Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 14:23:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/04_2023/6nts_0510_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/04_2023/6nts_0510.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/04_2023/6nts_0510_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/04_2023/6nts_0510_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/04_2023/6nts_0510_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/04_2023/6nts_0510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/04_2023/6nts_0510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/04_2023/6nts_0510_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/04_2023/6nts_0510_updated.pdb" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.001 sd= 0.033 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 S 57 5.16 5 C 6378 2.51 5 N 1654 2.21 5 O 1862 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 100": "OE1" <-> "OE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 122": "OD1" <-> "OD2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 312": "NH1" <-> "NH2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9956 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4543 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 556} Chain: "B" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2976 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Chain: "C" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2399 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'L2J': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.70, per 1000 atoms: 0.57 Number of scatterers: 9956 At special positions: 0 Unit cell: (96.824, 110.656, 118.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 57 16.00 F 3 9.00 O 1862 8.00 N 1654 7.00 C 6378 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: 4.48 Conformation dependent library (CDL) restraints added in 1.5 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2378 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 3 sheets defined 65.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 12 through 16 Processing helix chain 'A' and resid 25 through 42 removed outlier: 5.224A pdb=" N SER A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 58 removed outlier: 5.099A pdb=" N LEU A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 97 Proline residue: A 91 - end of helix Processing helix chain 'A' and resid 102 through 117 removed outlier: 4.156A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 removed outlier: 4.837A pdb=" N VAL A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.616A pdb=" N CYS A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 163 through 174 removed outlier: 3.692A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 removed outlier: 4.749A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 213 removed outlier: 5.081A pdb=" N ILE A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 218 through 234 removed outlier: 4.698A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 removed outlier: 4.398A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 252 Processing helix chain 'A' and resid 258 through 274 removed outlier: 5.172A pdb=" N THR A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLU A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 291 removed outlier: 4.743A pdb=" N VAL A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 297 through 311 removed outlier: 4.821A pdb=" N LYS A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 325 Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.767A pdb=" N LYS A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.924A pdb=" N SER A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 373 removed outlier: 3.806A pdb=" N ILE A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 378 through 386 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 397 through 413 removed outlier: 3.760A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Proline residue: A 406 - end of helix removed outlier: 5.059A pdb=" N GLU A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 434 Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 436 through 442 removed outlier: 3.666A pdb=" N ASP A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 451 Processing helix chain 'A' and resid 456 through 473 removed outlier: 4.004A pdb=" N GLU A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 491 removed outlier: 5.257A pdb=" N ILE A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Proline residue: A 484 - end of helix removed outlier: 3.941A pdb=" N MET A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 512 removed outlier: 3.734A pdb=" N THR A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 530 removed outlier: 5.227A pdb=" N LEU A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix removed outlier: 3.575A pdb=" N ALA A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 550 removed outlier: 4.549A pdb=" N ALA A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Proline residue: A 549 - end of helix Processing helix chain 'A' and resid 553 through 569 removed outlier: 3.601A pdb=" N GLN A 557 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix removed outlier: 3.814A pdb=" N GLN A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 586 Processing helix chain 'B' and resid 70 through 75 removed outlier: 4.203A pdb=" N LYS B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 92 through 110 removed outlier: 3.765A pdb=" N GLU B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 removed outlier: 4.384A pdb=" N SER B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 170 removed outlier: 4.230A pdb=" N LEU B 161 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.957A pdb=" N ARG B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 197 removed outlier: 4.305A pdb=" N LEU B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 removed outlier: 3.952A pdb=" N PHE B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 238 Processing helix chain 'B' and resid 246 through 259 removed outlier: 3.737A pdb=" N ILE B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 275 removed outlier: 3.713A pdb=" N LEU B 272 " --> pdb=" O HIS B 268 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 281 removed outlier: 3.698A pdb=" N THR B 281 " --> pdb=" O PRO B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 281' Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 289 through 300 removed outlier: 3.856A pdb=" N PHE B 299 " --> pdb=" O CYS B 295 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 316 removed outlier: 3.781A pdb=" N THR B 307 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B 308 " --> pdb=" O THR B 305 " (cutoff:3.500A) Proline residue: B 309 - end of helix removed outlier: 3.520A pdb=" N LYS B 316 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 336 removed outlier: 3.600A pdb=" N MET B 328 " --> pdb=" O GLN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 361 removed outlier: 4.465A pdb=" N LYS B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE B 348 " --> pdb=" O GLN B 344 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Proline residue: B 351 - end of helix removed outlier: 3.623A pdb=" N LYS B 358 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 376 removed outlier: 4.119A pdb=" N PHE B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TRP B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ASN B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 385 Processing helix chain 'B' and resid 392 through 401 removed outlier: 4.139A pdb=" N PHE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 397 " --> pdb=" O PRO B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 424 Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 25 through 41 removed outlier: 4.584A pdb=" N LYS C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 Processing helix chain 'C' and resid 93 through 106 Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.548A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 194 through 200 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing sheet with id= A, first strand: chain 'C' and resid 45 through 48 removed outlier: 7.250A pdb=" N THR C 156 " --> pdb=" O GLN C 46 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N VAL C 48 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU C 158 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 236 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU C 166 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER C 238 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 111 through 113 removed outlier: 6.302A pdb=" N TYR C 80 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR C 53 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 209 through 211 445 hydrogen bonds defined for protein. 1290 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: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.57: 10076 1.57 - 1.92: 84 1.92 - 2.27: 0 2.27 - 2.62: 0 2.62 - 2.97: 1 Bond restraints: 10161 Sorted by residual: bond pdb=" C10 MLL C 309 " pdb=" O9 MLL C 309 " ideal model delta sigma weight residual 1.427 2.965 -1.538 2.00e-02 2.50e+03 5.92e+03 bond pdb=" C02 L2J A 601 " pdb=" C03 L2J A 601 " ideal model delta sigma weight residual 1.404 1.293 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C MLL C 309 " pdb=" O9 MLL C 309 " ideal model delta sigma weight residual 1.327 1.231 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C01 L2J A 601 " pdb=" C06 L2J A 601 " ideal model delta sigma weight residual 1.392 1.488 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C05 L2J A 601 " pdb=" C06 L2J A 601 " ideal model delta sigma weight residual 1.389 1.473 -0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 10156 not shown) Histogram of bond angle deviations from ideal: 100.75 - 107.39: 325 107.39 - 114.04: 5841 114.04 - 120.68: 4517 120.68 - 127.32: 2985 127.32 - 133.97: 112 Bond angle restraints: 13780 Sorted by residual: angle pdb=" C MLL C 309 " pdb=" O9 MLL C 309 " pdb=" C10 MLL C 309 " ideal model delta sigma weight residual 117.67 133.31 -15.64 3.00e+00 1.11e-01 2.72e+01 angle pdb=" C07 L2J A 601 " pdb=" N01 L2J A 601 " pdb=" C18 L2J A 601 " ideal model delta sigma weight residual 109.49 123.82 -14.33 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C01 L2J A 601 " pdb=" C06 L2J A 601 " pdb=" C05 L2J A 601 " ideal model delta sigma weight residual 120.02 108.25 11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CA MLL C 309 " pdb=" C MLL C 309 " pdb=" O9 MLL C 309 " ideal model delta sigma weight residual 110.79 121.00 -10.21 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C03 L2J A 601 " pdb=" N01 L2J A 601 " pdb=" C18 L2J A 601 " ideal model delta sigma weight residual 109.45 117.08 -7.63 3.00e+00 1.11e-01 6.46e+00 ... (remaining 13775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.75: 5806 20.75 - 41.50: 288 41.50 - 62.25: 42 62.25 - 83.00: 15 83.00 - 103.75: 7 Dihedral angle restraints: 6158 sinusoidal: 2507 harmonic: 3651 Sorted by residual: dihedral pdb=" CA ARG A 537 " pdb=" C ARG A 537 " pdb=" N PHE A 538 " pdb=" CA PHE A 538 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" C15 L2J A 601 " pdb=" C13 L2J A 601 " pdb=" C14 L2J A 601 " pdb=" C18 L2J A 601 " ideal model delta sinusoidal sigma weight residual 52.96 -50.79 103.75 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" CA HIS B 364 " pdb=" C HIS B 364 " pdb=" N PHE B 365 " pdb=" CA PHE B 365 " ideal model delta harmonic sigma weight residual -180.00 -162.42 -17.58 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 6155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1117 0.029 - 0.058: 287 0.058 - 0.086: 116 0.086 - 0.115: 47 0.115 - 0.144: 5 Chirality restraints: 1572 Sorted by residual: chirality pdb=" C18 L2J A 601 " pdb=" C13 L2J A 601 " pdb=" C17 L2J A 601 " pdb=" N01 L2J A 601 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA VAL C 52 " pdb=" N VAL C 52 " pdb=" C VAL C 52 " pdb=" CB VAL C 52 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA PHE A 538 " pdb=" N PHE A 538 " pdb=" C PHE A 538 " pdb=" CB PHE A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1569 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 90 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.12e-01 pdb=" N PRO A 91 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 86 " 0.010 2.00e-02 2.50e+03 6.28e-03 7.89e-01 pdb=" CG TYR C 86 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR C 86 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 86 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 86 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 86 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 86 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 50 " -0.013 5.00e-02 4.00e+02 2.02e-02 6.53e-01 pdb=" N PRO C 51 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO C 51 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 51 " -0.011 5.00e-02 4.00e+02 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 40 2.51 - 3.11: 7922 3.11 - 3.71: 15892 3.71 - 4.30: 22155 4.30 - 4.90: 35777 Nonbonded interactions: 81786 Sorted by model distance: nonbonded pdb=" ND1 HIS C 241 " pdb="MN MN C 401 " model vdw 1.917 2.400 nonbonded pdb=" O GLY A 275 " pdb=" OG1 THR A 279 " model vdw 2.209 2.440 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 402 " model vdw 2.222 2.320 nonbonded pdb=" NE2 HIS C 59 " pdb="MN MN C 402 " model vdw 2.235 2.400 nonbonded pdb=" O GLY A 513 " pdb=" OG1 THR A 517 " model vdw 2.264 2.440 ... (remaining 81781 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=0.64 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: 2.040 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: 0.000 Extract box with map and model: 8.680 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.450 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 : 0.016 1.538 10161 Z= 1.026 Angle : 0.511 15.645 13780 Z= 0.246 Chirality : 0.034 0.144 1572 Planarity : 0.002 0.023 1764 Dihedral : 13.232 103.750 3780 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.00 % 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: -2.08 (0.22), residues: 1231 helix: -1.17 (0.17), residues: 793 sheet: -1.94 (0.87), residues: 35 loop : -1.41 (0.30), residues: 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2783 time to fit residues: 46.1517 Evaluate side-chains 47 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 31 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN C 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10161 Z= 0.223 Angle : 0.628 9.792 13780 Z= 0.304 Chirality : 0.042 0.253 1572 Planarity : 0.003 0.035 1764 Dihedral : 4.562 63.129 1337 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.90 % 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: -0.76 (0.24), residues: 1231 helix: -0.22 (0.19), residues: 809 sheet: -0.83 (0.98), residues: 31 loop : -0.78 (0.32), residues: 391 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 63 average time/residue: 0.2507 time to fit residues: 23.0907 Evaluate side-chains 47 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 1.314 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1111 time to fit residues: 2.7027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 30 optimal weight: 0.1980 chunk 111 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 10161 Z= 0.183 Angle : 0.560 12.565 13780 Z= 0.270 Chirality : 0.040 0.142 1572 Planarity : 0.003 0.031 1764 Dihedral : 4.106 53.739 1337 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.54 % 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: -0.18 (0.25), residues: 1231 helix: 0.20 (0.19), residues: 811 sheet: 0.61 (1.36), residues: 21 loop : -0.57 (0.33), residues: 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 49 average time/residue: 0.2115 time to fit residues: 16.5354 Evaluate side-chains 41 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1182 time to fit residues: 1.9179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 10161 Z= 0.178 Angle : 0.540 7.519 13780 Z= 0.265 Chirality : 0.039 0.144 1572 Planarity : 0.003 0.035 1764 Dihedral : 4.137 56.051 1337 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.45 % 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: 0.22 (0.25), residues: 1231 helix: 0.51 (0.19), residues: 815 sheet: -0.25 (1.09), residues: 31 loop : -0.36 (0.35), residues: 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 0.2050 time to fit residues: 16.0469 Evaluate side-chains 41 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 1.209 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0884 time to fit residues: 2.2166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN A 444 ASN B 228 GLN ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 10161 Z= 0.282 Angle : 0.671 10.616 13780 Z= 0.327 Chirality : 0.042 0.160 1572 Planarity : 0.004 0.058 1764 Dihedral : 4.563 52.970 1337 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 0.81 % 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: 0.17 (0.25), residues: 1231 helix: 0.51 (0.19), residues: 801 sheet: 1.14 (1.41), residues: 21 loop : -0.54 (0.32), residues: 409 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 1.326 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 41 average time/residue: 0.1938 time to fit residues: 13.6148 Evaluate side-chains 35 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1203 time to fit residues: 2.8574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.0870 chunk 114 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 10161 Z= 0.149 Angle : 0.561 7.489 13780 Z= 0.270 Chirality : 0.039 0.196 1572 Planarity : 0.003 0.035 1764 Dihedral : 4.290 56.472 1337 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.45 % 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: 0.46 (0.25), residues: 1231 helix: 0.72 (0.19), residues: 809 sheet: 0.33 (1.27), residues: 26 loop : -0.37 (0.33), residues: 396 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 1.402 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 39 average time/residue: 0.2115 time to fit residues: 13.6541 Evaluate side-chains 37 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0961 time to fit residues: 2.2609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 10161 Z= 0.156 Angle : 0.556 7.677 13780 Z= 0.266 Chirality : 0.039 0.149 1572 Planarity : 0.003 0.034 1764 Dihedral : 4.120 55.261 1337 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.18 % 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: 0.60 (0.26), residues: 1231 helix: 0.83 (0.19), residues: 811 sheet: 0.28 (1.27), residues: 26 loop : -0.31 (0.34), residues: 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 1.422 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.1978 time to fit residues: 11.8800 Evaluate side-chains 34 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 1.343 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1121 time to fit residues: 2.0829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 0.0270 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 10161 Z= 0.155 Angle : 0.549 7.622 13780 Z= 0.262 Chirality : 0.039 0.147 1572 Planarity : 0.003 0.034 1764 Dihedral : 4.053 55.505 1337 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.18 % 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: 0.67 (0.26), residues: 1231 helix: 0.89 (0.19), residues: 809 sheet: -0.12 (1.21), residues: 26 loop : -0.27 (0.34), residues: 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 1.320 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 34 average time/residue: 0.2011 time to fit residues: 11.8956 Evaluate side-chains 31 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 1.408 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1017 time to fit residues: 2.1666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 116 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 10161 Z= 0.160 Angle : 0.564 9.072 13780 Z= 0.266 Chirality : 0.039 0.146 1572 Planarity : 0.003 0.034 1764 Dihedral : 4.050 55.467 1337 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.09 % 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: 0.71 (0.26), residues: 1231 helix: 0.92 (0.19), residues: 809 sheet: -0.19 (1.19), residues: 26 loop : -0.24 (0.34), residues: 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 1.306 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.2066 time to fit residues: 11.2855 Evaluate side-chains 31 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 1.410 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1294 time to fit residues: 1.9724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 77 optimal weight: 0.0980 chunk 103 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 10161 Z= 0.141 Angle : 0.564 12.423 13780 Z= 0.264 Chirality : 0.038 0.146 1572 Planarity : 0.003 0.034 1764 Dihedral : 3.999 55.811 1337 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.00 % 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: 0.80 (0.26), residues: 1231 helix: 0.99 (0.20), residues: 803 sheet: -0.10 (1.19), residues: 26 loop : -0.18 (0.34), residues: 402 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.233 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2092 time to fit residues: 11.6180 Evaluate side-chains 31 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.0070 chunk 85 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.047270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.040099 restraints weight = 64014.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.041286 restraints weight = 35646.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.042102 restraints weight = 23412.606| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 10161 Z= 0.136 Angle : 0.556 12.566 13780 Z= 0.259 Chirality : 0.038 0.149 1572 Planarity : 0.003 0.034 1764 Dihedral : 3.939 55.729 1337 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.00 % 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: 0.88 (0.26), residues: 1231 helix: 1.05 (0.20), residues: 802 sheet: -0.31 (1.10), residues: 31 loop : -0.12 (0.34), residues: 398 =============================================================================== Job complete usr+sys time: 1682.05 seconds wall clock time: 31 minutes 54.87 seconds (1914.87 seconds total)