Starting phenix.real_space_refine on Sun Sep 29 14:08:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njn_12392/09_2024/7njn_12392_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njn_12392/09_2024/7njn_12392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njn_12392/09_2024/7njn_12392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njn_12392/09_2024/7njn_12392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njn_12392/09_2024/7njn_12392_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njn_12392/09_2024/7njn_12392_trim.cif" } resolution = 2.64 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 23550 2.51 5 N 6397 2.21 5 O 7174 1.98 5 H 37299 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74548 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 7631 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 481} Chain breaks: 2 Chain: "B" Number of atoms: 7639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 7639 Classifications: {'peptide': 505} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 483} Chain breaks: 2 Chain: "C" Number of atoms: 8129 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 536, 8109 Classifications: {'peptide': 536} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 511} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 536, 8109 Classifications: {'peptide': 536} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 511} Chain breaks: 2 bond proxies already assigned to first conformer: 8147 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: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7166 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "G" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4513 Classifications: {'peptide': 293} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 283} 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: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "M" 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: "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: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "P" 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: "Q" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1156 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "R" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1187 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: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} 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: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2172 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "d" Number of atoms: 6592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 6592 Classifications: {'peptide': 433} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 421} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 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: 2 residue: pdb=" N APHE C 354 " occ=0.60 ... (38 atoms not shown) pdb=" HZ BPHE C 354 " occ=0.40 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 33.97, per 1000 atoms: 0.46 Number of scatterers: 74548 At special positions: 0 Unit cell: (134.46, 127.82, 253.98, 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 7174 8.00 N 6397 7.00 C 23550 6.00 H 37299 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: 15.09 Conformation dependent library (CDL) restraints added in 5.3 seconds 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8872 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 0 sheets defined 55.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' 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: 3.775A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 5.033A 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: 3.657A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.548A 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 309 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 393 through 405 removed outlier: 4.710A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (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: 4.751A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 478 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.836A pdb=" N LYS A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 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: 3.741A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.679A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.738A 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 311 removed outlier: 3.559A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 384 through 405 removed outlier: 4.599A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.762A 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 464 through 477 Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'C' and resid 10 through 21 removed outlier: 4.989A pdb=" N ILE C 15 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.756A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.879A 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 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.719A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.505A 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: 3.540A 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 407 Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 461 through 477 removed outlier: 4.905A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 489 Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.935A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' 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: 4.828A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 318 through 326 removed outlier: 4.432A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.651A 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: 4.721A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 412 Processing helix chain 'D' and resid 420 through 423 No H-bonds generated for 'chain 'D' and resid 420 through 423' Processing helix chain 'D' and resid 432 through 443 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 194 through 206 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 243 removed outlier: 5.141A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.957A 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: 4.227A pdb=" N ARG E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 318 through 324 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 363 through 388 removed outlier: 4.408A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 412 Processing helix chain 'E' and resid 417 through 419 No H-bonds generated for 'chain 'E' and resid 417 through 419' 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 470 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: 4.730A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 270 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: 4.505A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 Processing helix chain 'F' and resid 358 through 361 No H-bonds generated for 'chain 'F' and resid 358 through 361' Processing helix chain 'F' and resid 363 through 381 Processing helix chain 'F' and resid 383 through 389 removed outlier: 3.624A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 396 through 412 Processing helix chain 'F' and resid 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 60 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 129 Processing helix chain 'G' and resid 147 through 163 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 79 removed outlier: 4.503A pdb=" N GLY L 51 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR L 55 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.504A pdb=" N GLY L 62 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU L 65 " --> pdb=" O GLY L 62 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE L 69 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 45 Processing helix chain 'M' and resid 47 through 78 removed outlier: 4.147A pdb=" N GLY M 51 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE M 54 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR M 55 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.686A pdb=" N VAL M 61 " --> pdb=" O PHE M 58 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU M 63 " --> pdb=" O THR M 60 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA M 67 " --> pdb=" O VAL M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 45 Processing helix chain 'N' and resid 47 through 79 removed outlier: 3.846A pdb=" N GLN N 50 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY N 51 " --> pdb=" O GLU N 48 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR N 55 " --> pdb=" O ARG N 52 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 4.045A pdb=" N GLU N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA N 66 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET N 75 " --> pdb=" O LEU N 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 45 Processing helix chain 'O' and resid 47 through 79 removed outlier: 4.531A pdb=" N GLY O 51 " --> pdb=" O GLU O 48 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE O 54 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 4.033A pdb=" N VAL O 61 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU O 65 " --> pdb=" O GLY O 62 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ALA O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE O 70 " --> pdb=" O ALA O 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 45 Processing helix chain 'P' and resid 47 through 79 removed outlier: 3.908A pdb=" N GLN P 50 " --> pdb=" O PRO P 47 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY P 51 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.919A pdb=" N VAL P 61 " --> pdb=" O PHE P 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 45 Processing helix chain 'Q' and resid 47 through 79 removed outlier: 3.849A pdb=" N GLN Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLY Q 51 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR Q 55 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) Proline residue: Q 56 - end of helix removed outlier: 3.618A pdb=" N VAL Q 79 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 45 Processing helix chain 'R' and resid 47 through 79 removed outlier: 4.001A pdb=" N GLN R 50 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY R 51 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE R 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 4.595A pdb=" N ALA R 66 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 45 Processing helix chain 'S' and resid 47 through 80 removed outlier: 3.716A pdb=" N GLY S 51 " --> pdb=" O GLU S 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU S 53 " --> pdb=" O GLN S 50 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE S 54 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.652A pdb=" N VAL S 61 " --> pdb=" O PHE S 58 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU S 65 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA S 66 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU S 72 " --> pdb=" O PHE S 69 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL S 79 " --> pdb=" O ALA S 76 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE S 80 " --> pdb=" O LEU S 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 45 Processing helix chain 'T' and resid 47 through 80 removed outlier: 4.891A pdb=" N GLY T 51 " --> pdb=" O GLU T 48 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR T 55 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 4.019A pdb=" N GLY T 62 " --> pdb=" O ILE T 59 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU T 65 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA T 67 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA T 76 " --> pdb=" O ALA T 73 " (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 87 through 108 Proline residue: a 91 - end of helix removed outlier: 4.060A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 4.470A 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 155 through 164 Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 168 through 205 Proline residue: a 172 - end of helix removed outlier: 4.832A pdb=" N LYS a 181 " --> pdb=" O GLU a 178 " (cutoff:3.500A) Proline residue: a 182 - end of helix removed outlier: 4.112A pdb=" N LEU a 187 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG a 188 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA a 195 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL a 200 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 244 removed outlier: 5.726A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.904A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 47 removed outlier: 3.697A pdb=" N VAL b 34 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 146 removed outlier: 3.881A pdb=" N GLU b 145 " --> pdb=" O ARG b 141 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 159 Processing helix chain 'd' and resid 2 through 138 removed outlier: 4.380A pdb=" N VAL d 23 " --> pdb=" O VAL d 19 " (cutoff:3.500A) Proline residue: d 24 - end of helix removed outlier: 3.784A pdb=" N ALA d 138 " --> pdb=" O ARG d 134 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 156 Processing helix chain 'd' and resid 174 through 193 removed outlier: 3.775A pdb=" N GLY d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLY d 193 " --> pdb=" O SER d 189 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 217 through 224 Processing helix chain 'd' and resid 232 through 241 Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 285 Processing helix chain 'd' and resid 289 through 305 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 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 441 1876 hydrogen bonds defined for protein. 4731 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: 28.61 Time building geometry restraints manager: 18.58 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: 37279 1.03 - 1.23: 56 1.23 - 1.42: 15288 1.42 - 1.62: 22323 1.62 - 1.81: 194 Bond restraints: 75140 Sorted by residual: bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" CG1 ILE B 504 " pdb=" CD1 ILE B 504 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.84e+00 bond pdb=" CB PRO C 530 " pdb=" CG PRO C 530 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.61e+00 bond pdb=" CG PRO F 344 " pdb=" CD PRO F 344 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.60e+00 bond pdb=" CG1 ILE S 30 " pdb=" CD1 ILE S 30 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.49e+00 ... (remaining 75135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 133426 1.43 - 2.85: 2401 2.85 - 4.28: 261 4.28 - 5.70: 31 5.70 - 7.13: 19 Bond angle restraints: 136138 Sorted by residual: angle pdb=" N ILE C 337 " pdb=" CA ILE C 337 " pdb=" C ILE C 337 " ideal model delta sigma weight residual 112.29 108.56 3.73 9.40e-01 1.13e+00 1.57e+01 angle pdb=" C ASP F 254 " pdb=" N ASN F 255 " pdb=" CA ASN F 255 " ideal model delta sigma weight residual 121.70 127.58 -5.88 1.80e+00 3.09e-01 1.07e+01 angle pdb=" C ASP E 254 " pdb=" N ASN E 255 " pdb=" CA ASN E 255 " ideal model delta sigma weight residual 121.70 127.55 -5.85 1.80e+00 3.09e-01 1.06e+01 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 127.40 -5.70 1.80e+00 3.09e-01 1.00e+01 angle pdb=" N VAL A 519 " pdb=" CA VAL A 519 " pdb=" C VAL A 519 " ideal model delta sigma weight residual 111.91 109.25 2.66 8.90e-01 1.26e+00 8.92e+00 ... (remaining 136133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.91: 33424 28.91 - 57.82: 1550 57.82 - 86.72: 142 86.72 - 115.63: 9 115.63 - 144.54: 2 Dihedral angle restraints: 35127 sinusoidal: 19467 harmonic: 15660 Sorted by residual: dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 84.54 -144.54 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 172.87 127.14 1 2.00e+01 2.50e-03 3.85e+01 dihedral pdb=" O1B ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PB ADP E 600 " pdb=" PA ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -150.00 89.99 1 2.00e+01 2.50e-03 2.40e+01 ... (remaining 35124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 5148 0.059 - 0.118: 736 0.118 - 0.176: 62 0.176 - 0.235: 2 0.235 - 0.294: 10 Chirality restraints: 5958 Sorted by residual: chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C3' ATP B 600 " pdb=" C2' ATP B 600 " pdb=" C4' ATP B 600 " pdb=" O3' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP A 600 " pdb=" C2' ATP A 600 " pdb=" C4' ATP A 600 " pdb=" O3' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 5955 not shown) Planarity restraints: 11412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 529 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.35e+00 pdb=" N PRO C 530 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 530 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 530 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR a 95 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.33e+00 pdb=" C THR a 95 " -0.032 2.00e-02 2.50e+03 pdb=" O THR a 95 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE a 96 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 467 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C PHE B 467 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE B 467 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU B 468 " 0.010 2.00e-02 2.50e+03 ... (remaining 11409 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 2677 2.13 - 2.75: 143636 2.75 - 3.37: 228227 3.37 - 3.98: 294474 3.98 - 4.60: 463616 Nonbonded interactions: 1132630 Sorted by model distance: nonbonded pdb=" H VAL D 277 " pdb=" OE2 GLU G 292 " model vdw 1.516 2.450 nonbonded pdb="HH22 ARG G 71 " pdb=" O PHE G 161 " model vdw 1.534 2.450 nonbonded pdb=" O PRO a 91 " pdb=" HG1 THR a 95 " model vdw 1.535 2.450 nonbonded pdb="HH22 ARG H 55 " pdb=" O ASP H 59 " model vdw 1.544 2.450 nonbonded pdb=" O ILE a 77 " pdb=" H ILE a 81 " model vdw 1.558 2.450 ... (remaining 1132625 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 9 through 22 or (resid 29 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3)) or resid 30 through 353 or resi \ d 355 through 406 or resid 415 through 521 or resid 600 through 601)) selection = (chain 'B' and ((resid 9 and (name N or name CA or name C or name O or name CB o \ r name HA or name HB1 or name HB2 or name HB3)) or resid 10 through 22 or resid \ 29 through 353 or resid 355 through 406 or resid 415 through 521 or resid 600 th \ rough 601)) selection = (chain 'C' and ((resid 9 and (name N or name CA or name C or name O or name CB o \ r name HA or name HB1 or name HB2 or name HB3)) or resid 10 through 22 or (resid \ 29 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 or name H \ G3)) or resid 30 through 353 or resid 355 through 406 or resid 415 through 521 o \ r 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 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 9 through 452 or resid 455 through 471)) } ncs_group { reference = (chain 'L' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'M' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'N' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'O' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'P' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = chain 'Q' selection = (chain 'R' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'S' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'T' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) } 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=0.40 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: 8.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.030 Extract box with map and model: 2.990 Check model and map are aligned: 0.420 Set scattering table: 0.530 Process input model: 133.510 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.310 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.004 0.063 37841 Z= 0.252 Angle : 0.516 7.130 51321 Z= 0.276 Chirality : 0.042 0.294 5958 Planarity : 0.004 0.072 6714 Dihedral : 14.883 144.541 13853 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.48 (0.12), residues: 4875 helix: 1.68 (0.10), residues: 2620 sheet: -0.25 (0.21), residues: 532 loop : 0.48 (0.16), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 21 HIS 0.005 0.001 HIS A 43 PHE 0.024 0.001 PHE Q 74 TYR 0.009 0.001 TYR d 401 ARG 0.007 0.000 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 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 391 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 4.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 ILE cc_start: 0.8190 (mt) cc_final: 0.7831 (mt) REVERT: P 58 PHE cc_start: 0.6955 (m-10) cc_final: 0.6247 (m-10) REVERT: S 75 MET cc_start: 0.8515 (tmm) cc_final: 0.8300 (tmm) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 3.0807 time to fit residues: 1458.3958 Evaluate side-chains 258 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 4.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 9.9990 chunk 366 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 246 optimal weight: 0.5980 chunk 195 optimal weight: 0.8980 chunk 378 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN E 377 GLN N 50 GLN O 6 ASN O 71 ASN a 104 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN b 131 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37841 Z= 0.222 Angle : 0.512 7.736 51321 Z= 0.270 Chirality : 0.040 0.143 5958 Planarity : 0.004 0.071 6714 Dihedral : 7.139 132.197 5401 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 0.39 % Allowed : 6.56 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.35 (0.12), residues: 4875 helix: 1.60 (0.10), residues: 2634 sheet: -0.61 (0.20), residues: 555 loop : 0.51 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 218 HIS 0.005 0.001 HIS B 479 PHE 0.017 0.001 PHE P 58 TYR 0.025 0.001 TYR a 145 ARG 0.006 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 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 295 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 281 time to evaluate : 5.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 54 PHE cc_start: 0.8614 (m-10) cc_final: 0.8374 (m-80) REVERT: S 75 MET cc_start: 0.8602 (tmm) cc_final: 0.8259 (tmm) REVERT: a 73 MET cc_start: 0.8186 (mmt) cc_final: 0.7824 (mmt) outliers start: 14 outliers final: 11 residues processed: 288 average time/residue: 2.7262 time to fit residues: 968.2261 Evaluate side-chains 273 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 262 time to evaluate : 4.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain S residue 45 ARG Chi-restraints excluded: chain a residue 117 ASP Chi-restraints excluded: chain a residue 151 TRP Chi-restraints excluded: chain d residue 351 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 365 optimal weight: 5.9990 chunk 298 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 439 optimal weight: 4.9990 chunk 474 optimal weight: 9.9990 chunk 391 optimal weight: 4.9990 chunk 435 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 352 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 421 GLN H 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 37841 Z= 0.336 Angle : 0.528 8.437 51321 Z= 0.279 Chirality : 0.041 0.155 5958 Planarity : 0.004 0.055 6714 Dihedral : 7.086 121.532 5401 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.27 % Rotamer: Outliers : 0.70 % Allowed : 7.50 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.23 (0.12), residues: 4875 helix: 1.49 (0.10), residues: 2642 sheet: -0.72 (0.21), residues: 540 loop : 0.46 (0.16), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 201 HIS 0.004 0.001 HIS A 43 PHE 0.015 0.001 PHE a 97 TYR 0.025 0.001 TYR a 145 ARG 0.007 0.000 ARG E 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 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 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 272 time to evaluate : 4.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7395 (mm-30) REVERT: L 32 ASP cc_start: 0.8516 (m-30) cc_final: 0.8036 (m-30) REVERT: S 21 MET cc_start: 0.8492 (mmm) cc_final: 0.8104 (mmm) REVERT: S 75 MET cc_start: 0.8634 (tmm) cc_final: 0.8369 (tmm) REVERT: a 73 MET cc_start: 0.8198 (mmt) cc_final: 0.7868 (mmt) REVERT: b 82 GLN cc_start: 0.7760 (tp-100) cc_final: 0.7535 (tp-100) outliers start: 26 outliers final: 11 residues processed: 287 average time/residue: 2.7093 time to fit residues: 969.0453 Evaluate side-chains 270 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 258 time to evaluate : 4.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain E residue 466 LYS Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain a residue 117 ASP Chi-restraints excluded: chain a residue 151 TRP 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: 5.9990 chunk 228 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 209 optimal weight: 0.2980 chunk 295 optimal weight: 3.9990 chunk 440 optimal weight: 5.9990 chunk 466 optimal weight: 6.9990 chunk 230 optimal weight: 0.9990 chunk 417 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 GLN M 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 37841 Z= 0.349 Angle : 0.533 8.900 51321 Z= 0.281 Chirality : 0.041 0.157 5958 Planarity : 0.004 0.058 6714 Dihedral : 7.077 116.298 5401 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 0.73 % Allowed : 8.20 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.15 (0.12), residues: 4875 helix: 1.44 (0.10), residues: 2640 sheet: -0.78 (0.21), residues: 535 loop : 0.39 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 201 HIS 0.005 0.001 HIS A 43 PHE 0.014 0.001 PHE F 257 TYR 0.023 0.001 TYR a 145 ARG 0.005 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 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 300 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 273 time to evaluate : 4.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 444 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8128 (mttt) REVERT: a 73 MET cc_start: 0.8247 (mmt) cc_final: 0.7893 (mmt) outliers start: 27 outliers final: 14 residues processed: 291 average time/residue: 2.6710 time to fit residues: 955.0973 Evaluate side-chains 264 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 249 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 466 LYS Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 117 ASP Chi-restraints excluded: chain a residue 151 TRP Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 347 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 398 optimal weight: 4.9990 chunk 322 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 238 optimal weight: 0.7980 chunk 419 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 71 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 37841 Z= 0.243 Angle : 0.507 8.403 51321 Z= 0.266 Chirality : 0.040 0.151 5958 Planarity : 0.004 0.059 6714 Dihedral : 6.965 114.042 5401 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.55 % Favored : 97.39 % Rotamer: Outliers : 0.83 % Allowed : 8.70 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.24 (0.12), residues: 4875 helix: 1.53 (0.10), residues: 2640 sheet: -0.83 (0.21), residues: 515 loop : 0.42 (0.16), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.003 0.001 HIS A 43 PHE 0.015 0.001 PHE a 97 TYR 0.020 0.001 TYR a 145 ARG 0.003 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 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 299 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 268 time to evaluate : 4.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: F 444 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8100 (mttt) REVERT: a 73 MET cc_start: 0.8223 (mmt) cc_final: 0.7818 (mmt) outliers start: 31 outliers final: 12 residues processed: 288 average time/residue: 2.6523 time to fit residues: 941.9300 Evaluate side-chains 267 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 253 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 466 LYS Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain M residue 70 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain a residue 151 TRP Chi-restraints excluded: chain d residue 155 GLU 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: 0.9990 chunk 92 optimal weight: 0.4980 chunk 274 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 467 optimal weight: 1.9990 chunk 387 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 245 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 71 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 37841 Z= 0.168 Angle : 0.484 7.684 51321 Z= 0.251 Chirality : 0.039 0.143 5958 Planarity : 0.004 0.057 6714 Dihedral : 6.739 109.844 5401 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.46 % Favored : 97.47 % Rotamer: Outliers : 0.76 % Allowed : 9.19 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.39 (0.13), residues: 4875 helix: 1.68 (0.10), residues: 2643 sheet: -0.92 (0.22), residues: 515 loop : 0.50 (0.16), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 201 HIS 0.003 0.001 HIS a 16 PHE 0.019 0.001 PHE R 74 TYR 0.021 0.001 TYR a 145 ARG 0.003 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 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 313 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 285 time to evaluate : 4.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 466 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8255 (ttpm) REVERT: F 444 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8079 (mttt) REVERT: H 50 MET cc_start: 0.8177 (tmm) cc_final: 0.7866 (tmm) outliers start: 28 outliers final: 11 residues processed: 304 average time/residue: 2.7031 time to fit residues: 1008.5595 Evaluate side-chains 270 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 258 time to evaluate : 4.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain E residue 466 LYS Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain a residue 117 ASP Chi-restraints excluded: chain a residue 151 TRP Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain b residue 95 GLN Chi-restraints excluded: chain d residue 81 GLU Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 341 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 393 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 465 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 71 ASN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 37841 Z= 0.400 Angle : 0.541 9.120 51321 Z= 0.285 Chirality : 0.042 0.163 5958 Planarity : 0.004 0.055 6714 Dihedral : 7.010 113.792 5401 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.77 % Favored : 97.17 % Rotamer: Outliers : 0.81 % Allowed : 9.63 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.24 (0.12), residues: 4875 helix: 1.54 (0.10), residues: 2645 sheet: -0.82 (0.21), residues: 525 loop : 0.42 (0.16), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 201 HIS 0.007 0.001 HIS A 43 PHE 0.014 0.001 PHE a 97 TYR 0.018 0.002 TYR a 145 ARG 0.005 0.000 ARG B 311 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 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 287 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 256 time to evaluate : 4.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7401 (mm-30) REVERT: F 444 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8111 (mttt) REVERT: H 50 MET cc_start: 0.8179 (tmm) cc_final: 0.7944 (tmm) REVERT: O 21 MET cc_start: 0.7854 (mmp) cc_final: 0.7653 (tpt) REVERT: a 73 MET cc_start: 0.8203 (mmt) cc_final: 0.7746 (mmt) outliers start: 31 outliers final: 17 residues processed: 276 average time/residue: 2.7606 time to fit residues: 933.4156 Evaluate side-chains 266 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 247 time to evaluate : 4.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 466 LYS Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain a residue 117 ASP Chi-restraints excluded: chain a residue 151 TRP Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain d residue 108 LEU Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 295 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 230 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 365 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 37841 Z= 0.241 Angle : 0.507 8.380 51321 Z= 0.264 Chirality : 0.040 0.152 5958 Planarity : 0.004 0.054 6714 Dihedral : 6.915 111.597 5401 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.25 % Rotamer: Outliers : 0.57 % Allowed : 10.15 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.29 (0.12), residues: 4875 helix: 1.61 (0.10), residues: 2635 sheet: -0.89 (0.22), residues: 517 loop : 0.42 (0.16), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 201 HIS 0.003 0.001 HIS A 43 PHE 0.015 0.001 PHE R 74 TYR 0.019 0.001 TYR a 145 ARG 0.004 0.000 ARG d 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 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 287 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 266 time to evaluate : 4.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: D 466 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8278 (ttpm) REVERT: F 444 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8096 (mttt) REVERT: H 50 MET cc_start: 0.8148 (tmm) cc_final: 0.7788 (tmm) REVERT: H 83 ASN cc_start: 0.7120 (p0) cc_final: 0.6875 (p0) REVERT: O 21 MET cc_start: 0.7830 (mmp) cc_final: 0.7618 (tpt) REVERT: a 73 MET cc_start: 0.8205 (mmt) cc_final: 0.7755 (mmt) REVERT: b 59 GLU cc_start: 0.8192 (tt0) cc_final: 0.7982 (pt0) outliers start: 21 outliers final: 13 residues processed: 280 average time/residue: 2.8022 time to fit residues: 969.4529 Evaluate side-chains 271 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 256 time to evaluate : 4.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain E residue 466 LYS Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain a residue 117 ASP Chi-restraints excluded: chain a residue 151 TRP Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain d residue 81 GLU Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 2.9990 chunk 445 optimal weight: 7.9990 chunk 406 optimal weight: 4.9990 chunk 433 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 340 optimal weight: 3.9990 chunk 133 optimal weight: 0.0770 chunk 392 optimal weight: 3.9990 chunk 410 optimal weight: 2.9990 chunk 432 optimal weight: 4.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 37841 Z= 0.343 Angle : 0.534 9.085 51321 Z= 0.280 Chirality : 0.041 0.167 5958 Planarity : 0.004 0.054 6714 Dihedral : 7.022 111.275 5401 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 0.57 % Allowed : 10.23 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.20 (0.12), residues: 4875 helix: 1.54 (0.10), residues: 2630 sheet: -0.86 (0.22), residues: 526 loop : 0.35 (0.16), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 201 HIS 0.006 0.001 HIS A 43 PHE 0.016 0.001 PHE a 97 TYR 0.018 0.001 TYR a 145 ARG 0.005 0.000 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 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 283 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 261 time to evaluate : 4.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7408 (mm-30) REVERT: F 444 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8103 (mttt) REVERT: H 50 MET cc_start: 0.8156 (tmm) cc_final: 0.7927 (tmm) REVERT: a 73 MET cc_start: 0.8231 (mmt) cc_final: 0.7789 (mmt) REVERT: b 59 GLU cc_start: 0.8219 (tt0) cc_final: 0.7994 (pt0) outliers start: 22 outliers final: 15 residues processed: 274 average time/residue: 2.7492 time to fit residues: 918.0967 Evaluate side-chains 269 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 252 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain E residue 466 LYS Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain a residue 117 ASP Chi-restraints excluded: chain a residue 151 TRP Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain d residue 81 GLU Chi-restraints excluded: chain d residue 108 LEU Chi-restraints excluded: chain d residue 155 GLU 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: 2.9990 chunk 279 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 481 optimal weight: 3.9990 chunk 442 optimal weight: 0.0470 chunk 383 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37841 Z= 0.226 Angle : 0.509 9.051 51321 Z= 0.265 Chirality : 0.040 0.157 5958 Planarity : 0.004 0.054 6714 Dihedral : 6.874 109.531 5401 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.27 % Rotamer: Outliers : 0.62 % Allowed : 10.23 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.27 (0.12), residues: 4875 helix: 1.61 (0.10), residues: 2627 sheet: -0.92 (0.22), residues: 517 loop : 0.38 (0.16), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 201 HIS 0.003 0.001 HIS A 43 PHE 0.017 0.001 PHE O 69 TYR 0.019 0.001 TYR a 145 ARG 0.005 0.000 ARG H 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9750 Ramachandran restraints generated. 4875 Oldfield, 0 Emsley, 4875 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 284 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 261 time to evaluate : 4.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7398 (mm-30) REVERT: D 466 LYS cc_start: 0.8565 (ttmm) cc_final: 0.8287 (ttpm) REVERT: F 444 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8083 (mttt) REVERT: H 50 MET cc_start: 0.8132 (tmm) cc_final: 0.7909 (tmm) REVERT: a 73 MET cc_start: 0.8226 (mmt) cc_final: 0.7781 (mmt) REVERT: b 59 GLU cc_start: 0.8216 (tt0) cc_final: 0.7994 (pt0) REVERT: b 86 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8603 (mp0) outliers start: 23 outliers final: 13 residues processed: 277 average time/residue: 2.7433 time to fit residues: 934.2187 Evaluate side-chains 271 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 256 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain E residue 371 GLU Chi-restraints excluded: chain E residue 466 LYS Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain S residue 75 MET Chi-restraints excluded: chain a residue 117 ASP Chi-restraints excluded: chain a residue 151 TRP Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain b residue 95 GLN Chi-restraints excluded: chain d residue 81 GLU Chi-restraints excluded: chain d residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 0.9990 chunk 408 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 353 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 383 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 394 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.084068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057481 restraints weight = 277908.496| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.68 r_work: 0.2837 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37841 Z= 0.220 Angle : 0.504 8.851 51321 Z= 0.261 Chirality : 0.040 0.155 5958 Planarity : 0.004 0.054 6714 Dihedral : 6.772 108.098 5401 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 0.52 % Allowed : 10.54 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 1.33 (0.13), residues: 4875 helix: 1.67 (0.10), residues: 2625 sheet: -0.93 (0.22), residues: 517 loop : 0.41 (0.16), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.003 0.001 HIS A 43 PHE 0.017 0.001 PHE P 58 TYR 0.019 0.001 TYR a 145 ARG 0.003 0.000 ARG d 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18291.07 seconds wall clock time: 314 minutes 9.14 seconds (18849.14 seconds total)