Starting phenix.real_space_refine on Fri Mar 15 00:20:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm2_13510/03_2024/7pm2_13510_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm2_13510/03_2024/7pm2_13510.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm2_13510/03_2024/7pm2_13510_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm2_13510/03_2024/7pm2_13510_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm2_13510/03_2024/7pm2_13510_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm2_13510/03_2024/7pm2_13510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm2_13510/03_2024/7pm2_13510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm2_13510/03_2024/7pm2_13510_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm2_13510/03_2024/7pm2_13510_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Br 1 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6475 2.51 5 N 1721 2.21 5 O 1893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "A ARG 542": "NH1" <-> "NH2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 570": "OD1" <-> "OD2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 763": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 179": "OD1" <-> "OD2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C ARG 372": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10156 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6117 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 27, 'TRANS': 721} Chain breaks: 4 Chain: "C" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2980 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Inner-chain residues flagged as termini: ['pdbres="PHE C 375 "'] Classifications: {'peptide': 371, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351, None: 4} Not linked: pdbres="PHE C 375 " pdbres="ADP C 401 " Not linked: pdbres="ADP C 401 " pdbres="PO4 C 402 " Not linked: pdbres="PO4 C 402 " pdbres=" MG C 403 " Not linked: pdbres=" MG C 403 " pdbres="9UE C 404 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.69, per 1000 atoms: 0.56 Number of scatterers: 10156 At special positions: 0 Unit cell: (104.5, 133.1, 148.5, 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) Br 1 34.99 S 62 16.00 P 3 15.00 Mg 1 11.99 O 1893 8.00 N 1721 7.00 C 6475 6.00 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 - 3.50 Amino acid : False - 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: 4.41 Conformation dependent library (CDL) restraints added in 2.0 seconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 14 sheets defined 49.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.202A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.365A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.755A pdb=" N ASN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 152 removed outlier: 3.530A pdb=" N GLU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 183 removed outlier: 3.595A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 207 removed outlier: 3.696A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.597A pdb=" N SER A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 5.616A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 286 through 291 removed outlier: 4.160A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLY A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 291' Processing helix chain 'A' and resid 301 through 314 removed outlier: 4.264A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.565A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.652A pdb=" N ASP A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 393 through 423 Processing helix chain 'A' and resid 449 through 480 removed outlier: 3.632A pdb=" N GLN A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 499 removed outlier: 3.648A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.613A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.553A pdb=" N VAL A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 removed outlier: 3.637A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.604A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 714 removed outlier: 4.098A pdb=" N SER A 709 " --> pdb=" O GLN A 705 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.698A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 791 Processing helix chain 'C' and resid 55 through 64 removed outlier: 3.780A pdb=" N LYS C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 62 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.516A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.627A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.181A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.627A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 removed outlier: 3.527A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 4.144A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.531A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 294 removed outlier: 4.439A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 333 through 348 removed outlier: 4.333A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 374 removed outlier: 3.783A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS C 374 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= B, first strand: chain 'A' and resid 12 through 16 Processing sheet with id= C, first strand: chain 'A' and resid 37 through 41 Processing sheet with id= D, first strand: chain 'A' and resid 100 through 103 Processing sheet with id= E, first strand: chain 'A' and resid 655 through 658 removed outlier: 3.950A pdb=" N SER A 158 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 377 through 381 Processing sheet with id= G, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= H, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.655A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.853A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= K, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= L, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= M, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.575A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 238 through 241 424 hydrogen bonds defined for protein. 1173 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: 2.91 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2792 1.33 - 1.47: 2913 1.47 - 1.60: 4562 1.60 - 1.73: 3 1.73 - 1.86: 102 Bond restraints: 10372 Sorted by residual: bond pdb=" C4 9UE C 404 " pdb=" C5 9UE C 404 " ideal model delta sigma weight residual 0.880 1.501 -0.621 2.00e-02 2.50e+03 9.64e+02 bond pdb=" C11 9UE C 404 " pdb=" C12 9UE C 404 " ideal model delta sigma weight residual 2.064 1.522 0.542 2.00e-02 2.50e+03 7.36e+02 bond pdb=" C9 9UE C 404 " pdb=" N1 9UE C 404 " ideal model delta sigma weight residual 1.863 1.363 0.500 2.00e-02 2.50e+03 6.26e+02 bond pdb=" O 9UE C 404 " pdb=" C4 9UE C 404 " ideal model delta sigma weight residual 0.887 1.333 -0.446 2.00e-02 2.50e+03 4.97e+02 bond pdb=" C7 9UE C 404 " pdb=" C8 9UE C 404 " ideal model delta sigma weight residual 1.139 1.533 -0.394 2.00e-02 2.50e+03 3.88e+02 ... (remaining 10367 not shown) Histogram of bond angle deviations from ideal: 97.69 - 105.56: 230 105.56 - 113.43: 5637 113.43 - 121.30: 5673 121.30 - 129.18: 2396 129.18 - 137.05: 72 Bond angle restraints: 14008 Sorted by residual: angle pdb=" C20 9UE C 404 " pdb=" C21 9UE C 404 " pdb=" C28 9UE C 404 " ideal model delta sigma weight residual 73.46 132.11 -58.65 3.00e+00 1.11e-01 3.82e+02 angle pdb=" C20 9UE C 404 " pdb=" C21 9UE C 404 " pdb=" C22 9UE C 404 " ideal model delta sigma weight residual 176.54 122.93 53.61 3.00e+00 1.11e-01 3.19e+02 angle pdb=" C21 9UE C 404 " pdb=" C28 9UE C 404 " pdb="BR 9UE C 404 " ideal model delta sigma weight residual 78.92 131.17 -52.25 3.00e+00 1.11e-01 3.03e+02 angle pdb=" C13 9UE C 404 " pdb=" C14 9UE C 404 " pdb=" C16 9UE C 404 " ideal model delta sigma weight residual 67.70 114.26 -46.56 3.00e+00 1.11e-01 2.41e+02 angle pdb=" N3 9UE C 404 " pdb=" C28 9UE C 404 " pdb="BR 9UE C 404 " ideal model delta sigma weight residual 73.72 117.15 -43.43 3.00e+00 1.11e-01 2.10e+02 ... (remaining 14003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.11: 6081 32.11 - 64.22: 117 64.22 - 96.33: 39 96.33 - 128.43: 6 128.43 - 160.54: 5 Dihedral angle restraints: 6248 sinusoidal: 2569 harmonic: 3679 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 169.96 130.04 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" CA LYS A 584 " pdb=" C LYS A 584 " pdb=" N LYS A 585 " pdb=" CA LYS A 585 " ideal model delta harmonic sigma weight residual -180.00 -150.75 -29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ILE C 289 " pdb=" C ILE C 289 " pdb=" N ARG C 290 " pdb=" CA ARG C 290 " ideal model delta harmonic sigma weight residual -180.00 -150.86 -29.14 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 6245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 1519 0.165 - 0.330: 6 0.330 - 0.495: 0 0.495 - 0.660: 1 0.660 - 0.824: 1 Chirality restraints: 1527 Sorted by residual: chirality pdb=" C6 9UE C 404 " pdb=" N 9UE C 404 " pdb=" C29 9UE C 404 " pdb=" C5 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.65 -1.82 -0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" C12 9UE C 404 " pdb=" C11 9UE C 404 " pdb=" C13 9UE C 404 " pdb=" C17 9UE C 404 " both_signs ideal model delta sigma weight residual False 2.99 2.46 0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" C1 9UE C 404 " pdb=" C 9UE C 404 " pdb=" C15 9UE C 404 " pdb=" C2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.65 -2.38 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1524 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 701 " 0.160 9.50e-02 1.11e+02 9.19e-02 4.41e+01 pdb=" NE ARG A 701 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG A 701 " 0.109 2.00e-02 2.50e+03 pdb=" NH1 ARG A 701 " -0.039 2.00e-02 2.50e+03 pdb=" NH2 ARG A 701 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 710 " -0.135 9.50e-02 1.11e+02 7.88e-02 3.39e+01 pdb=" NE ARG A 710 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG A 710 " -0.096 2.00e-02 2.50e+03 pdb=" NH1 ARG A 710 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG A 710 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 92 " 0.140 9.50e-02 1.11e+02 7.50e-02 2.37e+01 pdb=" NE ARG A 92 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 92 " 0.078 2.00e-02 2.50e+03 pdb=" NH1 ARG A 92 " -0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG A 92 " -0.021 2.00e-02 2.50e+03 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 113 2.65 - 3.21: 9744 3.21 - 3.77: 14925 3.77 - 4.34: 21129 4.34 - 4.90: 34231 Nonbonded interactions: 80142 Sorted by model distance: nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 403 " model vdw 2.085 2.170 nonbonded pdb=" OH TYR A 528 " pdb=" O ALA A 547 " model vdw 2.182 2.440 nonbonded pdb=" NH1 ARG A 213 " pdb=" O THR A 443 " model vdw 2.197 2.520 nonbonded pdb=" OG SER A 78 " pdb=" O ALA A 753 " model vdw 2.237 2.440 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.237 2.440 ... (remaining 80137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.130 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: 0.010 Extract box with map and model: 6.990 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 31.560 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.014 0.621 10372 Z= 0.970 Angle : 1.417 58.645 14008 Z= 0.623 Chirality : 0.057 0.824 1527 Planarity : 0.008 0.093 1793 Dihedral : 16.756 160.542 3876 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.45 (0.21), residues: 1238 helix: -1.72 (0.17), residues: 585 sheet: 0.38 (0.38), residues: 157 loop : -0.14 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 356 HIS 0.009 0.002 HIS A 418 PHE 0.020 0.002 PHE A 673 TYR 0.036 0.006 TYR C 198 ARG 0.111 0.011 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8141 (m-80) cc_final: 0.7475 (m-10) REVERT: B 110 ARG cc_start: 0.8848 (mtt-85) cc_final: 0.8508 (mtt-85) REVERT: B 121 THR cc_start: 0.8417 (p) cc_final: 0.8175 (p) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2708 time to fit residues: 66.5568 Evaluate side-chains 94 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.0040 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.0570 chunk 112 optimal weight: 0.5980 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 136 ASN A 39 GLN A 264 GLN A 395 HIS A 455 ASN A 463 GLN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 642 ASN A 726 GLN C 12 ASN C 59 GLN C 246 GLN C 280 ASN C 353 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10372 Z= 0.193 Angle : 0.844 46.337 14008 Z= 0.372 Chirality : 0.043 0.267 1527 Planarity : 0.004 0.051 1793 Dihedral : 11.803 175.409 1397 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.20 % Allowed : 6.46 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.55 (0.22), residues: 1238 helix: 0.42 (0.20), residues: 599 sheet: 0.46 (0.36), residues: 171 loop : 0.53 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 414 HIS 0.010 0.001 HIS C 371 PHE 0.018 0.001 PHE C 255 TYR 0.013 0.001 TYR A 711 ARG 0.007 0.001 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 ILE cc_start: 0.7491 (mt) cc_final: 0.7289 (mp) REVERT: B 31 GLN cc_start: 0.8676 (mt0) cc_final: 0.8471 (mp10) REVERT: B 110 ARG cc_start: 0.8856 (mtt-85) cc_final: 0.8475 (mtt-85) REVERT: A 749 ILE cc_start: 0.9056 (tt) cc_final: 0.8850 (tt) REVERT: A 783 MET cc_start: 0.8445 (tpp) cc_final: 0.8006 (tpp) outliers start: 13 outliers final: 9 residues processed: 129 average time/residue: 0.2156 time to fit residues: 40.2631 Evaluate side-chains 97 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 88 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN A 125 ASN ** A 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10372 Z= 0.216 Angle : 0.804 47.022 14008 Z= 0.345 Chirality : 0.042 0.167 1527 Planarity : 0.004 0.034 1793 Dihedral : 11.594 179.984 1397 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 1.48 % Allowed : 8.77 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.23), residues: 1238 helix: 1.16 (0.21), residues: 593 sheet: 0.63 (0.37), residues: 171 loop : 0.76 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 414 HIS 0.009 0.001 HIS C 275 PHE 0.015 0.001 PHE C 255 TYR 0.017 0.001 TYR A 711 ARG 0.005 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8152 (m-80) cc_final: 0.7893 (m-10) REVERT: B 31 GLN cc_start: 0.8816 (mt0) cc_final: 0.8575 (mp10) REVERT: B 93 PHE cc_start: 0.8717 (m-80) cc_final: 0.8511 (m-80) REVERT: B 110 ARG cc_start: 0.8908 (mtt-85) cc_final: 0.8471 (mtt-85) REVERT: A 787 TYR cc_start: 0.8048 (t80) cc_final: 0.7826 (t80) REVERT: C 132 MET cc_start: 0.8790 (tmm) cc_final: 0.8510 (ppp) outliers start: 16 outliers final: 10 residues processed: 109 average time/residue: 0.2197 time to fit residues: 35.1403 Evaluate side-chains 95 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.0470 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN A 418 HIS ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN C 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10372 Z= 0.190 Angle : 0.781 47.218 14008 Z= 0.332 Chirality : 0.041 0.142 1527 Planarity : 0.003 0.034 1793 Dihedral : 11.228 171.980 1397 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.57 % Allowed : 9.33 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.51 (0.24), residues: 1238 helix: 1.42 (0.22), residues: 593 sheet: 0.67 (0.37), residues: 171 loop : 0.79 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 414 HIS 0.009 0.001 HIS C 275 PHE 0.014 0.001 PHE C 255 TYR 0.012 0.001 TYR B 86 ARG 0.004 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8979 (mt0) cc_final: 0.8751 (mp10) REVERT: B 93 PHE cc_start: 0.8629 (m-80) cc_final: 0.8422 (m-80) REVERT: B 110 ARG cc_start: 0.8964 (mtt-85) cc_final: 0.8620 (mtt-85) REVERT: B 140 ASN cc_start: 0.8899 (p0) cc_final: 0.8675 (t0) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.2032 time to fit residues: 31.4583 Evaluate side-chains 100 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10372 Z= 0.182 Angle : 0.773 47.236 14008 Z= 0.323 Chirality : 0.040 0.140 1527 Planarity : 0.003 0.036 1793 Dihedral : 10.970 164.003 1397 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.48 % Allowed : 9.88 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.66 (0.24), residues: 1238 helix: 1.58 (0.22), residues: 602 sheet: 0.73 (0.38), residues: 173 loop : 0.80 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 523 HIS 0.008 0.001 HIS C 275 PHE 0.015 0.001 PHE B 70 TYR 0.017 0.001 TYR A 787 ARG 0.003 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8996 (mt0) cc_final: 0.8728 (mp10) REVERT: B 93 PHE cc_start: 0.8654 (m-80) cc_final: 0.8144 (m-80) REVERT: B 110 ARG cc_start: 0.8960 (mtt-85) cc_final: 0.8618 (mtt-85) REVERT: B 140 ASN cc_start: 0.8925 (p0) cc_final: 0.8651 (t0) REVERT: C 227 MET cc_start: 0.8929 (tpp) cc_final: 0.8698 (ttm) REVERT: C 289 ILE cc_start: 0.8778 (mm) cc_final: 0.8400 (tt) outliers start: 16 outliers final: 12 residues processed: 107 average time/residue: 0.2009 time to fit residues: 31.7466 Evaluate side-chains 101 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 0.0020 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10372 Z= 0.208 Angle : 0.779 47.222 14008 Z= 0.326 Chirality : 0.040 0.145 1527 Planarity : 0.003 0.034 1793 Dihedral : 10.825 157.347 1397 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.85 % Allowed : 9.70 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.66 (0.24), residues: 1238 helix: 1.63 (0.22), residues: 603 sheet: 0.64 (0.38), residues: 173 loop : 0.77 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 374 HIS 0.008 0.001 HIS C 275 PHE 0.013 0.001 PHE C 255 TYR 0.012 0.001 TYR B 86 ARG 0.003 0.000 ARG A 792 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.9033 (mt0) cc_final: 0.8775 (mp10) REVERT: B 93 PHE cc_start: 0.8654 (m-80) cc_final: 0.8156 (m-80) REVERT: B 110 ARG cc_start: 0.8974 (mtt-85) cc_final: 0.8638 (mtt-85) REVERT: B 140 ASN cc_start: 0.8996 (p0) cc_final: 0.8690 (t0) REVERT: A 92 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7626 (mtt90) REVERT: A 783 MET cc_start: 0.7448 (tpp) cc_final: 0.7217 (tpp) REVERT: A 790 MET cc_start: 0.5655 (tmm) cc_final: 0.5411 (ttp) REVERT: C 289 ILE cc_start: 0.8771 (mm) cc_final: 0.8437 (tt) outliers start: 20 outliers final: 12 residues processed: 110 average time/residue: 0.2166 time to fit residues: 34.9590 Evaluate side-chains 102 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 0.0020 chunk 66 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10372 Z= 0.176 Angle : 0.769 47.252 14008 Z= 0.320 Chirality : 0.040 0.152 1527 Planarity : 0.003 0.035 1793 Dihedral : 10.669 152.562 1397 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.75 % Allowed : 10.34 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.69 (0.24), residues: 1238 helix: 1.71 (0.22), residues: 596 sheet: 0.55 (0.38), residues: 174 loop : 0.77 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 414 HIS 0.007 0.001 HIS C 275 PHE 0.012 0.001 PHE C 255 TYR 0.011 0.001 TYR A 787 ARG 0.002 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 1.305 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: B 70 PHE cc_start: 0.7849 (t80) cc_final: 0.7645 (t80) REVERT: B 93 PHE cc_start: 0.8626 (m-80) cc_final: 0.8151 (m-80) REVERT: B 110 ARG cc_start: 0.8971 (mtt-85) cc_final: 0.8610 (mtt-85) REVERT: B 140 ASN cc_start: 0.9010 (p0) cc_final: 0.8694 (t0) REVERT: A 92 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7603 (mtt90) REVERT: C 132 MET cc_start: 0.8971 (ppp) cc_final: 0.8689 (ppp) REVERT: C 152 VAL cc_start: 0.9182 (t) cc_final: 0.8962 (m) outliers start: 19 outliers final: 12 residues processed: 110 average time/residue: 0.2015 time to fit residues: 32.4767 Evaluate side-chains 101 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 93 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10372 Z= 0.198 Angle : 0.789 47.212 14008 Z= 0.330 Chirality : 0.040 0.143 1527 Planarity : 0.003 0.034 1793 Dihedral : 10.635 150.735 1397 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.57 % Allowed : 10.80 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.70 (0.24), residues: 1238 helix: 1.75 (0.22), residues: 592 sheet: 0.51 (0.38), residues: 174 loop : 0.73 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.007 0.001 HIS C 275 PHE 0.012 0.001 PHE B 19 TYR 0.013 0.001 TYR B 86 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.8640 (m-80) cc_final: 0.8136 (m-80) REVERT: B 110 ARG cc_start: 0.8990 (mtt-85) cc_final: 0.8631 (mtt-85) REVERT: B 140 ASN cc_start: 0.9023 (p0) cc_final: 0.8687 (t0) REVERT: A 92 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7590 (mtt90) REVERT: A 177 MET cc_start: 0.7877 (mpp) cc_final: 0.7621 (mpp) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.2372 time to fit residues: 35.8948 Evaluate side-chains 98 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10372 Z= 0.309 Angle : 0.828 47.095 14008 Z= 0.355 Chirality : 0.042 0.139 1527 Planarity : 0.003 0.033 1793 Dihedral : 10.769 148.838 1397 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.57 % Allowed : 11.08 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.52 (0.24), residues: 1238 helix: 1.66 (0.22), residues: 592 sheet: 0.47 (0.39), residues: 170 loop : 0.56 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 79 HIS 0.009 0.001 HIS C 371 PHE 0.013 0.001 PHE C 255 TYR 0.015 0.001 TYR A 711 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.8671 (m-80) cc_final: 0.8190 (m-80) REVERT: B 110 ARG cc_start: 0.8982 (mtt-85) cc_final: 0.8637 (mtt-85) REVERT: B 140 ASN cc_start: 0.9050 (p0) cc_final: 0.8697 (t0) REVERT: A 92 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7674 (mtt90) REVERT: A 386 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8852 (p) REVERT: C 81 ASP cc_start: 0.7649 (m-30) cc_final: 0.7425 (m-30) outliers start: 17 outliers final: 12 residues processed: 100 average time/residue: 0.2245 time to fit residues: 32.3906 Evaluate side-chains 100 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10372 Z= 0.169 Angle : 0.797 47.198 14008 Z= 0.332 Chirality : 0.040 0.138 1527 Planarity : 0.003 0.035 1793 Dihedral : 10.555 145.899 1397 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.29 % Allowed : 11.36 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.56 (0.24), residues: 1238 helix: 1.71 (0.22), residues: 588 sheet: 0.47 (0.39), residues: 170 loop : 0.56 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 79 HIS 0.006 0.001 HIS C 275 PHE 0.026 0.001 PHE B 70 TYR 0.015 0.001 TYR A 787 ARG 0.003 0.000 ARG B 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.8606 (m-80) cc_final: 0.8180 (m-80) REVERT: B 110 ARG cc_start: 0.8977 (mtt-85) cc_final: 0.8621 (mtt-85) REVERT: B 140 ASN cc_start: 0.9001 (p0) cc_final: 0.8643 (t0) REVERT: A 92 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7713 (mtt90) REVERT: A 386 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8855 (p) REVERT: C 81 ASP cc_start: 0.7510 (m-30) cc_final: 0.7247 (m-30) outliers start: 14 outliers final: 11 residues processed: 103 average time/residue: 0.2274 time to fit residues: 33.8264 Evaluate side-chains 103 residues out of total 1094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 708 PHE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 0.0000 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 41 optimal weight: 0.0040 chunk 101 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.083488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061719 restraints weight = 30335.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.063975 restraints weight = 14679.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.065467 restraints weight = 9126.509| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10372 Z= 0.178 Angle : 0.797 47.157 14008 Z= 0.331 Chirality : 0.040 0.170 1527 Planarity : 0.003 0.034 1793 Dihedral : 10.461 143.797 1397 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.48 % Allowed : 11.54 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.58 (0.24), residues: 1238 helix: 1.71 (0.22), residues: 594 sheet: 0.46 (0.39), residues: 170 loop : 0.60 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.006 0.001 HIS C 275 PHE 0.011 0.001 PHE C 255 TYR 0.011 0.001 TYR A 711 ARG 0.003 0.000 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1990.13 seconds wall clock time: 36 minutes 54.77 seconds (2214.77 seconds total)