Starting phenix.real_space_refine on Sun Sep 29 13:35:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njr_12412/09_2024/7njr_12412_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njr_12412/09_2024/7njr_12412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njr_12412/09_2024/7njr_12412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njr_12412/09_2024/7njr_12412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njr_12412/09_2024/7njr_12412_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njr_12412/09_2024/7njr_12412_trim.cif" } resolution = 2.56 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 23564 2.51 5 N 6401 2.21 5 O 7173 1.98 5 H 37321 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 74587 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 7732 Classifications: {'peptide': 511} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 489} Chain: "B" Number of atoms: 7638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 7638 Classifications: {'peptide': 505} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 483} Chain breaks: 2 Chain: "C" Number of atoms: 7921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 521, 7900 Classifications: {'peptide': 521} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 496} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 521, 7900 Classifications: {'peptide': 521} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 496} Chain breaks: 2 bond proxies already assigned to first conformer: 7939 Chain: "D" Number of atoms: 7162 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Conformer: "B" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} bond proxies already assigned to first conformer: 7190 Chain: "E" Number of atoms: 7087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 7087 Classifications: {'peptide': 464} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain: "F" Number of atoms: 7144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "G" Number of atoms: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 4567 Classifications: {'peptide': 297} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 287} Chain breaks: 1 Chain: "H" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1802 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2172 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "d" Number of atoms: 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: 1 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 36.03, per 1000 atoms: 0.48 Number of scatterers: 74587 At special positions: 0 Unit cell: (134.46, 126.99, 251.49, 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 7173 8.00 N 6401 7.00 C 23564 6.00 H 37321 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.62 Conformation dependent library (CDL) restraints added in 5.8 seconds 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8878 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 0 sheets defined 55.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 178 through 195 removed outlier: 4.134A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.660A 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: 3.680A pdb=" N ASN A 263 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.945A pdb=" N ARG A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 393 through 406 removed outlier: 4.934A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 5.055A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 476 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 9 through 21 removed outlier: 3.840A pdb=" N VAL B 19 " --> pdb=" O GLU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.839A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.672A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.558A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 384 through 406 removed outlier: 5.478A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 441 through 452 removed outlier: 3.606A pdb=" N GLY B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 477 removed outlier: 4.860A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE B 467 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.600A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.710A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.713A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 301 through 311 removed outlier: 3.938A pdb=" N ARG C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 478 removed outlier: 4.917A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.777A 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 510 Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 180 removed outlier: 3.868A pdb=" N ARG D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 243 removed outlier: 4.740A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.558A 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: 4.343A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.655A 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: 4.652A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.768A 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 417 through 423 removed outlier: 4.406A pdb=" N GLN D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR D 423 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 461 through 471 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 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 194 through 206 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.867A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 276 through 278 No H-bonds generated for 'chain 'E' and resid 276 through 278' Processing helix chain 'E' and resid 283 through 293 removed outlier: 4.006A pdb=" N ARG E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 318 through 324 Processing helix chain 'E' and resid 335 through 339 Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 363 through 389 removed outlier: 4.248A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 396 through 411 Processing helix chain 'E' and resid 417 through 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 470 Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'F' and resid 194 through 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 245 removed outlier: 5.138A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN F 245 " --> pdb=" O PHE F 241 " (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: 4.536A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 Processing helix chain 'F' and resid 358 through 361 No H-bonds generated for 'chain 'F' and resid 358 through 361' Processing helix chain 'F' and resid 363 through 389 removed outlier: 4.493A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.915A 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 417 through 423 removed outlier: 3.689A pdb=" N GLU F 420 " --> pdb=" O MET F 417 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 444 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'G' and resid 4 through 59 Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 92 through 110 Processing helix chain 'G' and resid 121 through 130 Processing helix chain 'G' and resid 147 through 164 Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 228 through 303 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 92 through 98 Processing helix chain 'H' and resid 104 through 117 Processing helix chain 'L' and resid 5 through 45 Processing helix chain 'L' and resid 47 through 79 removed outlier: 4.490A pdb=" N GLY L 51 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR L 55 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Proline residue: L 56 - end of helix Processing helix chain 'M' and resid 5 through 45 Processing helix chain 'M' and resid 47 through 49 No H-bonds generated for 'chain 'M' and resid 47 through 49' Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'N' and resid 5 through 45 Processing helix chain 'N' and resid 47 through 78 removed outlier: 4.160A pdb=" N GLY N 51 " --> pdb=" O GLU N 48 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE N 54 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR N 55 " --> pdb=" O ARG N 52 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.799A pdb=" N LEU N 77 " --> pdb=" O PHE N 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE N 78 " --> pdb=" O MET N 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 45 Processing helix chain 'O' and resid 47 through 79 removed outlier: 4.772A pdb=" N GLY O 51 " --> pdb=" O GLU O 48 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR O 55 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.924A pdb=" N VAL O 79 " --> pdb=" O ALA O 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 45 Processing helix chain 'P' and resid 47 through 79 removed outlier: 4.731A pdb=" N GLY P 51 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE P 54 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.992A pdb=" N GLU P 65 " --> pdb=" O GLY P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 45 Processing helix chain 'Q' and resid 47 through 79 removed outlier: 4.393A pdb=" N GLY Q 51 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU Q 53 " --> pdb=" O GLN Q 50 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE Q 54 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR Q 55 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) Proline residue: Q 56 - end of helix Processing helix chain 'R' and resid 5 through 45 Processing helix chain 'R' and resid 47 through 79 removed outlier: 3.673A pdb=" N GLN R 50 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY R 51 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE R 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR R 55 " --> pdb=" O ARG R 52 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 4.065A pdb=" N GLU R 65 " --> pdb=" O GLY R 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 45 Processing helix chain 'S' and resid 47 through 79 removed outlier: 3.705A pdb=" N GLN S 50 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY S 51 " --> pdb=" O GLU S 48 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE S 54 " --> pdb=" O GLY S 51 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR S 55 " --> pdb=" O ARG S 52 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 4.550A pdb=" N ALA S 66 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL S 79 " --> pdb=" O ALA S 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 45 Processing helix chain 'T' and resid 47 through 79 removed outlier: 4.841A pdb=" N GLY T 51 " --> pdb=" O GLU T 48 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR T 55 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 4.565A 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: 4.445A 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 153 Processing helix chain 'a' and resid 155 through 164 Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 168 through 205 Proline residue: a 172 - end of helix Proline residue: a 182 - end of helix removed outlier: 4.095A pdb=" N LEU a 187 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG a 188 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ALA a 195 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL a 200 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 243 removed outlier: 5.910A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.747A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 45 removed outlier: 3.693A pdb=" N VAL b 34 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 145 removed outlier: 3.843A pdb=" N ALA b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY b 143 " --> pdb=" O GLN b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 159 Processing helix chain 'd' and resid 2 through 136 removed outlier: 4.853A pdb=" N VAL d 23 " --> pdb=" O VAL d 19 " (cutoff:3.500A) Proline residue: d 24 - end of helix Processing helix chain 'd' and resid 140 through 156 Processing helix chain 'd' and resid 174 through 193 removed outlier: 3.688A pdb=" N GLY d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLY d 193 " --> pdb=" O SER d 189 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 217 through 224 Processing helix chain 'd' and resid 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 305 Processing helix chain 'd' and resid 307 through 314 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 350 Processing helix chain 'd' and resid 357 through 372 removed outlier: 4.211A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 401 Processing helix chain 'd' and resid 413 through 415 No H-bonds generated for 'chain 'd' and resid 413 through 415' Processing helix chain 'd' and resid 432 through 441 1901 hydrogen bonds defined for protein. 4809 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: 26.16 Time building geometry restraints manager: 19.20 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: 37301 1.03 - 1.23: 31 1.23 - 1.42: 15320 1.42 - 1.61: 22338 1.61 - 1.81: 194 Bond restraints: 75184 Sorted by residual: bond pdb=" CG1 ILE M 30 " pdb=" CD1 ILE M 30 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.10e+00 bond pdb=" CG1 ILE L 30 " pdb=" CD1 ILE L 30 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.10e+00 bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.89e+00 bond pdb=" CB MET N 21 " pdb=" CG MET N 21 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CB MET M 21 " pdb=" CG MET M 21 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.43e+00 ... (remaining 75179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 134498 1.55 - 3.11: 1490 3.11 - 4.66: 192 4.66 - 6.22: 31 6.22 - 7.77: 10 Bond angle restraints: 136221 Sorted by residual: angle pdb=" C ASP F 254 " pdb=" N ASN F 255 " pdb=" CA ASN F 255 " ideal model delta sigma weight residual 121.70 127.61 -5.91 1.80e+00 3.09e-01 1.08e+01 angle pdb=" C ASP E 254 " pdb=" N ASN E 255 " pdb=" CA ASN E 255 " ideal model delta sigma weight residual 121.70 127.35 -5.65 1.80e+00 3.09e-01 9.86e+00 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 127.22 -5.52 1.80e+00 3.09e-01 9.41e+00 angle pdb=" C ILE N 20 " pdb=" N MET N 21 " pdb=" CA MET N 21 " ideal model delta sigma weight residual 122.06 116.84 5.22 1.86e+00 2.89e-01 7.87e+00 angle pdb=" C3' ATP B 600 " pdb=" C4' ATP B 600 " pdb=" O4' ATP B 600 " ideal model delta sigma weight residual 105.22 101.58 3.64 1.30e+00 5.94e-01 7.86e+00 ... (remaining 136216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.48: 33516 29.48 - 58.95: 1525 58.95 - 88.43: 107 88.43 - 117.90: 5 117.90 - 147.38: 3 Dihedral angle restraints: 35156 sinusoidal: 19479 harmonic: 15677 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 87.38 -147.38 1 2.00e+01 2.50e-03 4.42e+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 300.00 157.12 142.88 1 2.00e+01 2.50e-03 4.31e+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 300.00 175.37 124.64 1 2.00e+01 2.50e-03 3.76e+01 ... (remaining 35153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 5183 0.059 - 0.119: 696 0.119 - 0.178: 69 0.178 - 0.238: 2 0.238 - 0.297: 10 Chirality restraints: 5960 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 2.21e+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 2.15e+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 2.05e+00 ... (remaining 5957 not shown) Planarity restraints: 11423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE a 99 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C PHE a 99 " -0.038 2.00e-02 2.50e+03 pdb=" O PHE a 99 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE a 100 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE a 97 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C PHE a 97 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE a 97 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL a 98 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 66 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C ALA L 66 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA L 66 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA L 67 " -0.010 2.00e-02 2.50e+03 ... (remaining 11420 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 3181 2.15 - 2.76: 147329 2.76 - 3.37: 226476 3.37 - 3.99: 295419 3.99 - 4.60: 464031 Nonbonded interactions: 1136436 Sorted by model distance: nonbonded pdb=" O PHE R 58 " pdb=" H GLY R 62 " model vdw 1.537 2.450 nonbonded pdb=" OD2 ASP C 273 " pdb=" HG SER C 275 " model vdw 1.541 2.450 nonbonded pdb=" O PHE N 58 " pdb=" H GLY N 62 " model vdw 1.564 2.450 nonbonded pdb=" O ALA G 77 " pdb=" H VAL G 115 " model vdw 1.571 2.450 nonbonded pdb=" HG SER d 262 " pdb=" OD1 ASN d 266 " model vdw 1.588 2.450 ... (remaining 1136431 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 11 through 22 or (resid 30 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3)) or resid 31 through 173 or res \ id 175 through 407 or (resid 414 and (name N or name CA or name C or name O or n \ ame CB or name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) o \ r resid 415 through 515 or resid 518 through 519 or resid 521 or resid 600 throu \ gh 601)) selection = (chain 'B' and ((resid 11 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD1 \ 3)) or resid 12 through 22 or (resid 30 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name OE1 or name OE2 or name HA or name H \ B2 or name HB3 or name HG2 or name HG3)) or resid 31 through 173 or resid 175 th \ rough 515 or resid 518 through 519 or resid 521 or resid 600 through 601)) selection = (chain 'C' and ((resid 11 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD1 \ 3)) or resid 12 through 173 or resid 175 through 407 or (resid 414 and (name N o \ r name CA or name C or name O or name CB or name CG or name OD1 or name OD2 or n \ ame HA or name HB2 or name HB3)) or resid 415 through 514 or resid 532 or resid \ 537 through 538 or resid 540 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 452 or resid 455 through 471)) selection = (chain 'E' and (resid 8 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 452 or resid 455 t \ hrough 471)) selection = (chain 'F' and (resid 8 through 452 or resid 455 through 471)) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = (chain 'P' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 208.110 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: 1.130 Extract box with map and model: 3.470 Check model and map are aligned: 0.450 Set scattering table: 0.580 Process input model: 133.910 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.370 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:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 362.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37863 Z= 0.255 Angle : 0.518 7.770 51357 Z= 0.276 Chirality : 0.042 0.297 5960 Planarity : 0.004 0.041 6721 Dihedral : 14.798 147.381 13862 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.12), residues: 4882 helix: 1.48 (0.10), residues: 2649 sheet: -0.08 (0.21), residues: 579 loop : 0.52 (0.17), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.004 0.001 HIS A 259 PHE 0.021 0.001 PHE A 245 TYR 0.014 0.001 TYR B 18 ARG 0.008 0.000 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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 351 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 4.926 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: H 8 ILE cc_start: 0.8750 (mp) cc_final: 0.8229 (pt) REVERT: a 205 MET cc_start: 0.8035 (mmt) cc_final: 0.6451 (ttt) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 2.8885 time to fit residues: 1231.5219 Evaluate side-chains 242 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 4.710 ------------------------------------------------------------------------------- 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: 2.9990 chunk 366 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 378 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 230 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 GLN O 46 GLN ** P 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 50 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN ** b 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 37863 Z= 0.363 Angle : 0.546 8.982 51357 Z= 0.291 Chirality : 0.042 0.172 5960 Planarity : 0.005 0.069 6721 Dihedral : 7.479 139.860 5407 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 0.73 % Allowed : 5.42 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.12), residues: 4882 helix: 1.51 (0.10), residues: 2599 sheet: -0.32 (0.20), residues: 587 loop : 0.47 (0.16), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.004 0.001 HIS A 259 PHE 0.017 0.001 PHE C 245 TYR 0.022 0.002 TYR a 145 ARG 0.006 0.000 ARG a 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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 281 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 253 time to evaluate : 4.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 456 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: H 8 ILE cc_start: 0.8860 (mp) cc_final: 0.8355 (pt) REVERT: R 32 ASP cc_start: 0.8450 (m-30) cc_final: 0.8243 (m-30) REVERT: a 205 MET cc_start: 0.8046 (mmt) cc_final: 0.6425 (ttt) REVERT: b 73 LYS cc_start: 0.8018 (tmtt) cc_final: 0.7734 (tmtt) REVERT: b 76 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8058 (pp20) outliers start: 28 outliers final: 11 residues processed: 271 average time/residue: 2.9844 time to fit residues: 998.9684 Evaluate side-chains 249 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 236 time to evaluate : 4.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain G residue 271 ASP Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 80 SER Chi-restraints excluded: chain a residue 243 GLN Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 365 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 439 optimal weight: 5.9990 chunk 474 optimal weight: 4.9990 chunk 391 optimal weight: 3.9990 chunk 435 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 352 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN N 50 GLN O 46 GLN R 50 GLN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN ** b 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37863 Z= 0.293 Angle : 0.520 8.975 51357 Z= 0.276 Chirality : 0.041 0.167 5960 Planarity : 0.004 0.053 6721 Dihedral : 7.361 131.142 5407 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.82 % Rotamer: Outliers : 0.60 % Allowed : 6.43 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.12), residues: 4882 helix: 1.54 (0.10), residues: 2599 sheet: -0.47 (0.20), residues: 590 loop : 0.49 (0.16), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.004 0.001 HIS A 259 PHE 0.017 0.001 PHE S 74 TYR 0.021 0.001 TYR a 145 ARG 0.005 0.000 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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 263 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 240 time to evaluate : 5.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8028 (tttp) REVERT: E 456 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: H 8 ILE cc_start: 0.8861 (mp) cc_final: 0.8356 (pt) REVERT: a 205 MET cc_start: 0.8040 (mmt) cc_final: 0.6426 (ttt) REVERT: a 245 MET cc_start: 0.8083 (mtp) cc_final: 0.7827 (mtp) outliers start: 23 outliers final: 10 residues processed: 255 average time/residue: 3.0191 time to fit residues: 969.9637 Evaluate side-chains 245 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 233 time to evaluate : 5.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain d residue 220 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 295 optimal weight: 0.5980 chunk 440 optimal weight: 3.9990 chunk 466 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 417 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN N 50 GLN O 46 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN ** b 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 37863 Z= 0.381 Angle : 0.542 9.093 51357 Z= 0.288 Chirality : 0.042 0.173 5960 Planarity : 0.004 0.049 6721 Dihedral : 7.371 128.466 5407 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.45 % Rotamer: Outliers : 0.76 % Allowed : 7.32 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.12), residues: 4882 helix: 1.47 (0.10), residues: 2600 sheet: -0.57 (0.20), residues: 577 loop : 0.46 (0.16), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS A 259 PHE 0.016 0.001 PHE C 245 TYR 0.020 0.002 TYR a 145 ARG 0.007 0.000 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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 270 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 241 time to evaluate : 4.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8061 (tttp) REVERT: E 456 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7522 (m-80) REVERT: H 8 ILE cc_start: 0.8895 (mp) cc_final: 0.8397 (pt) REVERT: a 205 MET cc_start: 0.8036 (mmt) cc_final: 0.6433 (ttt) REVERT: b 76 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8073 (pp20) outliers start: 29 outliers final: 13 residues processed: 260 average time/residue: 2.7305 time to fit residues: 869.0548 Evaluate side-chains 250 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 234 time to evaluate : 4.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 6 ASN Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 76 GLU Chi-restraints excluded: chain d residue 220 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 347 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 398 optimal weight: 2.9990 chunk 322 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 419 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN N 50 GLN O 46 GLN R 50 GLN ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN ** b 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37863 Z= 0.279 Angle : 0.514 9.114 51357 Z= 0.272 Chirality : 0.040 0.166 5960 Planarity : 0.004 0.054 6721 Dihedral : 7.210 129.398 5407 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Rotamer: Outliers : 0.70 % Allowed : 8.20 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.12), residues: 4882 helix: 1.55 (0.10), residues: 2600 sheet: -0.66 (0.20), residues: 581 loop : 0.52 (0.16), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS A 259 PHE 0.016 0.001 PHE F 257 TYR 0.020 0.001 TYR a 145 ARG 0.008 0.000 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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 272 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 245 time to evaluate : 4.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8077 (tttp) REVERT: E 456 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: H 8 ILE cc_start: 0.8896 (mp) cc_final: 0.8402 (pt) REVERT: a 205 MET cc_start: 0.8023 (mmt) cc_final: 0.6395 (ttt) REVERT: b 76 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8057 (pp20) outliers start: 27 outliers final: 13 residues processed: 261 average time/residue: 2.6475 time to fit residues: 851.2353 Evaluate side-chains 251 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 235 time to evaluate : 4.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain P residue 6 ASN Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 76 GLU Chi-restraints excluded: chain d residue 220 ASN 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: 3.9990 chunk 92 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 115 optimal weight: 0.2980 chunk 467 optimal weight: 5.9990 chunk 387 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 245 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 GLN O 46 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN ** b 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 37863 Z= 0.311 Angle : 0.524 9.152 51357 Z= 0.276 Chirality : 0.040 0.167 5960 Planarity : 0.004 0.058 6721 Dihedral : 7.135 129.160 5407 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 0.83 % Allowed : 8.62 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.12), residues: 4882 helix: 1.57 (0.10), residues: 2598 sheet: -0.70 (0.20), residues: 581 loop : 0.50 (0.16), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS A 259 PHE 0.015 0.001 PHE F 257 TYR 0.020 0.001 TYR a 145 ARG 0.010 0.000 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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 275 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 4.487 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: A 418 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8098 (tttp) REVERT: E 456 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7571 (m-80) REVERT: G 206 MET cc_start: 0.8200 (mtm) cc_final: 0.7952 (mtp) REVERT: H 8 ILE cc_start: 0.8902 (mp) cc_final: 0.8416 (pt) REVERT: N 50 GLN cc_start: 0.8068 (tm130) cc_final: 0.7737 (tp40) REVERT: a 205 MET cc_start: 0.8026 (mmt) cc_final: 0.6421 (ttt) REVERT: b 76 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8079 (pp20) outliers start: 32 outliers final: 18 residues processed: 265 average time/residue: 2.6851 time to fit residues: 872.1962 Evaluate side-chains 257 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 236 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain P residue 6 ASN Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 76 GLU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain d residue 220 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 393 optimal weight: 1.9990 chunk 260 optimal weight: 0.9990 chunk 465 optimal weight: 7.9990 chunk 291 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN O 46 GLN R 50 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN ** b 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 37863 Z= 0.356 Angle : 0.536 9.149 51357 Z= 0.284 Chirality : 0.041 0.168 5960 Planarity : 0.004 0.064 6721 Dihedral : 7.108 117.681 5407 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 0.86 % Allowed : 9.24 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.12), residues: 4882 helix: 1.52 (0.10), residues: 2598 sheet: -0.71 (0.20), residues: 577 loop : 0.47 (0.16), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 218 HIS 0.004 0.001 HIS A 259 PHE 0.015 0.001 PHE F 257 TYR 0.019 0.002 TYR a 145 ARG 0.010 0.000 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 243 time to evaluate : 4.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8094 (tttp) REVERT: E 456 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: H 8 ILE cc_start: 0.8904 (mp) cc_final: 0.8418 (pt) REVERT: a 205 MET cc_start: 0.8030 (mmt) cc_final: 0.6398 (ttt) REVERT: b 76 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8080 (pp20) outliers start: 33 outliers final: 18 residues processed: 264 average time/residue: 2.7459 time to fit residues: 894.5516 Evaluate side-chains 254 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 233 time to evaluate : 4.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain E residue 384 ASP Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 76 GLU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain d residue 220 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 295 optimal weight: 0.9990 chunk 317 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 365 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 GLN D 453 GLN B E 425 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 GLN O 46 GLN ** P 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37863 Z= 0.199 Angle : 0.498 8.794 51357 Z= 0.261 Chirality : 0.040 0.168 5960 Planarity : 0.004 0.069 6721 Dihedral : 6.794 113.234 5407 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.74 % Rotamer: Outliers : 0.60 % Allowed : 9.76 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.12), residues: 4882 helix: 1.66 (0.10), residues: 2605 sheet: -0.73 (0.21), residues: 572 loop : 0.57 (0.16), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 218 HIS 0.004 0.001 HIS A 259 PHE 0.016 0.001 PHE F 257 TYR 0.020 0.001 TYR a 145 ARG 0.010 0.000 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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 268 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 4.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8103 (tttp) REVERT: E 456 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: G 206 MET cc_start: 0.8184 (mtm) cc_final: 0.7946 (mtp) REVERT: H 8 ILE cc_start: 0.8893 (mp) cc_final: 0.8391 (pt) REVERT: N 50 GLN cc_start: 0.8082 (tm130) cc_final: 0.7724 (tp40) REVERT: a 205 MET cc_start: 0.7973 (mmt) cc_final: 0.6379 (ttt) outliers start: 23 outliers final: 13 residues processed: 261 average time/residue: 2.6966 time to fit residues: 861.4589 Evaluate side-chains 251 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 7.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain G residue 271 ASP Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain d residue 220 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 3.9990 chunk 445 optimal weight: 5.9990 chunk 406 optimal weight: 4.9990 chunk 433 optimal weight: 8.9990 chunk 261 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 chunk 133 optimal weight: 0.0670 chunk 392 optimal weight: 1.9990 chunk 410 optimal weight: 4.9990 chunk 432 optimal weight: 0.7980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 46 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN b 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37863 Z= 0.235 Angle : 0.503 9.845 51357 Z= 0.263 Chirality : 0.040 0.165 5960 Planarity : 0.004 0.073 6721 Dihedral : 6.742 113.751 5407 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % Rotamer: Outliers : 0.60 % Allowed : 10.00 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.12), residues: 4882 helix: 1.69 (0.10), residues: 2605 sheet: -0.73 (0.21), residues: 572 loop : 0.58 (0.16), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.003 0.001 HIS A 259 PHE 0.016 0.001 PHE F 257 TYR 0.020 0.001 TYR a 145 ARG 0.012 0.000 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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 268 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 4.514 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: A 418 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8102 (tttp) REVERT: E 456 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: G 206 MET cc_start: 0.8204 (mtm) cc_final: 0.7965 (mtp) REVERT: H 8 ILE cc_start: 0.8894 (mp) cc_final: 0.8399 (pt) REVERT: a 205 MET cc_start: 0.7977 (mmt) cc_final: 0.6373 (ttt) outliers start: 23 outliers final: 15 residues processed: 261 average time/residue: 2.7088 time to fit residues: 865.2950 Evaluate side-chains 258 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 241 time to evaluate : 4.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain G residue 271 ASP Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain O residue 46 GLN Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 59 GLU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain d residue 220 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 0.8980 chunk 458 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 481 optimal weight: 0.5980 chunk 442 optimal weight: 0.9980 chunk 383 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 295 optimal weight: 0.5980 chunk 234 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 GLN O 46 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37863 Z= 0.180 Angle : 0.497 9.505 51357 Z= 0.259 Chirality : 0.040 0.200 5960 Planarity : 0.004 0.078 6721 Dihedral : 6.666 111.930 5407 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % Rotamer: Outliers : 0.57 % Allowed : 10.08 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.13), residues: 4882 helix: 1.73 (0.10), residues: 2606 sheet: -0.75 (0.21), residues: 566 loop : 0.62 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS A 259 PHE 0.016 0.001 PHE F 257 TYR 0.020 0.001 TYR a 145 ARG 0.013 0.000 ARG G 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 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 268 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 246 time to evaluate : 4.625 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: A 418 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8062 (tttt) REVERT: E 456 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7521 (m-80) REVERT: G 206 MET cc_start: 0.8206 (mtm) cc_final: 0.7970 (mtp) REVERT: H 8 ILE cc_start: 0.8892 (mp) cc_final: 0.8398 (pt) REVERT: L 46 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: N 50 GLN cc_start: 0.8122 (tm130) cc_final: 0.7674 (tp40) REVERT: O 46 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7138 (mp10) REVERT: a 205 MET cc_start: 0.7948 (mmt) cc_final: 0.6361 (ttt) outliers start: 22 outliers final: 11 residues processed: 261 average time/residue: 2.7966 time to fit residues: 901.1059 Evaluate side-chains 258 residues out of total 3837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 243 time to evaluate : 4.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain G residue 271 ASP Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain O residue 46 GLN Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain d residue 220 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 0.9990 chunk 408 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 383 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 394 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 425 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.077591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.057074 restraints weight = 275041.371| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.64 r_work: 0.2797 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.225 37863 Z= 0.234 Angle : 0.596 59.200 51357 Z= 0.331 Chirality : 0.040 0.295 5960 Planarity : 0.004 0.078 6721 Dihedral : 6.667 112.055 5407 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 0.52 % Allowed : 10.31 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.13), residues: 4882 helix: 1.73 (0.10), residues: 2606 sheet: -0.75 (0.21), residues: 566 loop : 0.62 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.004 0.001 HIS A 259 PHE 0.016 0.001 PHE F 257 TYR 0.020 0.001 TYR a 145 ARG 0.009 0.000 ARG G 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18077.22 seconds wall clock time: 314 minutes 26.76 seconds (18866.76 seconds total)