Starting phenix.real_space_refine on Sat Dec 9 03:41:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/12_2023/6nts_0510_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/12_2023/6nts_0510.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/12_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_0510/12_2023/6nts_0510_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/12_2023/6nts_0510_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/12_2023/6nts_0510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/12_2023/6nts_0510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/12_2023/6nts_0510_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nts_0510/12_2023/6nts_0510_updated.pdb" } resolution = 3.63 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= -0.001 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-1.21rc1-5172/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: 5.57, per 1000 atoms: 0.56 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: 4.05 Conformation dependent library (CDL) restraints added in 1.7 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: 2.16 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: 2.55 Time building geometry restraints manager: 4.38 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: 5810 20.75 - 41.50: 289 41.50 - 62.25: 42 62.25 - 83.00: 15 83.00 - 103.75: 7 Dihedral angle restraints: 6163 sinusoidal: 2512 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 6160 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: 1.680 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: 8.180 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.650 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:2.810 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: 0.7686 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 : 13.236 103.750 3785 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 % Allowed : 0.54 % Favored : 99.46 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.000 TRP A 257 HIS 0.003 0.000 HIS B 364 PHE 0.008 0.001 PHE A 538 TYR 0.013 0.001 TYR C 86 ARG 0.002 0.000 ARG C 185 *********************** 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 : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2730 time to fit residues: 45.5594 Evaluate side-chains 47 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5829 ------------------------------------------------------------------------------- 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: 0.8001 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10161 Z= 0.230 Angle : 0.628 9.705 13780 Z= 0.304 Chirality : 0.041 0.221 1572 Planarity : 0.003 0.036 1764 Dihedral : 4.438 57.106 1342 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.09 % Allowed : 6.52 % Favored : 92.40 % 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: -0.77 (0.24), residues: 1231 helix: -0.24 (0.19), residues: 809 sheet: -0.81 (0.98), residues: 31 loop : -0.77 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 477 HIS 0.011 0.001 HIS C 241 PHE 0.029 0.001 PHE A 538 TYR 0.015 0.001 TYR C 86 ARG 0.006 0.000 ARG A 21 *********************** 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 66 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 63 average time/residue: 0.2459 time to fit residues: 22.8709 Evaluate side-chains 49 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1105 time to fit residues: 2.9790 ------------------------------------------------------------------------------- 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: 9.9990 chunk 34 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 chunk 111 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 0.0770 overall best weight: 0.5736 ------------------------------------------------------------------------------- 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: 0.8028 moved from start: 0.2959 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= 0.149 Angle : 0.536 12.292 13780 Z= 0.259 Chirality : 0.039 0.141 1572 Planarity : 0.003 0.031 1764 Dihedral : 4.067 55.216 1342 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.54 % Allowed : 8.05 % Favored : 91.40 % 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: -0.23 (0.25), residues: 1231 helix: 0.16 (0.19), residues: 806 sheet: -0.67 (1.01), residues: 31 loop : -0.50 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 156 HIS 0.005 0.001 HIS B 289 PHE 0.027 0.001 PHE A 538 TYR 0.010 0.001 TYR B 400 ARG 0.003 0.000 ARG A 249 *********************** 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 55 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 52 average time/residue: 0.2373 time to fit residues: 18.7129 Evaluate side-chains 42 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1130 time to fit residues: 2.0514 ------------------------------------------------------------------------------- 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: 4.9990 chunk 84 optimal weight: 0.5980 chunk 58 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN B 111 ASN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10161 Z= 0.254 Angle : 0.629 10.314 13780 Z= 0.309 Chirality : 0.042 0.249 1572 Planarity : 0.004 0.032 1764 Dihedral : 4.417 54.466 1342 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.90 % Allowed : 10.23 % Favored : 88.87 % 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: -0.01 (0.25), residues: 1231 helix: 0.32 (0.19), residues: 816 sheet: -0.18 (1.11), residues: 31 loop : -0.44 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 156 HIS 0.004 0.001 HIS B 289 PHE 0.020 0.002 PHE A 538 TYR 0.011 0.001 TYR B 238 ARG 0.007 0.001 ARG A 21 *********************** 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 50 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 1.095 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 49 average time/residue: 0.1676 time to fit residues: 13.8215 Evaluate side-chains 41 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0925 time to fit residues: 2.6725 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN A 557 GLN ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10161 Z= 0.187 Angle : 0.549 7.888 13780 Z= 0.269 Chirality : 0.040 0.194 1572 Planarity : 0.003 0.033 1764 Dihedral : 4.265 55.878 1342 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.90 % Allowed : 11.13 % Favored : 87.96 % 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: 0.32 (0.25), residues: 1231 helix: 0.55 (0.19), residues: 819 sheet: -0.33 (1.08), residues: 31 loop : -0.24 (0.35), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 156 HIS 0.005 0.001 HIS B 289 PHE 0.019 0.001 PHE A 538 TYR 0.009 0.001 TYR C 107 ARG 0.004 0.000 ARG A 537 *********************** 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 49 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 1.069 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 47 average time/residue: 0.1980 time to fit residues: 15.0239 Evaluate side-chains 40 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1149 time to fit residues: 2.3875 ------------------------------------------------------------------------------- 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: 0.6980 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 55 optimal weight: 0.0370 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.7262 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10161 Z= 0.278 Angle : 0.628 8.565 13780 Z= 0.310 Chirality : 0.042 0.162 1572 Planarity : 0.004 0.035 1764 Dihedral : 4.523 53.828 1342 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.54 % Allowed : 13.21 % Favored : 86.24 % 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: 0.49 (0.19), residues: 815 sheet: -0.36 (1.06), residues: 31 loop : -0.39 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 477 HIS 0.005 0.001 HIS C 63 PHE 0.020 0.002 PHE A 538 TYR 0.012 0.001 TYR B 107 ARG 0.007 0.001 ARG A 221 *********************** 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 40 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 1.195 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 0.1802 time to fit residues: 12.4498 Evaluate side-chains 37 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1019 time to fit residues: 2.1632 ------------------------------------------------------------------------------- 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: 4.9990 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10161 Z= 0.195 Angle : 0.570 8.860 13780 Z= 0.277 Chirality : 0.040 0.145 1572 Planarity : 0.003 0.034 1764 Dihedral : 4.381 56.185 1342 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.54 % Allowed : 13.48 % Favored : 85.97 % 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: 0.50 (0.25), residues: 1231 helix: 0.69 (0.19), residues: 808 sheet: -0.25 (1.09), residues: 31 loop : -0.14 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.005 0.001 HIS B 289 PHE 0.019 0.001 PHE A 538 TYR 0.011 0.001 TYR B 107 ARG 0.006 0.000 ARG A 221 *********************** 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 40 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 1.127 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 0.1892 time to fit residues: 12.5578 Evaluate side-chains 36 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0921 time to fit residues: 2.1299 ------------------------------------------------------------------------------- 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: 0.8980 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10161 Z= 0.166 Angle : 0.554 8.480 13780 Z= 0.267 Chirality : 0.039 0.154 1572 Planarity : 0.003 0.034 1764 Dihedral : 4.226 57.006 1342 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.09 % Allowed : 14.03 % Favored : 85.88 % 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 (0.25), residues: 1231 helix: 0.78 (0.19), residues: 813 sheet: -0.61 (1.00), residues: 31 loop : -0.21 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 477 HIS 0.003 0.001 HIS B 289 PHE 0.017 0.001 PHE A 538 TYR 0.025 0.001 TYR A 60 ARG 0.006 0.000 ARG A 221 *********************** 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 36 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 1.277 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.2154 time to fit residues: 12.9011 Evaluate side-chains 35 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1214 time to fit residues: 1.8487 ------------------------------------------------------------------------------- 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: 2.9990 chunk 110 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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: 0.8374 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10161 Z= 0.204 Angle : 0.571 8.967 13780 Z= 0.278 Chirality : 0.040 0.159 1572 Planarity : 0.003 0.034 1764 Dihedral : 4.291 56.658 1342 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.09 % Allowed : 14.03 % Favored : 85.88 % 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: 0.64 (0.25), residues: 1231 helix: 0.83 (0.19), residues: 808 sheet: -0.91 (0.94), residues: 31 loop : -0.12 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.006 0.001 HIS B 289 PHE 0.019 0.001 PHE A 538 TYR 0.010 0.001 TYR B 107 ARG 0.006 0.000 ARG A 221 *********************** 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 36 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 1.268 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.2028 time to fit residues: 12.7314 Evaluate side-chains 35 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 1.314 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1055 time to fit residues: 2.6735 ------------------------------------------------------------------------------- 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: 0.8980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 77 optimal weight: 0.0770 chunk 103 optimal weight: 4.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.6211 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= 0.146 Angle : 0.556 12.372 13780 Z= 0.266 Chirality : 0.039 0.154 1572 Planarity : 0.003 0.034 1764 Dihedral : 4.200 57.442 1342 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.09 % Allowed : 14.12 % Favored : 85.79 % 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: 0.70 (0.25), residues: 1231 helix: 0.89 (0.19), residues: 805 sheet: -0.82 (0.94), residues: 31 loop : -0.10 (0.34), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 477 HIS 0.005 0.001 HIS B 289 PHE 0.017 0.001 PHE A 538 TYR 0.010 0.001 TYR B 107 ARG 0.005 0.000 ARG A 221 ********************** 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 39 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 1.303 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.1832 time to fit residues: 12.1469 Evaluate side-chains 36 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0999 time to fit residues: 1.4700 ------------------------------------------------------------------------------- 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: 0.1980 chunk 89 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 0.0770 chunk 5 optimal weight: 10.0000 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.047097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.039909 restraints weight = 63900.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.041084 restraints weight = 35657.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.041899 restraints weight = 23517.182| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 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 = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.6186 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= 0.130 Angle : 0.546 11.186 13780 Z= 0.261 Chirality : 0.038 0.161 1572 Planarity : 0.003 0.034 1764 Dihedral : 4.110 57.171 1342 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.09 % Allowed : 14.30 % Favored : 85.61 % 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: 0.75 (0.25), residues: 1231 helix: 0.92 (0.19), residues: 804 sheet: -0.66 (0.96), residues: 31 loop : -0.07 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 257 HIS 0.004 0.001 HIS B 289 PHE 0.016 0.001 PHE A 538 TYR 0.025 0.001 TYR B 107 ARG 0.005 0.000 ARG A 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1742.11 seconds wall clock time: 32 minutes 55.16 seconds (1975.16 seconds total)