Starting phenix.real_space_refine on Sun Sep 29 14:08:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njp_12402/09_2024/7njp_12402_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njp_12402/09_2024/7njp_12402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njp_12402/09_2024/7njp_12402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njp_12402/09_2024/7njp_12402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njp_12402/09_2024/7njp_12402_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njp_12402/09_2024/7njp_12402_trim.cif" } resolution = 2.84 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 23556 2.51 5 N 6393 2.21 5 O 7172 1.98 5 H 37305 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74554 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 7688 Classifications: {'peptide': 509} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 487} Chain breaks: 1 Chain: "B" Number of atoms: 7715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 7715 Classifications: {'peptide': 510} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 488} Chain breaks: 1 Chain: "C" Number of atoms: 8009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 526, 7967 Classifications: {'peptide': 526} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 502} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 526, 7967 Classifications: {'peptide': 526} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 502} Chain breaks: 2 bond proxies already assigned to first conformer: 7982 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: 4551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 4551 Classifications: {'peptide': 296} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 286} Chain breaks: 1 Chain: "H" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1802 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "M" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1187 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "O" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1156 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "P" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "Q" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "R" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1187 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1175 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2172 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "d" Number of atoms: 6656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6656 Classifications: {'peptide': 438} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 425} 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: 2 residue: pdb=" N APHE C 354 " occ=0.80 ... (38 atoms not shown) pdb=" HZ BPHE C 354 " occ=0.20 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 33.82, per 1000 atoms: 0.45 Number of scatterers: 74554 At special positions: 0 Unit cell: (141.93, 126.16, 250.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 107 16.00 P 16 15.00 Mg 5 11.99 O 7172 8.00 N 6393 7.00 C 23556 6.00 H 37305 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: 16.57 Conformation dependent library (CDL) restraints added in 5.8 seconds 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8876 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 0 sheets defined 55.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 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 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 178 through 195 removed outlier: 4.247A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.819A 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: 3.741A pdb=" N ASN A 263 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 406 removed outlier: 4.982A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' 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: 4.682A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.659A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 194 removed outlier: 3.796A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.821A 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: 3.718A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 301 through 311 removed outlier: 3.602A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 384 through 405 removed outlier: 4.985A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.780A 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: 4.815A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 178 through 195 removed outlier: 3.763A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.622A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (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: 4.182A 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 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 478 removed outlier: 4.951A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER C 478 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 489 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.615A pdb=" N LYS C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 176 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: 4.936A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 5.031A 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: 4.276A 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 389 removed outlier: 4.681A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 412 Processing helix chain 'D' and resid 420 through 423 No H-bonds generated for 'chain 'D' and resid 420 through 423' Processing helix chain 'D' and resid 432 through 443 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'E' and resid 26 through 28 No H-bonds generated for 'chain 'E' and resid 26 through 28' Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 209 through 212 Processing helix chain 'E' and resid 224 through 243 removed outlier: 5.153A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.774A 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 292 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 325 removed outlier: 3.628A pdb=" N ALA E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 339 Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 363 through 389 removed outlier: 4.460A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 412 Processing helix chain 'E' and resid 417 through 419 No H-bonds generated for 'chain 'E' and resid 417 through 419' Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 461 through 469 Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'F' and resid 194 through 207 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 243 removed outlier: 4.971A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.633A 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: 4.476A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 358 through 361 No H-bonds generated for 'chain 'F' and resid 358 through 361' Processing helix chain 'F' and resid 363 through 389 removed outlier: 4.337A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 412 Processing helix chain 'F' and resid 418 through 423 removed outlier: 3.939A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 444 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'G' and resid 4 through 60 Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 66 through 68 No H-bonds generated for 'chain 'G' and resid 66 through 68' Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 121 through 130 Processing helix chain 'G' and resid 147 through 163 Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 228 through 303 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 92 through 98 Processing helix chain 'H' and resid 104 through 117 Processing helix chain 'L' and resid 5 through 45 Processing helix chain 'L' and resid 47 through 80 removed outlier: 3.623A pdb=" N GLN L 50 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY L 51 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE L 54 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR L 55 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 3.646A pdb=" N ALA L 66 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE L 80 " --> pdb=" O LEU L 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 45 Processing helix chain 'M' and resid 47 through 79 removed outlier: 4.391A pdb=" N GLY M 51 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE M 54 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR M 55 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.763A pdb=" N GLY M 62 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA M 67 " --> pdb=" O VAL M 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL M 79 " --> pdb=" O ALA M 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 45 Processing helix chain 'N' and resid 49 through 80 removed outlier: 4.081A pdb=" N PHE N 54 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR N 55 " --> pdb=" O ARG N 52 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.535A pdb=" N VAL N 61 " --> pdb=" O PHE N 58 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE N 80 " --> pdb=" O LEU N 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 45 Processing helix chain 'O' and resid 47 through 80 removed outlier: 3.669A pdb=" N GLY O 51 " --> pdb=" O GLU O 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU O 53 " --> pdb=" O GLN O 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE O 54 " --> pdb=" O GLY O 51 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR O 55 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.961A pdb=" N ALA O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE O 80 " --> pdb=" O LEU O 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 45 Processing helix chain 'P' and resid 47 through 80 removed outlier: 3.735A pdb=" N GLN P 50 " --> pdb=" O PRO P 47 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY P 51 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.554A pdb=" N GLU P 65 " --> pdb=" O GLY P 62 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE P 80 " --> pdb=" O LEU P 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 45 Processing helix chain 'Q' and resid 47 through 80 removed outlier: 3.631A pdb=" N GLN Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLY Q 51 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR Q 55 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) Proline residue: Q 56 - end of helix removed outlier: 3.623A pdb=" N GLU Q 65 " --> pdb=" O GLY Q 62 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL Q 79 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE Q 80 " --> pdb=" O LEU Q 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 45 Processing helix chain 'R' and resid 47 through 80 removed outlier: 3.604A pdb=" N GLN R 50 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY R 51 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE R 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR R 55 " --> pdb=" O ARG R 52 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 4.314A pdb=" N GLY R 62 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE R 80 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 45 Processing helix chain 'S' and resid 47 through 80 removed outlier: 3.859A pdb=" N GLN S 50 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY S 51 " --> pdb=" O GLU S 48 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE S 54 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.746A pdb=" N ILE S 70 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE S 80 " --> pdb=" O LEU S 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 45 Processing helix chain 'T' and resid 47 through 80 removed outlier: 4.258A pdb=" N GLY T 51 " --> pdb=" O GLU T 48 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE T 54 " --> pdb=" O GLY T 51 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR T 55 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.506A pdb=" N VAL T 61 " --> pdb=" O PHE T 58 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA T 66 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 51 Processing helix chain 'a' and resid 61 through 80 Processing helix chain 'a' and resid 87 through 108 Proline residue: a 91 - end of helix removed outlier: 3.722A pdb=" N VAL a 94 " --> pdb=" O PRO a 91 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR a 95 " --> pdb=" O LEU a 92 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE a 99 " --> pdb=" O ILE a 96 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE a 100 " --> pdb=" O PHE a 97 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE a 102 " --> pdb=" O PHE a 99 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU a 106 " --> pdb=" O SER a 103 " (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 164 removed outlier: 6.618A pdb=" N ILE a 155 " --> pdb=" O TRP a 151 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N VAL a 156 " --> pdb=" O ARG a 152 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY a 157 " --> pdb=" O ARG a 153 " (cutoff:3.500A) Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 168 through 205 Proline residue: a 172 - end of helix Proline residue: a 182 - end of helix removed outlier: 3.945A pdb=" N LEU a 187 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG a 188 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA a 195 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL a 200 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 243 removed outlier: 6.026A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.657A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 45 removed outlier: 3.865A pdb=" N VAL b 34 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 160 removed outlier: 4.528A pdb=" N SER b 146 " --> pdb=" O SER b 142 " (cutoff:3.500A) removed outlier: 4.609A 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: 5.583A pdb=" N ASP b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLY b 150 " --> pdb=" O SER b 146 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU b 151 " --> pdb=" O SER b 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 138 removed outlier: 4.135A pdb=" N VAL d 23 " --> pdb=" O VAL d 19 " (cutoff:3.500A) Proline residue: d 24 - end of helix removed outlier: 3.677A pdb=" N GLU d 70 " --> pdb=" O LYS d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 156 removed outlier: 3.516A pdb=" N GLN d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 191 Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 217 through 224 Processing helix chain 'd' and resid 231 through 241 Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 286 Processing helix chain 'd' and resid 289 through 304 Processing helix chain 'd' and resid 307 through 314 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 350 Processing helix chain 'd' and resid 357 through 372 removed outlier: 4.123A 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 432 through 441 1895 hydrogen bonds defined for protein. 4689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.19 Time building geometry restraints manager: 20.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 37285 1.03 - 1.23: 22 1.23 - 1.42: 15324 1.42 - 1.61: 22327 1.61 - 1.81: 194 Bond restraints: 75152 Sorted by residual: bond pdb=" CG1 ILE R 30 " pdb=" CD1 ILE R 30 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.30e+00 bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" CG PRO F 344 " pdb=" CD PRO F 344 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.70e-02 1.37e+03 1.36e+00 bond pdb=" CG1 ILE S 30 " pdb=" CD1 ILE S 30 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.34e+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 1.25e+00 ... (remaining 75147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 132942 1.35 - 2.70: 2902 2.70 - 4.05: 253 4.05 - 5.39: 43 5.39 - 6.74: 24 Bond angle restraints: 136164 Sorted by residual: angle pdb=" C ASP E 254 " pdb=" N ASN E 255 " pdb=" CA ASN E 255 " ideal model delta sigma weight residual 121.70 127.60 -5.90 1.80e+00 3.09e-01 1.08e+01 angle pdb=" N GLU b 102 " pdb=" CA GLU b 102 " pdb=" CB GLU b 102 " ideal model delta sigma weight residual 110.28 115.21 -4.93 1.55e+00 4.16e-01 1.01e+01 angle pdb=" C ASP F 254 " pdb=" N ASN F 255 " pdb=" CA ASN F 255 " ideal model delta sigma weight residual 121.70 127.15 -5.45 1.80e+00 3.09e-01 9.18e+00 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 127.10 -5.40 1.80e+00 3.09e-01 8.99e+00 angle pdb=" C ASP C 272 " pdb=" N ASP C 273 " pdb=" CA ASP C 273 " ideal model delta sigma weight residual 121.70 126.82 -5.12 1.80e+00 3.09e-01 8.09e+00 ... (remaining 136159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.10: 33867 34.10 - 68.19: 1209 68.19 - 102.29: 65 102.29 - 136.39: 1 136.39 - 170.48: 1 Dihedral angle restraints: 35143 sinusoidal: 19462 harmonic: 15681 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 -60.00 110.48 -170.48 1 2.00e+01 2.50e-03 4.77e+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 300.00 167.56 132.44 1 2.00e+01 2.50e-03 4.02e+01 dihedral pdb=" O1B ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PB ADP E 600 " pdb=" PA ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -155.58 95.57 1 2.00e+01 2.50e-03 2.63e+01 ... (remaining 35140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5222 0.060 - 0.119: 672 0.119 - 0.179: 55 0.179 - 0.239: 2 0.239 - 0.299: 10 Chirality restraints: 5961 Sorted by residual: chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.04e+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 2.03e+00 ... (remaining 5958 not shown) Planarity restraints: 11419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 484 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C ASP B 484 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP B 484 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 485 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 26 " 0.208 9.50e-02 1.11e+02 6.94e-02 5.28e+00 pdb=" NE ARG E 26 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG E 26 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG E 26 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 26 " 0.003 2.00e-02 2.50e+03 pdb="HH11 ARG E 26 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG E 26 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG E 26 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG E 26 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY T 22 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C GLY T 22 " -0.032 2.00e-02 2.50e+03 pdb=" O GLY T 22 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY T 23 " 0.011 2.00e-02 2.50e+03 ... (remaining 11416 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 3388 2.15 - 2.77: 147988 2.77 - 3.38: 225980 3.38 - 3.99: 292046 3.99 - 4.60: 459362 Nonbonded interactions: 1128764 Sorted by model distance: nonbonded pdb="HH21 ARG H 55 " pdb=" O ASP H 59 " model vdw 1.543 2.450 nonbonded pdb=" O GLY B 485 " pdb=" HG1 THR B 489 " model vdw 1.554 2.450 nonbonded pdb=" O PRO a 207 " pdb=" H GLN a 211 " model vdw 1.563 2.450 nonbonded pdb=" OG SER d 176 " pdb=" H SER d 262 " model vdw 1.584 2.450 nonbonded pdb=" O PHE a 190 " pdb=" H PHE a 194 " model vdw 1.587 2.450 ... (remaining 1128759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 173 or resid 175 through 353 or resid 356 throug \ h 406 or (resid 414 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 415 t \ hrough 521 or resid 600 through 601)) selection = (chain 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or resid 8 through 22 \ or (resid 29 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 or name HG2 \ or name HG3)) or resid 30 through 173 or resid 175 through 353 or resid 356 thr \ ough 521 or resid 600 through 601)) selection = (chain 'C' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or resid 8 through 17 \ 3 or resid 175 through 353 or resid 356 through 406 or (resid 414 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name OD2 or na \ me HA or name HB2 or name HB3)) or resid 415 through 521 or resid 600 through 60 \ 1)) } ncs_group { reference = (chain 'D' and (resid 8 through 452 or resid 455 through 471)) selection = (chain 'E' and (resid 8 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 452 or resid 455 t \ hrough 471)) selection = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 9 through 452 or resid 455 through 471)) } ncs_group { reference = (chain 'L' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'M' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'N' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = chain 'O' selection = (chain 'P' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'Q' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'R' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'S' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) selection = (chain 'T' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid \ 5 through 85)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.140 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: 1.070 Extract box with map and model: 3.340 Check model and map are aligned: 0.460 Set scattering table: 0.570 Process input model: 135.930 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.300 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:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 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 0.071 37847 Z= 0.208 Angle : 0.496 6.743 51337 Z= 0.264 Chirality : 0.041 0.299 5961 Planarity : 0.003 0.092 6715 Dihedral : 14.726 170.482 13847 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.26 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.13), residues: 4884 helix: 2.15 (0.10), residues: 2664 sheet: 0.09 (0.22), residues: 526 loop : 0.36 (0.16), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 218 HIS 0.004 0.001 HIS d 410 PHE 0.026 0.001 PHE C 245 TYR 0.025 0.001 TYR a 145 ARG 0.018 0.000 ARG d 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 360 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 4.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 32 ASP cc_start: 0.8459 (m-30) cc_final: 0.7952 (m-30) REVERT: O 21 MET cc_start: 0.8465 (mmm) cc_final: 0.8150 (mmm) REVERT: R 32 ASP cc_start: 0.8766 (m-30) cc_final: 0.8544 (m-30) REVERT: a 75 GLN cc_start: 0.8932 (tt0) cc_final: 0.8543 (tt0) REVERT: a 177 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8609 (tm-30) REVERT: a 192 ASN cc_start: 0.8705 (m110) cc_final: 0.8368 (m110) REVERT: d 57 MET cc_start: 0.7435 (mmp) cc_final: 0.7231 (mmp) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 2.6399 time to fit residues: 1179.0488 Evaluate side-chains 225 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 4.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 9.9990 chunk 366 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 378 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN ** S 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 37847 Z= 0.370 Angle : 0.550 7.338 51337 Z= 0.296 Chirality : 0.042 0.155 5961 Planarity : 0.005 0.043 6715 Dihedral : 7.061 148.059 5408 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer: Outliers : 0.42 % Allowed : 6.38 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.12), residues: 4884 helix: 1.69 (0.10), residues: 2669 sheet: -0.17 (0.23), residues: 517 loop : 0.24 (0.16), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.005 0.001 HIS H 38 PHE 0.020 0.001 PHE R 57 TYR 0.021 0.001 TYR a 145 ARG 0.009 0.000 ARG O 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 271 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 255 time to evaluate : 5.196 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: B 468 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: E 332 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: G 263 MET cc_start: 0.8588 (mmp) cc_final: 0.8179 (mmp) REVERT: L 21 MET cc_start: 0.7941 (mmm) cc_final: 0.7730 (mmm) REVERT: O 21 MET cc_start: 0.8524 (mmm) cc_final: 0.8145 (mmm) REVERT: R 32 ASP cc_start: 0.8794 (m-30) cc_final: 0.8591 (m-30) REVERT: a 25 MET cc_start: 0.6366 (tmm) cc_final: 0.5716 (tmm) REVERT: a 75 GLN cc_start: 0.8996 (tt0) cc_final: 0.8600 (tt0) REVERT: a 177 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8599 (tm-30) REVERT: a 192 ASN cc_start: 0.8791 (m110) cc_final: 0.8442 (m110) REVERT: b 73 LYS cc_start: 0.9478 (tppp) cc_final: 0.9267 (tmtp) REVERT: b 76 GLU cc_start: 0.8296 (mp0) cc_final: 0.8094 (mp0) outliers start: 16 outliers final: 7 residues processed: 264 average time/residue: 2.6157 time to fit residues: 866.7435 Evaluate side-chains 243 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 234 time to evaluate : 4.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain N residue 21 MET Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain d residue 240 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 365 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 chunk 120 optimal weight: 0.2980 chunk 439 optimal weight: 5.9990 chunk 474 optimal weight: 5.9990 chunk 391 optimal weight: 4.9990 chunk 435 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 352 optimal weight: 0.3980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN T 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37847 Z= 0.205 Angle : 0.500 6.141 51337 Z= 0.264 Chirality : 0.040 0.150 5961 Planarity : 0.004 0.044 6715 Dihedral : 6.704 126.301 5408 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.60 % Rotamer: Outliers : 0.62 % Allowed : 7.34 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.13), residues: 4884 helix: 1.69 (0.10), residues: 2676 sheet: -0.49 (0.22), residues: 525 loop : 0.34 (0.16), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.005 0.001 HIS d 58 PHE 0.018 0.001 PHE R 57 TYR 0.019 0.001 TYR a 145 ARG 0.005 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 292 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 268 time to evaluate : 4.834 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: E 384 ASP cc_start: 0.6195 (p0) cc_final: 0.5960 (p0) REVERT: L 21 MET cc_start: 0.7919 (mmm) cc_final: 0.7655 (mmm) REVERT: O 21 MET cc_start: 0.8516 (mmm) cc_final: 0.8229 (mmm) REVERT: R 21 MET cc_start: 0.7625 (ttp) cc_final: 0.7219 (mtm) REVERT: a 75 GLN cc_start: 0.9009 (tt0) cc_final: 0.8612 (tt0) REVERT: a 177 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8557 (tm-30) REVERT: a 192 ASN cc_start: 0.8780 (m110) cc_final: 0.8417 (m110) REVERT: b 73 LYS cc_start: 0.9487 (tppp) cc_final: 0.9256 (tmtp) outliers start: 24 outliers final: 7 residues processed: 282 average time/residue: 2.4982 time to fit residues: 905.1279 Evaluate side-chains 241 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 234 time to evaluate : 4.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain b residue 76 GLU Chi-restraints excluded: chain d residue 263 THR 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: 0.5980 chunk 209 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 440 optimal weight: 0.5980 chunk 466 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 417 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37847 Z= 0.240 Angle : 0.502 6.996 51337 Z= 0.264 Chirality : 0.040 0.164 5961 Planarity : 0.004 0.048 6715 Dihedral : 6.540 113.193 5408 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.87 % Favored : 97.09 % Rotamer: Outliers : 0.65 % Allowed : 8.20 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.13), residues: 4884 helix: 1.68 (0.10), residues: 2661 sheet: -0.63 (0.22), residues: 517 loop : 0.31 (0.16), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 218 HIS 0.003 0.001 HIS D 121 PHE 0.017 0.001 PHE R 57 TYR 0.018 0.001 TYR a 145 ARG 0.005 0.000 ARG d 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 269 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 244 time to evaluate : 4.639 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: E 384 ASP cc_start: 0.6199 (p0) cc_final: 0.5974 (p0) REVERT: L 32 ASP cc_start: 0.8342 (m-30) cc_final: 0.8134 (m-30) REVERT: O 21 MET cc_start: 0.8519 (mmm) cc_final: 0.8188 (mmm) REVERT: a 75 GLN cc_start: 0.9013 (tt0) cc_final: 0.8625 (tt0) REVERT: a 177 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8546 (tm-30) REVERT: a 192 ASN cc_start: 0.8788 (m110) cc_final: 0.8426 (m110) REVERT: d 263 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7815 (p) outliers start: 25 outliers final: 7 residues processed: 263 average time/residue: 2.3710 time to fit residues: 785.2447 Evaluate side-chains 242 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 234 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain b residue 76 GLU Chi-restraints excluded: chain d residue 263 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 347 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 398 optimal weight: 4.9990 chunk 322 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 238 optimal weight: 3.9990 chunk 419 optimal weight: 3.9990 chunk 117 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN T 71 ASN b 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 37847 Z= 0.427 Angle : 0.554 6.663 51337 Z= 0.295 Chirality : 0.042 0.182 5961 Planarity : 0.004 0.051 6715 Dihedral : 6.699 105.070 5408 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 0.83 % Allowed : 8.91 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.12), residues: 4884 helix: 1.52 (0.10), residues: 2660 sheet: -0.63 (0.22), residues: 516 loop : 0.15 (0.16), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 218 HIS 0.004 0.001 HIS C 259 PHE 0.018 0.001 PHE C 245 TYR 0.018 0.002 TYR a 145 ARG 0.005 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 269 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 237 time to evaluate : 4.621 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: G 263 MET cc_start: 0.8593 (mmp) cc_final: 0.8191 (mmp) REVERT: L 21 MET cc_start: 0.7930 (mmm) cc_final: 0.7696 (mmm) REVERT: L 48 GLU cc_start: 0.8237 (mp0) cc_final: 0.7801 (pt0) REVERT: O 21 MET cc_start: 0.8536 (mmm) cc_final: 0.8121 (mmm) REVERT: O 71 ASN cc_start: 0.8149 (t0) cc_final: 0.7825 (t0) REVERT: a 25 MET cc_start: 0.6151 (tmm) cc_final: 0.5935 (tmm) REVERT: a 75 GLN cc_start: 0.9055 (tt0) cc_final: 0.8692 (tt0) REVERT: a 83 MET cc_start: 0.8361 (tpt) cc_final: 0.8143 (tpp) REVERT: a 177 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8557 (tm-30) REVERT: a 192 ASN cc_start: 0.8769 (m110) cc_final: 0.8355 (m110) REVERT: d 57 MET cc_start: 0.7251 (mmt) cc_final: 0.6982 (mmp) REVERT: d 263 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7850 (p) outliers start: 32 outliers final: 16 residues processed: 257 average time/residue: 2.4903 time to fit residues: 800.9919 Evaluate side-chains 241 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 224 time to evaluate : 4.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain b residue 63 MET Chi-restraints excluded: chain b residue 76 GLU Chi-restraints excluded: chain b residue 130 ASP Chi-restraints excluded: chain d residue 240 LEU Chi-restraints excluded: chain d residue 263 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 2.9990 chunk 420 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 467 optimal weight: 0.9990 chunk 387 optimal weight: 6.9990 chunk 216 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN B 453 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37847 Z= 0.209 Angle : 0.502 6.694 51337 Z= 0.264 Chirality : 0.040 0.185 5961 Planarity : 0.004 0.071 6715 Dihedral : 6.519 100.775 5408 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.07 % Rotamer: Outliers : 0.57 % Allowed : 9.53 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.13), residues: 4884 helix: 1.62 (0.10), residues: 2672 sheet: -0.84 (0.22), residues: 510 loop : 0.30 (0.16), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.003 0.001 HIS C 259 PHE 0.096 0.001 PHE R 74 TYR 0.018 0.001 TYR a 145 ARG 0.009 0.000 ARG O 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 236 time to evaluate : 4.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 MET cc_start: 0.7966 (mmm) cc_final: 0.7736 (mmm) REVERT: O 21 MET cc_start: 0.8512 (mmm) cc_final: 0.8237 (mmm) REVERT: a 75 GLN cc_start: 0.9052 (tt0) cc_final: 0.8697 (tt0) REVERT: a 83 MET cc_start: 0.8330 (tpt) cc_final: 0.8112 (tpp) REVERT: a 177 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8558 (tm-30) REVERT: a 192 ASN cc_start: 0.8755 (m110) cc_final: 0.8372 (m110) REVERT: d 57 MET cc_start: 0.7269 (mmt) cc_final: 0.7001 (mmp) outliers start: 22 outliers final: 5 residues processed: 250 average time/residue: 2.3530 time to fit residues: 743.8548 Evaluate side-chains 231 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 226 time to evaluate : 4.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain T residue 41 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 341 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 393 optimal weight: 0.6980 chunk 260 optimal weight: 1.9990 chunk 465 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN M 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 37847 Z= 0.334 Angle : 0.532 8.455 51337 Z= 0.281 Chirality : 0.041 0.189 5961 Planarity : 0.004 0.050 6715 Dihedral : 6.558 95.612 5408 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 0.57 % Allowed : 10.00 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.13), residues: 4884 helix: 1.56 (0.10), residues: 2676 sheet: -0.77 (0.22), residues: 517 loop : 0.27 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.004 0.001 HIS D 121 PHE 0.061 0.001 PHE R 74 TYR 0.018 0.001 TYR a 145 ARG 0.008 0.000 ARG O 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 251 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 229 time to evaluate : 4.646 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: G 263 MET cc_start: 0.8579 (mmp) cc_final: 0.8192 (mmp) REVERT: O 21 MET cc_start: 0.8524 (mmm) cc_final: 0.8307 (mmm) REVERT: a 75 GLN cc_start: 0.9057 (tt0) cc_final: 0.8708 (tt0) REVERT: a 83 MET cc_start: 0.8308 (tpt) cc_final: 0.8056 (tpp) REVERT: a 177 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8556 (tm-30) REVERT: a 192 ASN cc_start: 0.8737 (m110) cc_final: 0.8325 (m110) REVERT: d 57 MET cc_start: 0.7264 (mmt) cc_final: 0.6987 (mmp) outliers start: 22 outliers final: 9 residues processed: 242 average time/residue: 2.4415 time to fit residues: 747.1712 Evaluate side-chains 231 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 222 time to evaluate : 4.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain b residue 130 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: 1.9990 chunk 278 optimal weight: 0.7980 chunk 140 optimal weight: 0.0050 chunk 91 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 295 optimal weight: 0.9980 chunk 317 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 365 optimal weight: 3.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN M 46 GLN T 71 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 37847 Z= 0.204 Angle : 0.508 8.676 51337 Z= 0.266 Chirality : 0.040 0.169 5961 Planarity : 0.004 0.050 6715 Dihedral : 6.434 91.093 5408 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.87 % Favored : 97.09 % Rotamer: Outliers : 0.36 % Allowed : 10.31 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.13), residues: 4884 helix: 1.64 (0.10), residues: 2680 sheet: -0.89 (0.22), residues: 503 loop : 0.37 (0.16), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.003 0.001 HIS D 121 PHE 0.016 0.001 PHE F 257 TYR 0.018 0.001 TYR a 145 ARG 0.007 0.000 ARG O 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 235 time to evaluate : 4.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 48 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7810 (mp0) REVERT: O 21 MET cc_start: 0.8525 (mmm) cc_final: 0.8286 (mmm) REVERT: S 63 LEU cc_start: 0.9199 (tp) cc_final: 0.8866 (tt) REVERT: a 75 GLN cc_start: 0.9051 (tt0) cc_final: 0.8699 (tt0) REVERT: a 83 MET cc_start: 0.8213 (tpt) cc_final: 0.7948 (tpp) REVERT: a 177 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8559 (tm-30) REVERT: a 192 ASN cc_start: 0.8736 (m110) cc_final: 0.8321 (m110) REVERT: d 57 MET cc_start: 0.7238 (mmt) cc_final: 0.6965 (mmp) outliers start: 14 outliers final: 7 residues processed: 245 average time/residue: 2.4389 time to fit residues: 767.2442 Evaluate side-chains 227 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 220 time to evaluate : 4.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain T residue 41 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 4.9990 chunk 445 optimal weight: 5.9990 chunk 406 optimal weight: 6.9990 chunk 433 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 chunk 188 optimal weight: 0.5980 chunk 340 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 392 optimal weight: 0.9980 chunk 410 optimal weight: 8.9990 chunk 432 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN M 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 37847 Z= 0.214 Angle : 0.513 8.935 51337 Z= 0.267 Chirality : 0.040 0.173 5961 Planarity : 0.004 0.050 6715 Dihedral : 6.360 89.597 5408 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 0.29 % Allowed : 10.52 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.13), residues: 4884 helix: 1.66 (0.10), residues: 2675 sheet: -0.93 (0.22), residues: 503 loop : 0.39 (0.17), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.003 0.001 HIS D 121 PHE 0.015 0.001 PHE F 257 TYR 0.018 0.001 TYR a 145 ARG 0.007 0.000 ARG O 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 239 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 228 time to evaluate : 5.055 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: L 48 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7864 (mp0) REVERT: O 21 MET cc_start: 0.8529 (mmm) cc_final: 0.8299 (mmm) REVERT: S 63 LEU cc_start: 0.9201 (tp) cc_final: 0.8865 (tt) REVERT: a 75 GLN cc_start: 0.9050 (tt0) cc_final: 0.8700 (tt0) REVERT: a 83 MET cc_start: 0.8155 (tpt) cc_final: 0.7836 (tpp) REVERT: a 177 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8563 (tm-30) REVERT: a 192 ASN cc_start: 0.8728 (m110) cc_final: 0.8312 (m110) REVERT: d 57 MET cc_start: 0.7261 (mmt) cc_final: 0.6987 (mmp) outliers start: 11 outliers final: 7 residues processed: 235 average time/residue: 2.4221 time to fit residues: 715.6639 Evaluate side-chains 232 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 225 time to evaluate : 4.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain T residue 41 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 2.9990 chunk 458 optimal weight: 4.9990 chunk 279 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 318 optimal weight: 1.9990 chunk 481 optimal weight: 0.7980 chunk 442 optimal weight: 0.0270 chunk 383 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 295 optimal weight: 0.9980 chunk 234 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37847 Z= 0.172 Angle : 0.499 9.352 51337 Z= 0.259 Chirality : 0.039 0.194 5961 Planarity : 0.004 0.053 6715 Dihedral : 6.211 89.911 5408 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.75 % Favored : 97.21 % Rotamer: Outliers : 0.29 % Allowed : 10.62 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.13), residues: 4884 helix: 1.75 (0.10), residues: 2676 sheet: -0.98 (0.22), residues: 507 loop : 0.47 (0.17), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 218 HIS 0.002 0.001 HIS D 121 PHE 0.017 0.001 PHE R 57 TYR 0.019 0.001 TYR a 145 ARG 0.007 0.000 ARG O 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 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 253 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 242 time to evaluate : 4.638 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: F 192 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7312 (mm-30) REVERT: G 197 THR cc_start: 0.8724 (m) cc_final: 0.8365 (p) REVERT: L 48 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7878 (mp0) REVERT: S 63 LEU cc_start: 0.9202 (tp) cc_final: 0.8859 (tt) REVERT: a 67 GLU cc_start: 0.8728 (pt0) cc_final: 0.8391 (pt0) REVERT: a 75 GLN cc_start: 0.9046 (tt0) cc_final: 0.8702 (tt0) REVERT: a 83 MET cc_start: 0.8078 (tpt) cc_final: 0.7810 (tpp) REVERT: a 177 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8572 (tm-30) REVERT: a 192 ASN cc_start: 0.8733 (m110) cc_final: 0.8335 (m110) REVERT: d 57 MET cc_start: 0.7278 (mmt) cc_final: 0.7015 (mmp) outliers start: 11 outliers final: 10 residues processed: 248 average time/residue: 2.3786 time to fit residues: 748.9014 Evaluate side-chains 237 residues out of total 3833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 227 time to evaluate : 4.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain M residue 21 MET Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain T residue 41 SER Chi-restraints excluded: chain b residue 63 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 3.9990 chunk 408 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 353 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 383 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 394 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 399 GLN G 159 ASN M 46 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.080363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.056157 restraints weight = 330251.241| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.90 r_work: 0.2843 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 37847 Z= 0.386 Angle : 0.555 10.680 51337 Z= 0.292 Chirality : 0.041 0.164 5961 Planarity : 0.004 0.052 6715 Dihedral : 6.416 89.707 5408 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 0.31 % Allowed : 10.94 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.13), residues: 4884 helix: 1.60 (0.10), residues: 2679 sheet: -0.85 (0.22), residues: 516 loop : 0.30 (0.16), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 218 HIS 0.005 0.001 HIS B 266 PHE 0.015 0.001 PHE E 439 TYR 0.018 0.002 TYR a 145 ARG 0.007 0.000 ARG O 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16892.64 seconds wall clock time: 292 minutes 44.65 seconds (17564.65 seconds total)