Starting phenix.real_space_refine on Wed Mar 4 09:20:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rw8_24710/03_2026/7rw8_24710.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rw8_24710/03_2026/7rw8_24710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rw8_24710/03_2026/7rw8_24710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rw8_24710/03_2026/7rw8_24710.map" model { file = "/net/cci-nas-00/data/ceres_data/7rw8_24710/03_2026/7rw8_24710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rw8_24710/03_2026/7rw8_24710.cif" } resolution = 3.5 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8136 2.51 5 N 2113 2.21 5 O 2263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12572 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4389 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 22, 'TRANS': 575} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 15, 'ASP:plan': 18, 'ASN:plan1': 5, 'GLU:plan': 17, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 232 Chain: "B" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4086 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 26, 'TRANS': 552} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 515 Unresolved non-hydrogen angles: 618 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 25, 'ASN:plan1': 12, 'ARG:plan': 10, 'ASP:plan': 20, 'GLN:plan1': 10, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 305 Chain: "M" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2969 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 17, 'TRANS': 376} Chain breaks: 3 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 4, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 133 Chain: "S" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1128 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 140} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 4, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 2.74, per 1000 atoms: 0.22 Number of scatterers: 12572 At special positions: 0 Unit cell: (97.9, 110.36, 129.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2263 8.00 N 2113 7.00 C 8136 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 509.1 milliseconds 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3308 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 7 sheets defined 63.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.597A pdb=" N SER A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 46 Processing helix chain 'A' and resid 51 through 69 removed outlier: 3.587A pdb=" N GLY A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 83 removed outlier: 3.735A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.760A pdb=" N VAL A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.070A pdb=" N PHE A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.646A pdb=" N CYS A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 293 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.864A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.596A pdb=" N ARG A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.975A pdb=" N HIS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 382 through 396 Processing helix chain 'A' and resid 401 through 416 removed outlier: 3.901A pdb=" N GLU A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 435 removed outlier: 4.218A pdb=" N GLU A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 460 through 472 removed outlier: 3.734A pdb=" N ILE A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 4.017A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.504A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 removed outlier: 3.890A pdb=" N VAL A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.534A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 589 Processing helix chain 'A' and resid 591 through 599 removed outlier: 3.537A pdb=" N THR A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 598 " --> pdb=" O ILE A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 23 removed outlier: 3.659A pdb=" N ASN B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 43 removed outlier: 3.960A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 62 through 80 removed outlier: 3.563A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 86 removed outlier: 3.527A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.563A pdb=" N PHE B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 99 through 112 removed outlier: 4.028A pdb=" N ARG B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.903A pdb=" N THR B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 128 removed outlier: 3.589A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 127 " --> pdb=" O CYS B 123 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 128' Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.994A pdb=" N ARG B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 170 removed outlier: 4.263A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 removed outlier: 5.346A pdb=" N ALA B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 4.388A pdb=" N ASN B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.802A pdb=" N ILE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 284 through 292 removed outlier: 3.930A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.756A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.616A pdb=" N VAL B 323 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.948A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.729A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.590A pdb=" N ALA B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.559A pdb=" N GLU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 435 removed outlier: 3.556A pdb=" N GLU B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 461 through 471 removed outlier: 3.808A pdb=" N GLU B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 499 through 512 Processing helix chain 'B' and resid 516 through 531 Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.559A pdb=" N ALA B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 538 " --> pdb=" O PRO B 534 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 566 Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.595A pdb=" N PHE B 581 " --> pdb=" O PRO B 578 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 36 removed outlier: 3.776A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.534A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 128 through 133 removed outlier: 4.160A pdb=" N PHE M 132 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 42 removed outlier: 3.512A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 96 Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 127 through 141 Processing sheet with id=AA1, first strand: chain 'M' and resid 14 through 19 Processing sheet with id=AA2, first strand: chain 'M' and resid 116 through 117 removed outlier: 3.530A pdb=" N ASP M 117 " --> pdb=" O TYR M 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 245 through 248 removed outlier: 5.917A pdb=" N GLU M 271 " --> pdb=" O SER M 204 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER M 204 " --> pdb=" O GLU M 271 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET M 275 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG M 427 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL M 392 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU M 316 " --> pdb=" O ALA M 359 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA M 359 " --> pdb=" O LEU M 316 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 253 through 254 Processing sheet with id=AA5, first strand: chain 'M' and resid 287 through 294 removed outlier: 3.524A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.531A pdb=" N THR S 14 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN S 9 " --> pdb=" O THR S 14 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 118 through 119 794 hydrogen bonds defined for protein. 2325 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: 2.21 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4064 1.34 - 1.46: 1943 1.46 - 1.57: 6713 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 12808 Sorted by residual: bond pdb=" CG1 ILE A 17 " pdb=" CD1 ILE A 17 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.57e+00 bond pdb=" CB CYS A 171 " pdb=" SG CYS A 171 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CB VAL A 483 " pdb=" CG1 VAL A 483 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CB VAL B 298 " pdb=" CG1 VAL B 298 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CB MET S 117 " pdb=" CG MET S 117 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.81e-01 ... (remaining 12803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 17038 1.48 - 2.96: 388 2.96 - 4.44: 57 4.44 - 5.92: 17 5.92 - 7.40: 9 Bond angle restraints: 17509 Sorted by residual: angle pdb=" N ASN B 179 " pdb=" CA ASN B 179 " pdb=" C ASN B 179 " ideal model delta sigma weight residual 113.18 105.78 7.40 1.33e+00 5.65e-01 3.10e+01 angle pdb=" CA GLU A 601 " pdb=" C GLU A 601 " pdb=" O GLU A 601 " ideal model delta sigma weight residual 120.51 113.88 6.63 1.43e+00 4.89e-01 2.15e+01 angle pdb=" CA GLU A 601 " pdb=" C GLU A 601 " pdb=" N MET A 602 " ideal model delta sigma weight residual 116.84 123.58 -6.74 1.71e+00 3.42e-01 1.56e+01 angle pdb=" N HIS A 493 " pdb=" CA HIS A 493 " pdb=" C HIS A 493 " ideal model delta sigma weight residual 108.34 113.09 -4.75 1.31e+00 5.83e-01 1.32e+01 angle pdb=" C GLU A 600 " pdb=" N GLU A 601 " pdb=" CA GLU A 601 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 ... (remaining 17504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7048 18.00 - 35.99: 513 35.99 - 53.99: 83 53.99 - 71.99: 15 71.99 - 89.98: 10 Dihedral angle restraints: 7669 sinusoidal: 2595 harmonic: 5074 Sorted by residual: dihedral pdb=" CA HIS A 493 " pdb=" C HIS A 493 " pdb=" N GLU A 494 " pdb=" CA GLU A 494 " ideal model delta harmonic sigma weight residual 180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA TRP A 462 " pdb=" C TRP A 462 " pdb=" N TYR A 463 " pdb=" CA TYR A 463 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU B 248 " pdb=" C LEU B 248 " pdb=" N SER B 249 " pdb=" CA SER B 249 " ideal model delta harmonic sigma weight residual -180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1400 0.034 - 0.069: 577 0.069 - 0.103: 140 0.103 - 0.137: 45 0.137 - 0.172: 8 Chirality restraints: 2170 Sorted by residual: chirality pdb=" CG LEU B 68 " pdb=" CB LEU B 68 " pdb=" CD1 LEU B 68 " pdb=" CD2 LEU B 68 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA ILE S 58 " pdb=" N ILE S 58 " pdb=" C ILE S 58 " pdb=" CB ILE S 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA THR B 245 " pdb=" N THR B 245 " pdb=" C THR B 245 " pdb=" CB THR B 245 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2167 not shown) Planarity restraints: 2207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 179 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO A 180 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 64 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C GLU B 64 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU B 64 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU B 65 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 97 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO B 98 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " 0.029 5.00e-02 4.00e+02 ... (remaining 2204 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 75 2.63 - 3.20: 11575 3.20 - 3.77: 18770 3.77 - 4.33: 24370 4.33 - 4.90: 41725 Nonbonded interactions: 96515 Sorted by model distance: nonbonded pdb=" O ILE A 511 " pdb=" OG SER A 517 " model vdw 2.069 3.040 nonbonded pdb=" OE1 GLU B 297 " pdb=" OH TYR M 83 " model vdw 2.095 3.040 nonbonded pdb=" OD2 ASP A 444 " pdb=" OH TYR A 478 " model vdw 2.199 3.040 nonbonded pdb=" O VAL A 300 " pdb=" OG SER A 303 " model vdw 2.233 3.040 nonbonded pdb=" O LEU A 244 " pdb=" OG1 THR A 248 " model vdw 2.233 3.040 ... (remaining 96510 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.050 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.090 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12808 Z= 0.166 Angle : 0.581 7.401 17509 Z= 0.321 Chirality : 0.041 0.172 2170 Planarity : 0.004 0.055 2207 Dihedral : 13.413 89.982 4361 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.20), residues: 1696 helix: 1.59 (0.17), residues: 981 sheet: 1.03 (0.37), residues: 183 loop : -1.26 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.028 0.002 TYR B 70 PHE 0.019 0.002 PHE S 49 TRP 0.013 0.001 TRP A 462 HIS 0.004 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00391 (12808) covalent geometry : angle 0.58058 (17509) hydrogen bonds : bond 0.14062 ( 794) hydrogen bonds : angle 5.14739 ( 2325) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.449 Fit side-chains REVERT: S 29 GLN cc_start: 0.6340 (mm-40) cc_final: 0.5580 (mm-40) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0964 time to fit residues: 16.6663 Evaluate side-chains 74 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN B 305 ASN M 49 ASN M 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.065686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.048470 restraints weight = 55326.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.050265 restraints weight = 29937.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.051479 restraints weight = 20458.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.052230 restraints weight = 15885.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.052865 restraints weight = 13485.994| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12808 Z= 0.119 Angle : 0.517 10.690 17509 Z= 0.270 Chirality : 0.040 0.150 2170 Planarity : 0.004 0.042 2207 Dihedral : 3.892 23.885 1823 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.65 % Allowed : 4.96 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 1696 helix: 1.76 (0.17), residues: 996 sheet: 1.23 (0.38), residues: 181 loop : -1.12 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 278 TYR 0.026 0.001 TYR A 247 PHE 0.012 0.001 PHE M 105 TRP 0.014 0.001 TRP A 462 HIS 0.008 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00259 (12808) covalent geometry : angle 0.51689 (17509) hydrogen bonds : bond 0.03889 ( 794) hydrogen bonds : angle 4.24458 ( 2325) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.433 Fit side-chains REVERT: S 29 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8572 (mm-40) REVERT: S 33 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8389 (mm-30) outliers start: 8 outliers final: 1 residues processed: 95 average time/residue: 0.0770 time to fit residues: 12.1532 Evaluate side-chains 80 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 14 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 122 optimal weight: 0.0570 chunk 30 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN M 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.065927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.048675 restraints weight = 55771.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.050482 restraints weight = 30143.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.051708 restraints weight = 20525.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.052563 restraints weight = 15905.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053104 restraints weight = 13325.049| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 12808 Z= 0.105 Angle : 0.483 11.471 17509 Z= 0.249 Chirality : 0.039 0.139 2170 Planarity : 0.003 0.033 2207 Dihedral : 3.740 23.081 1823 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.65 % Allowed : 8.06 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.21), residues: 1696 helix: 1.96 (0.17), residues: 996 sheet: 1.19 (0.38), residues: 181 loop : -0.99 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 341 TYR 0.015 0.001 TYR B 70 PHE 0.015 0.001 PHE M 105 TRP 0.014 0.001 TRP A 462 HIS 0.005 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00233 (12808) covalent geometry : angle 0.48259 (17509) hydrogen bonds : bond 0.03207 ( 794) hydrogen bonds : angle 3.97547 ( 2325) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.457 Fit side-chains REVERT: M 77 MET cc_start: 0.8854 (tpp) cc_final: 0.8652 (tpp) REVERT: M 120 TYR cc_start: 0.8029 (m-80) cc_final: 0.7710 (m-80) REVERT: S 33 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8545 (mm-30) outliers start: 8 outliers final: 4 residues processed: 86 average time/residue: 0.0799 time to fit residues: 11.4180 Evaluate side-chains 79 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 95 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 110 optimal weight: 0.0060 chunk 59 optimal weight: 0.0770 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 154 optimal weight: 0.0970 overall best weight: 0.9954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 HIS M 412 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.065477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.048307 restraints weight = 55986.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.050103 restraints weight = 30254.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.051299 restraints weight = 20645.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.052133 restraints weight = 16041.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.052664 restraints weight = 13463.871| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12808 Z= 0.113 Angle : 0.471 11.767 17509 Z= 0.244 Chirality : 0.038 0.143 2170 Planarity : 0.003 0.033 2207 Dihedral : 3.656 22.899 1823 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.06 % Allowed : 8.71 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.21), residues: 1696 helix: 2.14 (0.17), residues: 993 sheet: 1.02 (0.38), residues: 187 loop : -0.94 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 53 TYR 0.018 0.001 TYR A 247 PHE 0.013 0.001 PHE M 105 TRP 0.012 0.001 TRP A 462 HIS 0.004 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00256 (12808) covalent geometry : angle 0.47051 (17509) hydrogen bonds : bond 0.03039 ( 794) hydrogen bonds : angle 3.87052 ( 2325) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.465 Fit side-chains REVERT: A 391 ASP cc_start: 0.8926 (m-30) cc_final: 0.8709 (m-30) REVERT: S 33 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8552 (mm-30) REVERT: S 53 ARG cc_start: 0.8962 (mtp85) cc_final: 0.8565 (mmt90) outliers start: 13 outliers final: 7 residues processed: 86 average time/residue: 0.0725 time to fit residues: 10.4458 Evaluate side-chains 82 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 168 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.064107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.046975 restraints weight = 55870.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.048704 restraints weight = 30219.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.049872 restraints weight = 20634.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.050694 restraints weight = 16077.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.051206 restraints weight = 13533.606| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12808 Z= 0.145 Angle : 0.498 13.484 17509 Z= 0.255 Chirality : 0.039 0.148 2170 Planarity : 0.003 0.037 2207 Dihedral : 3.681 23.238 1823 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.14 % Allowed : 9.68 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.21), residues: 1696 helix: 2.21 (0.17), residues: 997 sheet: 1.02 (0.38), residues: 187 loop : -0.94 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.012 0.001 TYR M 8 PHE 0.010 0.001 PHE M 105 TRP 0.010 0.001 TRP A 462 HIS 0.004 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00335 (12808) covalent geometry : angle 0.49838 (17509) hydrogen bonds : bond 0.03241 ( 794) hydrogen bonds : angle 3.89100 ( 2325) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.425 Fit side-chains REVERT: M 218 ASP cc_start: 0.8443 (t0) cc_final: 0.8219 (t0) REVERT: M 308 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8422 (mtmt) REVERT: S 33 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8591 (mm-30) outliers start: 14 outliers final: 7 residues processed: 90 average time/residue: 0.0833 time to fit residues: 12.1225 Evaluate side-chains 82 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 131 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 59 optimal weight: 0.0070 chunk 40 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 ASN B 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.064189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.047111 restraints weight = 55634.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.048850 restraints weight = 30064.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.050031 restraints weight = 20517.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.050854 restraints weight = 15944.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.051419 restraints weight = 13382.952| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12808 Z= 0.120 Angle : 0.476 12.761 17509 Z= 0.244 Chirality : 0.039 0.143 2170 Planarity : 0.003 0.034 2207 Dihedral : 3.648 22.791 1823 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.98 % Allowed : 10.33 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.21), residues: 1696 helix: 2.32 (0.17), residues: 997 sheet: 1.06 (0.38), residues: 187 loop : -0.92 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 247 TYR 0.010 0.001 TYR M 8 PHE 0.009 0.001 PHE M 93 TRP 0.013 0.001 TRP A 462 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00277 (12808) covalent geometry : angle 0.47612 (17509) hydrogen bonds : bond 0.03021 ( 794) hydrogen bonds : angle 3.81754 ( 2325) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.316 Fit side-chains REVERT: M 218 ASP cc_start: 0.8554 (t0) cc_final: 0.8292 (t0) REVERT: S 33 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8604 (mm-30) REVERT: S 53 ARG cc_start: 0.8974 (mtp85) cc_final: 0.8602 (mmt90) outliers start: 12 outliers final: 10 residues processed: 86 average time/residue: 0.0850 time to fit residues: 11.9115 Evaluate side-chains 86 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 0.0870 chunk 130 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 75 optimal weight: 9.9990 chunk 160 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 157 optimal weight: 0.0670 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.065518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.048515 restraints weight = 55310.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.050284 restraints weight = 29731.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.051487 restraints weight = 20222.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.052331 restraints weight = 15681.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.052824 restraints weight = 13132.338| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12808 Z= 0.085 Angle : 0.453 13.256 17509 Z= 0.232 Chirality : 0.038 0.149 2170 Planarity : 0.003 0.033 2207 Dihedral : 3.524 22.283 1823 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.49 % Allowed : 10.90 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.21), residues: 1696 helix: 2.40 (0.17), residues: 997 sheet: 1.16 (0.38), residues: 185 loop : -0.86 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 247 TYR 0.007 0.001 TYR M 8 PHE 0.009 0.001 PHE M 32 TRP 0.017 0.001 TRP A 462 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00184 (12808) covalent geometry : angle 0.45289 (17509) hydrogen bonds : bond 0.02631 ( 794) hydrogen bonds : angle 3.67360 ( 2325) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.462 Fit side-chains REVERT: B 253 SER cc_start: 0.7969 (p) cc_final: 0.7739 (p) REVERT: M 218 ASP cc_start: 0.8505 (t0) cc_final: 0.8213 (t0) REVERT: S 33 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8601 (mm-30) REVERT: S 53 ARG cc_start: 0.8974 (mtp85) cc_final: 0.8640 (mmt90) outliers start: 6 outliers final: 5 residues processed: 88 average time/residue: 0.0814 time to fit residues: 11.8098 Evaluate side-chains 83 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 112 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 76 optimal weight: 0.0770 chunk 29 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.064768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.047743 restraints weight = 55447.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.049496 restraints weight = 29991.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.050678 restraints weight = 20430.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.051517 restraints weight = 15860.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.051998 restraints weight = 13310.791| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12808 Z= 0.111 Angle : 0.465 12.953 17509 Z= 0.239 Chirality : 0.038 0.151 2170 Planarity : 0.003 0.034 2207 Dihedral : 3.509 22.706 1823 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.81 % Allowed : 11.07 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.21), residues: 1696 helix: 2.48 (0.17), residues: 996 sheet: 1.20 (0.38), residues: 181 loop : -0.86 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.010 0.001 TYR M 8 PHE 0.009 0.001 PHE M 56 TRP 0.012 0.001 TRP A 462 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00257 (12808) covalent geometry : angle 0.46532 (17509) hydrogen bonds : bond 0.02809 ( 794) hydrogen bonds : angle 3.69734 ( 2325) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.488 Fit side-chains REVERT: A 398 ASP cc_start: 0.8413 (t0) cc_final: 0.8128 (t70) REVERT: M 218 ASP cc_start: 0.8551 (t0) cc_final: 0.8242 (t0) REVERT: S 33 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8679 (mm-30) REVERT: S 53 ARG cc_start: 0.9000 (mtp85) cc_final: 0.8620 (mmt90) outliers start: 10 outliers final: 8 residues processed: 85 average time/residue: 0.0849 time to fit residues: 11.9051 Evaluate side-chains 85 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 143 optimal weight: 0.0370 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 156 optimal weight: 0.4980 chunk 153 optimal weight: 0.0030 chunk 152 optimal weight: 1.9990 overall best weight: 0.3668 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.065375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.048430 restraints weight = 55519.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.050228 restraints weight = 29803.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.051450 restraints weight = 20176.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.052300 restraints weight = 15567.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.052889 restraints weight = 13024.907| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12808 Z= 0.085 Angle : 0.456 13.670 17509 Z= 0.234 Chirality : 0.038 0.145 2170 Planarity : 0.003 0.036 2207 Dihedral : 3.440 22.503 1823 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.57 % Allowed : 11.55 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.21), residues: 1696 helix: 2.50 (0.17), residues: 995 sheet: 1.40 (0.40), residues: 168 loop : -0.86 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.007 0.001 TYR M 8 PHE 0.009 0.001 PHE M 93 TRP 0.017 0.001 TRP A 462 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00185 (12808) covalent geometry : angle 0.45566 (17509) hydrogen bonds : bond 0.02565 ( 794) hydrogen bonds : angle 3.60550 ( 2325) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.480 Fit side-chains REVERT: A 276 VAL cc_start: 0.8901 (t) cc_final: 0.8685 (p) REVERT: M 218 ASP cc_start: 0.8493 (t0) cc_final: 0.8172 (t0) REVERT: S 29 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8302 (mm-40) REVERT: S 33 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8617 (mm-30) REVERT: S 53 ARG cc_start: 0.8976 (mtp85) cc_final: 0.8546 (mmt180) outliers start: 7 outliers final: 4 residues processed: 85 average time/residue: 0.0776 time to fit residues: 10.8480 Evaluate side-chains 83 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 130 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 116 optimal weight: 0.1980 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.0050 chunk 127 optimal weight: 0.0050 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.065677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.048876 restraints weight = 55436.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.050677 restraints weight = 29622.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.051897 restraints weight = 19999.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.052736 restraints weight = 15386.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.053336 restraints weight = 12890.509| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12808 Z= 0.086 Angle : 0.465 14.114 17509 Z= 0.236 Chirality : 0.038 0.140 2170 Planarity : 0.003 0.037 2207 Dihedral : 3.372 22.501 1823 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.33 % Allowed : 11.80 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.21), residues: 1696 helix: 2.52 (0.17), residues: 997 sheet: 1.28 (0.39), residues: 179 loop : -0.78 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.008 0.001 TYR M 8 PHE 0.009 0.001 PHE A 16 TRP 0.015 0.001 TRP A 462 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00191 (12808) covalent geometry : angle 0.46520 (17509) hydrogen bonds : bond 0.02563 ( 794) hydrogen bonds : angle 3.60173 ( 2325) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.485 Fit side-chains REVERT: A 161 MET cc_start: 0.8421 (tmm) cc_final: 0.7976 (tpt) REVERT: A 398 ASP cc_start: 0.8447 (t0) cc_final: 0.8142 (t70) REVERT: M 218 ASP cc_start: 0.8428 (t0) cc_final: 0.8073 (t0) REVERT: S 29 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8295 (mm-40) REVERT: S 33 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8665 (mm-30) REVERT: S 53 ARG cc_start: 0.8974 (mtp85) cc_final: 0.8547 (mmt180) REVERT: S 82 GLU cc_start: 0.8804 (mm-30) cc_final: 0.7834 (mt-10) outliers start: 4 outliers final: 4 residues processed: 83 average time/residue: 0.0829 time to fit residues: 11.3411 Evaluate side-chains 80 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.0060 chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.065439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.048508 restraints weight = 55626.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.050306 restraints weight = 29917.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.051522 restraints weight = 20277.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.052372 restraints weight = 15670.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.052935 restraints weight = 13113.274| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12808 Z= 0.090 Angle : 0.464 14.099 17509 Z= 0.235 Chirality : 0.038 0.139 2170 Planarity : 0.003 0.037 2207 Dihedral : 3.368 22.586 1823 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.41 % Allowed : 12.04 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.21), residues: 1696 helix: 2.55 (0.17), residues: 998 sheet: 1.41 (0.40), residues: 168 loop : -0.75 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 277 TYR 0.009 0.001 TYR M 277 PHE 0.009 0.001 PHE M 93 TRP 0.014 0.001 TRP A 462 HIS 0.003 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00203 (12808) covalent geometry : angle 0.46380 (17509) hydrogen bonds : bond 0.02556 ( 794) hydrogen bonds : angle 3.59202 ( 2325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1844.08 seconds wall clock time: 32 minutes 38.49 seconds (1958.49 seconds total)