243 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 206 time to evaluate : 4.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 137 SER Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 82 GLN Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain d residue 64 ASP Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 265 SER Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 310 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 347 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 398 optimal weight: 2.9990 chunk 322 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 419 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 37896 Z= 0.310 Angle : 0.521 9.031 51405 Z= 0.275 Chirality : 0.040 0.153 5964 Planarity : 0.004 0.048 6729 Dihedral : 7.473 114.246 5433 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.66 % Favored : 97.32 % Rotamer: Outliers : 1.54 % Allowed : 16.34 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.53 (0.12), residues: 4890 helix: 1.81 (0.10), residues: 2653 sheet: -0.70 (0.21), residues: 530 loop : 0.49 (0.16), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.005 0.001 HIS A 266 PHE 0.017 0.001 PHE a 142 TYR 0.019 0.001 TYR a 145 ARG 0.004 0.000 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 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 276 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 217 time to evaluate : 4.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 26 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7369 (tmt-80) REVERT: E 219 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8008 (mt0) REVERT: E 400 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: F 173 MET cc_start: 0.8954 (mmt) cc_final: 0.8491 (mmt) REVERT: G 250 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: S 30 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8017 (mm) REVERT: T 48 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: a 72 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8215 (tp40) REVERT: a 199 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8709 (mm) REVERT: b 70 ASP cc_start: 0.7794 (m-30) cc_final: 0.7497 (t0) outliers start: 59 outliers final: 30 residues processed: 261 average time/residue: 2.8671 time to fit residues: 909.9753 Evaluate side-chains 247 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 210 time to evaluate : 4.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 234 SER Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 142 SER Chi-restraints excluded: chain d residue 64 ASP Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 185 GLU Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 310 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 2.9990 chunk 420 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 467 optimal weight: 2.9990 chunk 387 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 245 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN F 425 GLN N 50 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37896 Z= 0.184 Angle : 0.486 7.902 51405 Z= 0.255 Chirality : 0.039 0.149 5964 Planarity : 0.004 0.045 6729 Dihedral : 7.208 113.580 5429 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.38 % Favored : 97.60 % Rotamer: Outliers : 1.17 % Allowed : 16.78 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.65 (0.12), residues: 4890 helix: 1.94 (0.10), residues: 2651 sheet: -0.84 (0.21), residues: 530 loop : 0.57 (0.16), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS A 259 PHE 0.016 0.001 PHE a 142 TYR 0.018 0.001 TYR a 145 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 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 261 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 216 time to evaluate : 4.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 26 ARG cc_start: 0.7274 (mmt90) cc_final: 0.7064 (mpt-90) REVERT: E 26 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6899 (tmt-80) REVERT: E 219 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: E 400 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: F 173 MET cc_start: 0.8930 (mmt) cc_final: 0.8479 (mmt) REVERT: G 250 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: S 30 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7915 (mm) REVERT: T 48 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: a 72 GLN cc_start: 0.8424 (tp-100) cc_final: 0.8091 (tp40) REVERT: a 199 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8679 (mm) REVERT: b 70 ASP cc_start: 0.7785 (m-30) cc_final: 0.7493 (t0) REVERT: d 356 ARG cc_start: 0.7291 (mmm160) cc_final: 0.7005 (mtp85) outliers start: 45 outliers final: 25 residues processed: 250 average time/residue: 2.8557 time to fit residues: 871.0841 Evaluate side-chains 241 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 209 time to evaluate : 4.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain b residue 82 GLN Chi-restraints excluded: chain d residue 64 ASP Chi-restraints excluded: chain d residue 161 SER Chi-restraints excluded: chain d residue 185 GLU Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 310 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 341 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 393 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 465 optimal weight: 6.9990 chunk 291 optimal weight: 0.6980 chunk 283 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 37896 Z= 0.339 Angle : 0.527 8.833 51405 Z= 0.279 Chirality : 0.041 0.157 5964 Planarity : 0.004 0.047 6729 Dihedral : 7.431 113.296 5427 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.75 % Favored : 97.23 % Rotamer: Outliers : 1.41 % Allowed : 16.71 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.54 (0.12), residues: 4890 helix: 1.83 (0.10), residues: 2650 sheet: -0.79 (0.21), residues: 532 loop : 0.50 (0.16), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.004 0.001 HIS A 266 PHE 0.017 0.001 PHE a 142 TYR 0.020 0.001 TYR a 145 ARG 0.004 0.000 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 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 273 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 219 time to evaluate : 4.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 26 ARG cc_start: 0.7368 (mmt90) cc_final: 0.7147 (mmt180) REVERT: E 26 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7377 (tmt-80) REVERT: E 219 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.7998 (mt0) REVERT: F 173 MET cc_start: 0.8949 (mmt) cc_final: 0.8485 (mmt) REVERT: G 250 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: S 30 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.8019 (mm) REVERT: T 48 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: a 72 GLN cc_start: 0.8462 (tp-100) cc_final: 0.8060 (tp40) REVERT: a 199 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8693 (mm) REVERT: b 70 ASP cc_start: 0.7793 (m-30) cc_final: 0.7491 (t0) outliers start: 54 outliers final: 31 residues processed: 258 average time/residue: 2.9350 time to fit residues: 928.8544 Evaluate side-chains 250 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 213 time to evaluate : 4.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 48 GLU Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 82 GLN Chi-restraints excluded: chain d residue 64 ASP Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 161 SER Chi-restraints excluded: chain d residue 185 GLU Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 310 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 295 optimal weight: 0.5980 chunk 317 optimal weight: 2.9990 chunk 230 optimal weight: 0.5980 chunk 43 optimal weight: 0.1980 chunk 365 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN F 425 GLN N 50 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37896 Z= 0.172 Angle : 0.487 9.592 51405 Z= 0.254 Chirality : 0.039 0.148 5964 Planarity : 0.004 0.044 6729 Dihedral : 7.129 113.065 5427 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.34 % Favored : 97.64 % Rotamer: Outliers : 0.99 % Allowed : 17.23 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.67 (0.12), residues: 4890 helix: 1.96 (0.10), residues: 2652 sheet: -0.91 (0.21), residues: 531 loop : 0.60 (0.16), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS A 259 PHE 0.016 0.001 PHE a 142 TYR 0.018 0.001 TYR a 145 ARG 0.003 0.000 ARG O 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 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 258 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 220 time to evaluate : 4.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 26 ARG cc_start: 0.7347 (mmt90) cc_final: 0.7132 (mpt-90) REVERT: E 26 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6899 (tmt-80) REVERT: E 219 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7955 (mt0) REVERT: E 400 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: F 173 MET cc_start: 0.8911 (mmt) cc_final: 0.8464 (mmt) REVERT: G 250 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: a 72 GLN cc_start: 0.8419 (tp-100) cc_final: 0.8156 (tp40) REVERT: a 199 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8633 (mm) REVERT: b 70 ASP cc_start: 0.7745 (m-30) cc_final: 0.7482 (t0) outliers start: 38 outliers final: 25 residues processed: 247 average time/residue: 2.9620 time to fit residues: 898.2243 Evaluate side-chains 239 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 209 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 400 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 82 GLN Chi-restraints excluded: chain d residue 93 SER Chi-restraints excluded: chain d residue 161 SER Chi-restraints excluded: chain d residue 185 GLU Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 310 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 0.9980 chunk 445 optimal weight: 5.9990 chunk 406 optimal weight: 3.9990 chunk 433 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 340 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 392 optimal weight: 0.6980 chunk 410 optimal weight: 0.5980 chunk 432 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 410 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37896 Z= 0.193 Angle : 0.487 10.138 51405 Z= 0.254 Chirality : 0.039 0.141 5964 Planarity : 0.004 0.045 6729 Dihedral : 7.063 111.797 5427 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.42 % Favored : 97.56 % Rotamer: Outliers : 0.94 % Allowed : 17.10 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.72 (0.12), residues: 4890 helix: 2.00 (0.10), residues: 2650 sheet: -0.93 (0.21), residues: 531 loop : 0.62 (0.16), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.005 0.001 HIS d 410 PHE 0.017 0.001 PHE a 142 TYR 0.019 0.001 TYR a 145 ARG 0.004 0.000 ARG O 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 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 249 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 213 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 26 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6957 (tmt-80) REVERT: E 219 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: F 173 MET cc_start: 0.8912 (mmt) cc_final: 0.8470 (mmt) REVERT: G 250 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: S 30 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7924 (mm) REVERT: a 72 GLN cc_start: 0.8434 (tp-100) cc_final: 0.8168 (tp40) REVERT: a 199 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8627 (mm) REVERT: b 70 ASP cc_start: 0.7773 (m-30) cc_final: 0.7506 (t0) outliers start: 36 outliers final: 24 residues processed: 240 average time/residue: 2.9406 time to fit residues: 855.9309 Evaluate side-chains 237 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 208 time to evaluate : 4.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 227 ASP Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain a residue 69 LEU Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 82 GLN Chi-restraints excluded: chain d residue 161 SER Chi-restraints excluded: chain d residue 185 GLU Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 310 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 1.9990 chunk 458 optimal weight: 0.6980 chunk 279 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 481 optimal weight: 2.9990 chunk 442 optimal weight: 0.6980 chunk 383 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 295 optimal weight: 0.5980 chunk 234 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37896 Z= 0.203 Angle : 0.494 11.074 51405 Z= 0.257 Chirality : 0.039 0.193 5964 Planarity : 0.004 0.043 6729 Dihedral : 7.028 111.065 5425 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.38 % Favored : 97.60 % Rotamer: Outliers : 0.86 % Allowed : 17.33 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.72 (0.12), residues: 4890 helix: 2.00 (0.10), residues: 2650 sheet: -0.93 (0.21), residues: 532 loop : 0.63 (0.16), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.003 0.001 HIS A 266 PHE 0.016 0.001 PHE a 142 TYR 0.018 0.001 TYR a 145 ARG 0.005 0.000 ARG O 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9780 Ramachandran restraints generated. 4890 Oldfield, 0 Emsley, 4890 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 249 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 4.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 26 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6887 (tmt-80) REVERT: E 219 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: F 173 MET cc_start: 0.8902 (mmt) cc_final: 0.8461 (mmt) REVERT: G 250 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: a 72 GLN cc_start: 0.8437 (tp-100) cc_final: 0.8171 (tp40) REVERT: a 199 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8630 (mm) REVERT: b 70 ASP cc_start: 0.7758 (m-30) cc_final: 0.7497 (t0) outliers start: 33 outliers final: 24 residues processed: 243 average time/residue: 2.9051 time to fit residues: 859.2467 Evaluate side-chains 240 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 212 time to evaluate : 4.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 59 ILE Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain P residue 20 ILE Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 242 SER Chi-restraints excluded: chain b residue 82 GLN Chi-restraints excluded: chain d residue 161 SER Chi-restraints excluded: chain d residue 185 GLU Chi-restraints excluded: chain d residue 292 VAL Chi-restraints excluded: chain d residue 310 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 3.9990 chunk 408 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 353 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 383 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 394 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.074811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.055614 restraints weight = 273070.322| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.65 r_work: 0.2790 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 37896 Z= 0.251 Angle : 0.505 11.332 51405 Z= 0.264 Chirality : 0.040 0.145 5964 Planarity : 0.004 0.044 6729 Dihedral : 7.126 110.786 5425 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.54 % Favored : 97.44 % Rotamer: Outliers : 1.09 % Allowed : 17.02 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % 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: 1.68 (0.12), residues: 4890 helix: 1.96 (0.10), residues: 2650 sheet: -0.89 (0.21), residues: 532 loop : 0.62 (0.16), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 218 HIS 0.004 0.001 HIS A 266 PHE 0.017 0.001 PHE a 142 TYR 0.018 0.001 TYR a 145 ARG 0.004 0.000 ARG O 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18137.91 seconds wall clock time: 309 minutes 9.54 seconds (18549.54 seconds total)