Starting phenix.real_space_refine on Sun Sep 29 14:09:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njl_12382/09_2024/7njl_12382_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njl_12382/09_2024/7njl_12382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njl_12382/09_2024/7njl_12382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njl_12382/09_2024/7njl_12382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njl_12382/09_2024/7njl_12382_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njl_12382/09_2024/7njl_12382_trim.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 107 5.16 5 C 23615 2.51 5 N 6419 2.21 5 O 7199 1.98 5 H 37414 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74775 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 7704 Classifications: {'peptide': 509} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 487} 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: 8067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8067 Classifications: {'peptide': 533} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 508} Chain breaks: 2 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: 4590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 4590 Classifications: {'peptide': 298} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 287} Chain breaks: 1 Chain: "H" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1802 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 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: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} 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: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} 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: 6668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6668 Classifications: {'peptide': 439} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 426} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 31.17, per 1000 atoms: 0.42 Number of scatterers: 74775 At special positions: 0 Unit cell: (136.12, 129.48, 252.32, 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 7199 8.00 N 6419 7.00 C 23615 6.00 H 37414 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: 15.10 Conformation dependent library (CDL) restraints added in 5.1 seconds 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8902 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 0 sheets defined 55.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.82 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 removed outlier: 3.951A pdb=" N VAL A 19 " --> pdb=" O GLU A 16 " (cutoff:3.500A) 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 194 removed outlier: 3.723A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 243 through 263 Proline residue: A 250 - end of helix removed outlier: 3.696A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.565A 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 310 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 362 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 406 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: 4.722A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A 478 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 8 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 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.839A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.690A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.545A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 384 through 405 removed outlier: 4.596A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 461 through 477 removed outlier: 5.070A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 488 Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'C' and resid 8 through 21 removed outlier: 3.788A pdb=" N ILE C 15 " --> pdb=" O ILE C 11 " (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 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 178 through 195 removed outlier: 3.762A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 243 through 262 Proline residue: C 250 - end of helix removed outlier: 3.725A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 301 through 311 removed outlier: 3.631A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 415 through 430 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 477 removed outlier: 4.563A 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 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 206 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: 4.881A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.596A 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: 4.274A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.579A 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 388 removed outlier: 4.531A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 412 Processing helix chain 'D' and resid 420 through 423 No H-bonds generated for 'chain 'D' and resid 420 through 423' Processing helix chain 'D' and resid 432 through 443 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 166 through 180 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: 5.163A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.723A 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: 4.204A 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 removed outlier: 3.542A pdb=" N LYS E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 363 through 389 removed outlier: 4.274A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 396 through 411 Processing helix chain 'E' and resid 417 through 421 removed outlier: 3.740A pdb=" N GLN E 421 " --> pdb=" O ALA E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'F' and resid 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 244 removed outlier: 5.027A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 269 Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 283 through 293 Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.445A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.601A 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 389 removed outlier: 4.524A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 411 Processing helix chain 'F' and resid 420 through 423 No H-bonds generated for 'chain 'F' and resid 420 through 423' Processing helix chain 'F' and resid 432 through 443 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'G' and resid 4 through 42 Processing helix chain 'G' and resid 44 through 59 removed outlier: 3.610A pdb=" N ASN G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 109 removed outlier: 3.948A pdb=" N LEU G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 130 Processing helix chain 'G' and resid 147 through 165 removed outlier: 3.608A pdb=" N GLY G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA G 165 " --> pdb=" O PHE G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 303 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 92 through 100 removed outlier: 4.052A pdb=" N ALA H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) 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: 4.264A pdb=" N GLY L 51 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE L 54 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 3.941A pdb=" N VAL L 61 " --> pdb=" O PHE L 58 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY L 62 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU L 65 " --> pdb=" O GLY L 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 45 Processing helix chain 'M' and resid 47 through 79 removed outlier: 3.995A pdb=" N GLY M 51 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE M 54 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR M 55 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.938A pdb=" N VAL M 61 " --> pdb=" O PHE M 58 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL M 64 " --> pdb=" O VAL M 61 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU M 65 " --> pdb=" O GLY M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 45 Processing helix chain 'N' and resid 48 through 79 removed outlier: 3.803A pdb=" N GLY N 51 " --> pdb=" O GLU N 48 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 4.020A pdb=" N TYR N 68 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 45 Processing helix chain 'O' and resid 47 through 79 removed outlier: 4.885A pdb=" N GLY O 51 " --> pdb=" O GLU O 48 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR O 55 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.662A pdb=" N VAL O 61 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU O 65 " --> pdb=" O GLY O 62 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 45 Processing helix chain 'P' and resid 48 through 80 removed outlier: 3.912A pdb=" N GLY P 51 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU P 53 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE P 54 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.764A pdb=" N GLU P 65 " --> pdb=" O GLY P 62 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA P 66 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL P 79 " --> pdb=" O ALA P 76 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE P 80 " --> pdb=" O LEU P 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 45 removed outlier: 3.606A pdb=" N ARG Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 50 Processing helix chain 'Q' and resid 53 through 79 Processing helix chain 'R' and resid 5 through 45 Processing helix chain 'R' and resid 47 through 79 removed outlier: 5.190A pdb=" N GLY R 51 " --> pdb=" O GLU R 48 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 3.556A pdb=" N VAL R 61 " --> pdb=" O PHE R 58 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU R 65 " --> pdb=" O GLY R 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 45 Processing helix chain 'S' and resid 47 through 79 removed outlier: 4.379A pdb=" N GLY S 51 " --> pdb=" O GLU S 48 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE S 54 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 4.141A pdb=" N GLY S 62 " --> pdb=" O ILE S 59 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU S 65 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE S 69 " --> pdb=" O ALA S 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 45 Processing helix chain 'T' and resid 50 through 80 Proline residue: T 56 - end of helix removed outlier: 3.719A pdb=" N ASN T 71 " --> pdb=" O ALA T 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 52 Processing helix chain 'a' and resid 61 through 80 Processing helix chain 'a' and resid 89 through 108 removed outlier: 3.976A pdb=" N ALA a 107 " --> pdb=" O SER a 103 " (cutoff:3.500A) removed outlier: 4.485A 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 171 through 205 Proline residue: a 182 - end of helix removed outlier: 4.256A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET a 205 " --> pdb=" O ALA a 201 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 244 removed outlier: 5.928A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.850A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 47 removed outlier: 3.985A pdb=" N VAL b 34 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE b 37 " --> pdb=" O VAL b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 160 removed outlier: 4.092A pdb=" N SER b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY b 143 " --> pdb=" O GLN b 139 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU b 151 " --> pdb=" O SER b 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 138 removed outlier: 4.387A pdb=" N VAL d 23 " --> pdb=" O VAL d 19 " (cutoff:3.500A) Proline residue: d 24 - end of helix removed outlier: 3.578A pdb=" N GLU d 131 " --> pdb=" O ASN d 127 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 155 Processing helix chain 'd' and resid 174 through 191 Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 219 through 224 Processing helix chain 'd' and resid 231 through 240 Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 286 removed outlier: 3.509A pdb=" N ILE d 285 " --> pdb=" O ARG d 282 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 307 through 313 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 350 Processing helix chain 'd' and resid 357 through 372 removed outlier: 3.807A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 401 Processing helix chain 'd' and resid 413 through 415 No H-bonds generated for 'chain 'd' and resid 413 through 415' Processing helix chain 'd' and resid 432 through 441 1889 hydrogen bonds defined for protein. 4920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 27.43 Time building geometry restraints manager: 18.72 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: 37394 1.03 - 1.23: 21 1.23 - 1.42: 15359 1.42 - 1.62: 22400 1.62 - 1.81: 194 Bond restraints: 75368 Sorted by residual: bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" CG1 ILE T 20 " pdb=" CD1 ILE T 20 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.36e+00 bond pdb=" CG LEU a 179 " pdb=" CD2 LEU a 179 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 bond pdb=" CB MET R 21 " pdb=" CG MET R 21 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.24e+00 ... (remaining 75363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 134121 1.46 - 2.91: 2150 2.91 - 4.37: 229 4.37 - 5.82: 35 5.82 - 7.28: 19 Bond angle restraints: 136554 Sorted by residual: angle pdb=" N ILE a 11 " pdb=" CA ILE a 11 " pdb=" C ILE a 11 " ideal model delta sigma weight residual 113.53 109.51 4.02 9.80e-01 1.04e+00 1.68e+01 angle pdb=" N ILE A 35 " pdb=" CA ILE A 35 " pdb=" C ILE A 35 " ideal model delta sigma weight residual 112.96 109.19 3.77 1.00e+00 1.00e+00 1.42e+01 angle pdb=" N VAL E 164 " pdb=" CA VAL E 164 " pdb=" C VAL E 164 " ideal model delta sigma weight residual 113.20 109.91 3.29 9.60e-01 1.09e+00 1.17e+01 angle pdb=" C ASP E 254 " pdb=" N ASN E 255 " pdb=" CA ASN E 255 " ideal model delta sigma weight residual 121.70 127.07 -5.37 1.80e+00 3.09e-01 8.91e+00 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 127.05 -5.35 1.80e+00 3.09e-01 8.83e+00 ... (remaining 136549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.29: 33778 32.29 - 64.58: 1377 64.58 - 96.86: 79 96.86 - 129.15: 3 129.15 - 161.44: 1 Dihedral angle restraints: 35238 sinusoidal: 19537 harmonic: 15701 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 -60.00 101.44 -161.44 1 2.00e+01 2.50e-03 4.68e+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 300.00 178.75 121.26 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 47.84 -107.84 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 35235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 5165 0.059 - 0.118: 724 0.118 - 0.176: 75 0.176 - 0.235: 3 0.235 - 0.294: 10 Chirality restraints: 5977 Sorted by residual: chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C2' ATP F 600 " pdb=" C1' ATP F 600 " pdb=" C3' ATP F 600 " pdb=" O2' ATP F 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 5974 not shown) Planarity restraints: 11448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 21 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C MET R 21 " -0.031 2.00e-02 2.50e+03 pdb=" O MET R 21 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY R 22 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 17 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO F 18 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 18 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 18 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET Q 21 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C MET Q 21 " -0.026 2.00e-02 2.50e+03 pdb=" O MET Q 21 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY Q 22 " 0.009 2.00e-02 2.50e+03 ... (remaining 11445 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 2412 2.13 - 2.74: 141056 2.74 - 3.36: 230358 3.36 - 3.98: 295744 3.98 - 4.60: 465108 Nonbonded interactions: 1134678 Sorted by model distance: nonbonded pdb="HE21 GLN C 399 " pdb=" O LYS D 340 " model vdw 1.507 2.450 nonbonded pdb=" O PHE C 22 " pdb=" HE ARG b 158 " model vdw 1.511 2.450 nonbonded pdb=" OE1 GLU T 48 " pdb=" H GLU T 48 " model vdw 1.540 2.450 nonbonded pdb=" O GLU L 65 " pdb=" H PHE L 69 " model vdw 1.575 2.450 nonbonded pdb=" H ILE G 185 " pdb=" O ARG G 201 " model vdw 1.586 2.450 ... (remaining 1134673 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 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 7 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 HG3)) or resid 30 through 406 or (resid 414 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e OD2 or name HA or name HB2 or name HB3)) or resid 415 through 521 or resid 600 \ through 601)) selection = (chain 'B' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 7 through 22 or resid 29 through 521 or resid 600 through 601)) selection = (chain 'C' and (resid 6 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 406 or (res \ id 414 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 415 through 521 or \ resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 452 or resid 455 through 471)) selection = (chain 'E' and (resid 8 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 452 or resid 455 t \ hrough 471)) selection = (chain 'F' and ((resid 8 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = (chain 'P' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = chain 'Q' selection = (chain 'R' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 94.430 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: 1.120 Extract box with map and model: 3.120 Check model and map are aligned: 0.440 Set scattering table: 0.560 Process input model: 131.400 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 : 0.003 0.045 37954 Z= 0.175 Angle : 0.508 7.279 51475 Z= 0.269 Chirality : 0.042 0.294 5977 Planarity : 0.003 0.044 6735 Dihedral : 15.069 161.437 13899 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.35 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.12), residues: 4891 helix: 1.74 (0.10), residues: 2616 sheet: -0.16 (0.21), residues: 540 loop : 0.47 (0.16), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 218 HIS 0.004 0.001 HIS F 365 PHE 0.022 0.001 PHE T 58 TYR 0.019 0.001 TYR G 147 ARG 0.007 0.000 ARG B 426 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 422 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 4.409 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: N 60 THR cc_start: 0.8477 (t) cc_final: 0.7980 (p) REVERT: Q 32 ASP cc_start: 0.8552 (m-30) cc_final: 0.8330 (m-30) REVERT: S 32 ASP cc_start: 0.8211 (m-30) cc_final: 0.7498 (m-30) REVERT: b 70 ASP cc_start: 0.7941 (m-30) cc_final: 0.7698 (p0) outliers start: 0 outliers final: 1 residues processed: 422 average time/residue: 2.7979 time to fit residues: 1453.8373 Evaluate side-chains 298 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 297 time to evaluate : 5.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 2.9990 chunk 366 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 378 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 230 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 GLN R 71 ASN S 71 ASN a 104 ASN b 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37954 Z= 0.293 Angle : 0.543 8.322 51475 Z= 0.286 Chirality : 0.042 0.190 5977 Planarity : 0.004 0.063 6735 Dihedral : 7.491 142.371 5420 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 0.80 % Allowed : 6.64 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.12), residues: 4891 helix: 1.60 (0.10), residues: 2607 sheet: -0.36 (0.21), residues: 539 loop : 0.36 (0.16), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 218 HIS 0.007 0.001 HIS a 166 PHE 0.023 0.001 PHE L 74 TYR 0.019 0.001 TYR a 145 ARG 0.006 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 349 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 318 time to evaluate : 4.412 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: A 396 ASP cc_start: 0.7776 (m-30) cc_final: 0.7530 (m-30) REVERT: T 75 MET cc_start: 0.8229 (tmm) cc_final: 0.7916 (tmm) REVERT: a 177 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: b 70 ASP cc_start: 0.7988 (m-30) cc_final: 0.7773 (p0) outliers start: 31 outliers final: 9 residues processed: 340 average time/residue: 2.5391 time to fit residues: 1088.5740 Evaluate side-chains 306 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 296 time to evaluate : 4.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain a residue 222 ASP Chi-restraints excluded: chain b residue 163 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 365 optimal weight: 4.9990 chunk 298 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 439 optimal weight: 5.9990 chunk 474 optimal weight: 4.9990 chunk 391 optimal weight: 4.9990 chunk 435 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 352 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN N 46 GLN R 50 GLN b 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 37954 Z= 0.283 Angle : 0.531 7.887 51475 Z= 0.278 Chirality : 0.041 0.186 5977 Planarity : 0.004 0.079 6735 Dihedral : 7.416 130.693 5418 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.56 % Favored : 97.40 % Rotamer: Outliers : 0.83 % Allowed : 7.91 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.12), residues: 4891 helix: 1.53 (0.10), residues: 2606 sheet: -0.45 (0.21), residues: 548 loop : 0.30 (0.16), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 218 HIS 0.009 0.001 HIS a 166 PHE 0.014 0.001 PHE b 31 TYR 0.016 0.001 TYR a 145 ARG 0.007 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 341 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 309 time to evaluate : 4.338 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: A 473 GLU cc_start: 0.7733 (tp30) cc_final: 0.7118 (tp30) REVERT: B 487 ARG cc_start: 0.8374 (ttp-110) cc_final: 0.8111 (ttp-110) REVERT: L 21 MET cc_start: 0.8276 (mmm) cc_final: 0.8058 (mmp) REVERT: T 75 MET cc_start: 0.8301 (tmm) cc_final: 0.8044 (tmm) REVERT: T 79 VAL cc_start: 0.9120 (t) cc_final: 0.8894 (t) REVERT: a 177 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: b 70 ASP cc_start: 0.7962 (m-30) cc_final: 0.7727 (p0) REVERT: b 112 ASP cc_start: 0.7932 (m-30) cc_final: 0.7707 (m-30) outliers start: 32 outliers final: 14 residues processed: 330 average time/residue: 2.4618 time to fit residues: 1014.2382 Evaluate side-chains 310 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 295 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain a residue 222 ASP Chi-restraints excluded: chain b residue 163 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 4.9990 chunk 330 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 295 optimal weight: 1.9990 chunk 440 optimal weight: 5.9990 chunk 466 optimal weight: 0.6980 chunk 230 optimal weight: 1.9990 chunk 417 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 46 GLN R 50 GLN b 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 37954 Z= 0.313 Angle : 0.538 8.125 51475 Z= 0.282 Chirality : 0.041 0.186 5977 Planarity : 0.004 0.057 6735 Dihedral : 7.378 132.436 5418 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 0.91 % Allowed : 8.90 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.12), residues: 4891 helix: 1.49 (0.10), residues: 2610 sheet: -0.56 (0.21), residues: 542 loop : 0.27 (0.16), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 218 HIS 0.007 0.001 HIS a 166 PHE 0.016 0.001 PHE L 74 TYR 0.015 0.001 TYR a 145 ARG 0.007 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 337 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 302 time to evaluate : 4.336 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: B 190 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7604 (ttt-90) REVERT: B 487 ARG cc_start: 0.8358 (ttp-110) cc_final: 0.8095 (ttp-110) REVERT: C 159 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7914 (mtp) REVERT: a 177 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: b 70 ASP cc_start: 0.7957 (m-30) cc_final: 0.7728 (p0) REVERT: b 84 ASP cc_start: 0.8683 (m-30) cc_final: 0.8430 (m-30) outliers start: 35 outliers final: 18 residues processed: 323 average time/residue: 2.4955 time to fit residues: 1003.5531 Evaluate side-chains 312 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 291 time to evaluate : 4.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain T residue 37 ASN Chi-restraints excluded: chain T residue 59 ILE Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain a residue 222 ASP Chi-restraints excluded: chain b residue 163 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 3.9990 chunk 265 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 347 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 398 optimal weight: 3.9990 chunk 322 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 chunk 419 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN R 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37954 Z= 0.286 Angle : 0.531 8.369 51475 Z= 0.277 Chirality : 0.041 0.184 5977 Planarity : 0.004 0.057 6735 Dihedral : 7.328 137.734 5418 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 0.99 % Allowed : 9.60 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.12), residues: 4891 helix: 1.50 (0.10), residues: 2610 sheet: -0.63 (0.21), residues: 541 loop : 0.26 (0.16), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 218 HIS 0.008 0.001 HIS a 166 PHE 0.015 0.001 PHE b 31 TYR 0.015 0.001 TYR a 145 ARG 0.009 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 339 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 301 time to evaluate : 4.417 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: B 190 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7496 (ttt-90) REVERT: C 159 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7915 (mtp) REVERT: L 65 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8006 (mm-30) REVERT: a 73 MET cc_start: 0.9031 (mmt) cc_final: 0.8740 (mmt) REVERT: a 177 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: b 70 ASP cc_start: 0.7938 (m-30) cc_final: 0.7678 (p0) REVERT: b 84 ASP cc_start: 0.8660 (m-30) cc_final: 0.8418 (m-30) outliers start: 38 outliers final: 20 residues processed: 326 average time/residue: 2.4206 time to fit residues: 985.3122 Evaluate side-chains 315 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 292 time to evaluate : 4.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain F residue 180 ASN Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain T residue 37 ASN Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 222 ASP Chi-restraints excluded: chain b residue 163 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 1.9990 chunk 420 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 274 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 467 optimal weight: 3.9990 chunk 387 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN C 399 GLN D 425 GLN R 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37954 Z= 0.285 Angle : 0.530 8.106 51475 Z= 0.277 Chirality : 0.041 0.183 5977 Planarity : 0.004 0.062 6735 Dihedral : 7.300 144.287 5418 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 0.99 % Allowed : 9.96 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.12), residues: 4891 helix: 1.52 (0.10), residues: 2608 sheet: -0.66 (0.21), residues: 541 loop : 0.26 (0.16), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 218 HIS 0.008 0.001 HIS a 166 PHE 0.017 0.001 PHE L 74 TYR 0.015 0.001 TYR a 145 ARG 0.010 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 335 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 297 time to evaluate : 4.319 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: B 190 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.7492 (ttt-90) REVERT: C 159 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7926 (mtp) REVERT: L 32 ASP cc_start: 0.8281 (m-30) cc_final: 0.7878 (m-30) REVERT: a 73 MET cc_start: 0.9035 (mmt) cc_final: 0.8732 (mmt) REVERT: a 177 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: b 70 ASP cc_start: 0.7933 (m-30) cc_final: 0.7683 (p0) REVERT: b 84 ASP cc_start: 0.8660 (m-30) cc_final: 0.8418 (m-30) REVERT: b 136 GLN cc_start: 0.7489 (tm-30) cc_final: 0.7265 (tm-30) outliers start: 38 outliers final: 20 residues processed: 319 average time/residue: 2.4350 time to fit residues: 969.7050 Evaluate side-chains 317 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 294 time to evaluate : 4.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain T residue 37 ASN Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 222 ASP Chi-restraints excluded: chain b residue 163 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 266 optimal weight: 0.3980 chunk 341 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 393 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 465 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN R 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 37954 Z= 0.363 Angle : 0.558 8.256 51475 Z= 0.292 Chirality : 0.042 0.183 5977 Planarity : 0.004 0.070 6735 Dihedral : 7.427 158.036 5418 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.93 % Rotamer: Outliers : 1.01 % Allowed : 10.46 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.12), residues: 4891 helix: 1.44 (0.10), residues: 2606 sheet: -0.72 (0.21), residues: 544 loop : 0.23 (0.16), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 218 HIS 0.008 0.001 HIS a 166 PHE 0.018 0.002 PHE b 31 TYR 0.016 0.001 TYR a 240 ARG 0.012 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 333 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 294 time to evaluate : 4.353 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: B 190 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7551 (ttt-90) REVERT: T 75 MET cc_start: 0.8307 (tmm) cc_final: 0.8073 (tmm) REVERT: a 73 MET cc_start: 0.9050 (mmt) cc_final: 0.8729 (mmt) REVERT: a 177 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: b 70 ASP cc_start: 0.7944 (m-30) cc_final: 0.7695 (p0) REVERT: b 84 ASP cc_start: 0.8664 (m-30) cc_final: 0.8420 (m-30) outliers start: 39 outliers final: 23 residues processed: 318 average time/residue: 2.4835 time to fit residues: 995.5319 Evaluate side-chains 314 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 289 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain T residue 37 ASN Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 222 ASP Chi-restraints excluded: chain b residue 163 ASP 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: 0.9990 chunk 278 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 295 optimal weight: 1.9990 chunk 317 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 365 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN D 425 GLN R 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37954 Z= 0.237 Angle : 0.523 8.828 51475 Z= 0.272 Chirality : 0.041 0.183 5977 Planarity : 0.004 0.078 6735 Dihedral : 7.286 166.417 5418 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 0.86 % Allowed : 10.85 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.12), residues: 4891 helix: 1.56 (0.10), residues: 2605 sheet: -0.86 (0.21), residues: 536 loop : 0.27 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 218 HIS 0.009 0.001 HIS a 166 PHE 0.017 0.001 PHE L 74 TYR 0.015 0.001 TYR a 145 ARG 0.010 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 337 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 304 time to evaluate : 4.323 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: B 190 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.7492 (ttt-90) REVERT: N 32 ASP cc_start: 0.8713 (m-30) cc_final: 0.8413 (m-30) REVERT: a 177 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: b 84 ASP cc_start: 0.8664 (m-30) cc_final: 0.8397 (m-30) REVERT: b 136 GLN cc_start: 0.7438 (tm-30) cc_final: 0.7221 (tm-30) outliers start: 33 outliers final: 17 residues processed: 322 average time/residue: 2.4427 time to fit residues: 980.3010 Evaluate side-chains 308 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 289 time to evaluate : 4.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain T residue 37 ASN Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 222 ASP Chi-restraints excluded: chain b residue 163 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 0.0670 chunk 445 optimal weight: 3.9990 chunk 406 optimal weight: 2.9990 chunk 433 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 340 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 392 optimal weight: 0.8980 chunk 410 optimal weight: 0.9980 chunk 432 optimal weight: 2.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 GLN C 399 GLN R 50 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37954 Z= 0.209 Angle : 0.517 9.218 51475 Z= 0.267 Chirality : 0.040 0.182 5977 Planarity : 0.004 0.086 6735 Dihedral : 7.231 178.288 5418 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.80 % Favored : 97.16 % Rotamer: Outliers : 0.70 % Allowed : 11.34 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.12), residues: 4891 helix: 1.62 (0.10), residues: 2611 sheet: -0.89 (0.21), residues: 532 loop : 0.31 (0.16), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 218 HIS 0.010 0.001 HIS a 166 PHE 0.019 0.001 PHE b 31 TYR 0.015 0.001 TYR a 145 ARG 0.012 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 327 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 300 time to evaluate : 4.387 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: B 190 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.7493 (ttt-90) REVERT: N 32 ASP cc_start: 0.8724 (m-30) cc_final: 0.8488 (m-30) REVERT: Q 75 MET cc_start: 0.8464 (tmm) cc_final: 0.8186 (tmm) REVERT: a 177 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: b 84 ASP cc_start: 0.8651 (m-30) cc_final: 0.8411 (m-30) REVERT: b 136 GLN cc_start: 0.7421 (tm-30) cc_final: 0.7204 (tm-30) outliers start: 27 outliers final: 17 residues processed: 314 average time/residue: 2.4553 time to fit residues: 965.0273 Evaluate side-chains 310 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 291 time to evaluate : 4.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain T residue 37 ASN Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 222 ASP Chi-restraints excluded: chain b residue 163 ASP 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: 5.9990 chunk 279 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 481 optimal weight: 3.9990 chunk 442 optimal weight: 0.9990 chunk 383 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 295 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN R 50 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 37954 Z= 0.259 Angle : 0.530 10.747 51475 Z= 0.274 Chirality : 0.041 0.181 5977 Planarity : 0.004 0.085 6735 Dihedral : 7.217 166.621 5418 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 0.67 % Allowed : 11.68 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.12), residues: 4891 helix: 1.60 (0.10), residues: 2612 sheet: -0.82 (0.21), residues: 544 loop : 0.30 (0.16), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 218 HIS 0.010 0.001 HIS a 166 PHE 0.017 0.001 PHE L 74 TYR 0.015 0.001 TYR a 145 ARG 0.015 0.000 ARG F 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9782 Ramachandran restraints generated. 4891 Oldfield, 0 Emsley, 4891 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 319 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 293 time to evaluate : 4.350 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: A 51 MET cc_start: 0.8456 (mtm) cc_final: 0.8203 (mtm) REVERT: B 190 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.7506 (ttt-90) REVERT: N 32 ASP cc_start: 0.8705 (m-30) cc_final: 0.8462 (m-30) REVERT: Q 75 MET cc_start: 0.8472 (tmm) cc_final: 0.8189 (tmm) REVERT: a 177 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: b 84 ASP cc_start: 0.8643 (m-30) cc_final: 0.8417 (m-30) REVERT: b 136 GLN cc_start: 0.7427 (tm-30) cc_final: 0.7204 (tm-30) outliers start: 26 outliers final: 19 residues processed: 308 average time/residue: 2.4207 time to fit residues: 936.0533 Evaluate side-chains 313 residues out of total 3852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 292 time to evaluate : 4.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 PHE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain E residue 393 GLU Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 206 ASP Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain O residue 65 GLU Chi-restraints excluded: chain P residue 72 LEU Chi-restraints excluded: chain Q residue 55 THR Chi-restraints excluded: chain T residue 37 ASN Chi-restraints excluded: chain a residue 177 GLU Chi-restraints excluded: chain a residue 205 MET Chi-restraints excluded: chain a residue 222 ASP Chi-restraints excluded: chain b residue 163 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 0.6980 chunk 408 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 353 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 383 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 394 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.078789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.058639 restraints weight = 272233.545| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.62 r_work: 0.2861 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37954 Z= 0.216 Angle : 0.517 9.399 51475 Z= 0.267 Chirality : 0.040 0.181 5977 Planarity : 0.004 0.087 6735 Dihedral : 7.079 151.418 5418 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.72 % Favored : 97.24 % Rotamer: Outliers : 0.67 % Allowed : 11.68 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.12), residues: 4891 helix: 1.65 (0.10), residues: 2611 sheet: -0.95 (0.21), residues: 522 loop : 0.35 (0.16), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 218 HIS 0.011 0.001 HIS a 166 PHE 0.018 0.001 PHE b 31 TYR 0.016 0.001 TYR a 240 ARG 0.014 0.000 ARG F 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18423.76 seconds wall clock time: 313 minutes 38.77 seconds (18818.77 seconds total)