Starting phenix.real_space_refine on Fri Jul 3 11:06:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t1o_40973/07_2026/8t1o_40973.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t1o_40973/07_2026/8t1o_40973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t1o_40973/07_2026/8t1o_40973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t1o_40973/07_2026/8t1o_40973.map" model { file = "/net/cci-nas-00/data/ceres_data/8t1o_40973/07_2026/8t1o_40973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t1o_40973/07_2026/8t1o_40973.cif" } resolution = 3.3 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= -0.001 sd= 1.211 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 72 5.16 5 C 8811 2.51 5 N 2338 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13800 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4721 Classifications: {'peptide': 599} Link IDs: {'PTRANS': 22, 'TRANS': 576} Chain breaks: 1 Chain: "B" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4518 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 26, 'TRANS': 543} Chain: "M" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3297 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "S" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1190 Classifications: {'peptide': 141} Link IDs: {'TRANS': 140} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-1': 1, 'PIO:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.90, per 1000 atoms: 0.21 Number of scatterers: 13800 At special positions: 0 Unit cell: (107.36, 116.16, 125.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 3 15.00 O 2576 8.00 N 2338 7.00 C 8811 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: 0.97 Conformation dependent library (CDL) restraints added in 534.3 milliseconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 10 sheets defined 63.7% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 removed outlier: 3.660A pdb=" N CYS A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 45 Processing helix chain 'A' and resid 51 through 69 removed outlier: 3.618A pdb=" N GLY A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.702A pdb=" N SER A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.501A pdb=" N LYS A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 124 through 138 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 187 through 194 removed outlier: 4.649A pdb=" N ARG A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 200 through 216 removed outlier: 4.127A pdb=" N GLN A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 238 removed outlier: 4.434A pdb=" N SER A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.775A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.537A pdb=" N VAL A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.702A pdb=" N THR A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 401 through 414 Processing helix chain 'A' and resid 420 through 435 Processing helix chain 'A' and resid 438 through 453 removed outlier: 4.018A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 4.269A pdb=" N VAL A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TRP A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.519A pdb=" N GLN A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 removed outlier: 3.645A pdb=" N GLU A 506 " --> pdb=" O TYR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 531 removed outlier: 4.160A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 Processing helix chain 'A' and resid 555 through 565 Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.532A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.539A pdb=" N GLN A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 599 removed outlier: 3.667A pdb=" N LEU A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 23 Processing helix chain 'B' and resid 26 through 44 removed outlier: 3.540A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (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 removed outlier: 3.915A pdb=" N VAL B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 86 through 96 removed outlier: 4.497A pdb=" N SER B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 115 through 131 removed outlier: 3.753A pdb=" N THR B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 3.878A pdb=" N LYS B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.685A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 168 removed outlier: 3.513A pdb=" N GLN B 159 " --> pdb=" O MET B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 removed outlier: 3.559A pdb=" N VAL B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 214 removed outlier: 4.680A pdb=" N ASN B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 229 removed outlier: 3.530A pdb=" N ILE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR B 229 " --> pdb=" O CYS B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.650A pdb=" N ALA B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 removed outlier: 3.642A pdb=" N SER B 249 " --> pdb=" O PRO B 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 252 through 266 Processing helix chain 'B' and resid 274 through 292 removed outlier: 4.059A pdb=" N ASN B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Proline residue: B 286 - end of helix removed outlier: 4.023A pdb=" N LEU B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.679A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.652A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 350 through 362 Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.584A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.910A 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: 3.932A pdb=" N ASN B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.908A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 473 Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.785A pdb=" N VAL B 503 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 533 removed outlier: 3.677A pdb=" N ASP B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.654A pdb=" N ALA B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 566 Processing helix chain 'B' and resid 569 through 575 removed outlier: 3.966A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 36 removed outlier: 4.331A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP M 30 " --> pdb=" O ARG M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 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: 3.763A pdb=" N PHE M 132 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 157 removed outlier: 3.782A pdb=" N GLN M 148 " --> pdb=" O THR M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 261 Processing helix chain 'S' and resid 24 through 42 removed outlier: 3.703A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 96 Processing helix chain 'S' and resid 99 through 106 removed outlier: 3.660A pdb=" N LEU S 103 " --> pdb=" O CYS S 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 127 through 141 removed outlier: 3.518A pdb=" N VAL S 131 " --> pdb=" O SER S 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 19 Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117 Processing sheet with id=AA4, first strand: chain 'M' and resid 245 through 248 removed outlier: 4.002A pdb=" N ASP M 245 " --> pdb=" O ARG M 278 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY M 270 " --> pdb=" O SER M 204 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER M 204 " --> pdb=" O GLY M 270 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL M 200 " --> pdb=" O LEU M 274 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG M 276 " --> pdb=" O GLY M 198 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY M 198 " --> pdb=" O ARG M 276 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG M 278 " --> pdb=" O VAL M 196 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL M 196 " --> pdb=" O ARG M 278 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER M 193 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL M 181 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU M 183 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR M 431 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N MET M 185 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR M 433 " --> pdb=" O MET M 185 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ARG M 427 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL M 392 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER M 387 " --> pdb=" O ARG M 323 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE M 320 " --> pdb=" O ILE M 355 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE M 355 " --> pdb=" O ILE M 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 245 through 248 removed outlier: 4.002A pdb=" N ASP M 245 " --> pdb=" O ARG M 278 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY M 270 " --> pdb=" O SER M 204 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER M 204 " --> pdb=" O GLY M 270 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL M 200 " --> pdb=" O LEU M 274 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG M 276 " --> pdb=" O GLY M 198 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY M 198 " --> pdb=" O ARG M 276 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG M 278 " --> pdb=" O VAL M 196 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL M 196 " --> pdb=" O ARG M 278 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER M 193 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL M 181 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU M 183 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR M 431 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N MET M 185 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR M 433 " --> pdb=" O MET M 185 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 263 through 265 removed outlier: 4.236A pdb=" N ILE M 263 " --> pdb=" O PHE M 214 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR M 403 " --> pdb=" O GLY M 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 287 through 296 removed outlier: 3.585A pdb=" N ARG M 288 " --> pdb=" O LYS M 308 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS M 308 " --> pdb=" O ARG M 288 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE M 290 " --> pdb=" O VAL M 306 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL M 306 " --> pdb=" O ILE M 290 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS M 300 " --> pdb=" O VAL M 296 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL M 303 " --> pdb=" O ALA M 368 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA M 368 " --> pdb=" O VAL M 303 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL M 305 " --> pdb=" O ILE M 366 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE M 366 " --> pdb=" O VAL M 305 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER M 367 " --> pdb=" O VAL M 335 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL M 335 " --> pdb=" O SER M 367 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU M 369 " --> pdb=" O VAL M 333 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL M 333 " --> pdb=" O GLU M 369 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU M 371 " --> pdb=" O SER M 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 287 through 296 removed outlier: 3.585A pdb=" N ARG M 288 " --> pdb=" O LYS M 308 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS M 308 " --> pdb=" O ARG M 288 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE M 290 " --> pdb=" O VAL M 306 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL M 306 " --> pdb=" O ILE M 290 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS M 300 " --> pdb=" O VAL M 296 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE M 307 " --> pdb=" O SER M 364 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER M 364 " --> pdb=" O ILE M 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.234A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TRP S 19 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ARG S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE S 55 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE S 52 " --> pdb=" O PHE S 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 118 through 119 834 hydrogen bonds defined for protein. 2442 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: 2.15 Time building geometry restraints manager: 1.26 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: 4511 1.34 - 1.46: 2734 1.46 - 1.58: 6683 1.58 - 1.70: 4 1.70 - 1.81: 111 Bond restraints: 14043 Sorted by residual: bond pdb=" O4 PIO A 701 " pdb=" P4 PIO A 701 " ideal model delta sigma weight residual 1.710 1.644 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O5 PIO A 701 " pdb=" P5 PIO A 701 " ideal model delta sigma weight residual 1.699 1.649 0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" C THR B 245 " pdb=" N PRO B 246 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.19e-02 7.06e+03 2.40e+00 bond pdb=" CB VAL A 483 " pdb=" CG1 VAL A 483 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.35e+00 bond pdb=" CG GLU S 33 " pdb=" CD GLU S 33 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.35e+00 ... (remaining 14038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 18787 2.36 - 4.72: 193 4.72 - 7.08: 33 7.08 - 9.45: 3 9.45 - 11.81: 2 Bond angle restraints: 19018 Sorted by residual: angle pdb=" O1 PIO A 701 " pdb=" P1 PIO A 701 " pdb=" O13 PIO A 701 " ideal model delta sigma weight residual 97.64 109.45 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O11 PIO A 701 " pdb=" P1 PIO A 701 " pdb=" O12 PIO A 701 " ideal model delta sigma weight residual 121.09 109.30 11.79 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C GLU M 125 " pdb=" N THR M 126 " pdb=" CA THR M 126 " ideal model delta sigma weight residual 121.54 128.70 -7.16 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C GLN A 266 " pdb=" N CYS A 267 " pdb=" CA CYS A 267 " ideal model delta sigma weight residual 122.31 115.52 6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N GLU S 33 " pdb=" CA GLU S 33 " pdb=" CB GLU S 33 " ideal model delta sigma weight residual 110.28 115.29 -5.01 1.55e+00 4.16e-01 1.05e+01 ... (remaining 19013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7749 17.94 - 35.87: 709 35.87 - 53.81: 110 53.81 - 71.74: 28 71.74 - 89.68: 24 Dihedral angle restraints: 8620 sinusoidal: 3501 harmonic: 5119 Sorted by residual: dihedral pdb=" CA HIS B 250 " pdb=" C HIS B 250 " pdb=" N ALA B 251 " pdb=" CA ALA B 251 " ideal model delta harmonic sigma weight residual 180.00 155.72 24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA LEU B 196 " pdb=" C LEU B 196 " pdb=" N LEU B 197 " pdb=" CA LEU B 197 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO B 81 " pdb=" C PRO B 81 " pdb=" N ASP B 82 " pdb=" CA ASP B 82 " ideal model delta harmonic sigma weight residual 180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 8617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1452 0.034 - 0.068: 568 0.068 - 0.103: 134 0.103 - 0.137: 58 0.137 - 0.171: 3 Chirality restraints: 2215 Sorted by residual: chirality pdb=" CA GLU S 33 " pdb=" N GLU S 33 " pdb=" C GLU S 33 " pdb=" CB GLU S 33 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-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 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA PRO B 201 " pdb=" N PRO B 201 " pdb=" C PRO B 201 " pdb=" CB PRO B 201 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 2212 not shown) Planarity restraints: 2418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN S 29 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C GLN S 29 " 0.031 2.00e-02 2.50e+03 pdb=" O GLN S 29 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS S 30 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 124 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO A 125 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 270 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO B 271 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 271 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 271 " -0.023 5.00e-02 4.00e+02 ... (remaining 2415 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 253 2.70 - 3.25: 14047 3.25 - 3.80: 21398 3.80 - 4.35: 27670 4.35 - 4.90: 46716 Nonbonded interactions: 110084 Sorted by model distance: nonbonded pdb=" O LEU B 398 " pdb=" OG1 THR B 401 " model vdw 2.146 3.040 nonbonded pdb=" O LEU B 270 " pdb=" OG SER B 274 " model vdw 2.160 3.040 nonbonded pdb=" ND2 ASN B 200 " pdb=" OE1 GLN B 202 " model vdw 2.162 3.120 nonbonded pdb=" OH TYR A 95 " pdb=" OD2 ASP A 119 " model vdw 2.173 3.040 nonbonded pdb=" O ILE A 511 " pdb=" OG SER A 517 " model vdw 2.190 3.040 ... (remaining 110079 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 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 : 0.003 0.066 14043 Z= 0.151 Angle : 0.618 11.808 19018 Z= 0.323 Chirality : 0.041 0.171 2215 Planarity : 0.004 0.045 2418 Dihedral : 14.788 89.676 5284 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.93 (0.20), residues: 1712 helix: 1.38 (0.16), residues: 992 sheet: 0.66 (0.38), residues: 165 loop : -0.73 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 579 TYR 0.029 0.001 TYR B 70 PHE 0.016 0.001 PHE A 147 TRP 0.020 0.001 TRP A 462 HIS 0.006 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (14043) covalent geometry : angle 0.61791 / 0.32 (19018) hydrogen bonds : bond 0.13962 / 8.97 ( 801) hydrogen bonds : angle 6.13853 / 4.44 ( 2442) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 103 ASN cc_start: 0.7273 (t0) cc_final: 0.6994 (t0) REVERT: B 163 ASP cc_start: 0.7423 (p0) cc_final: 0.6855 (t0) REVERT: M 114 GLU cc_start: 0.7137 (tp30) cc_final: 0.6903 (tp30) REVERT: M 158 GLN cc_start: 0.7118 (tm-30) cc_final: 0.6836 (tp40) REVERT: M 410 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7911 (tptm) REVERT: S 33 GLU cc_start: 0.7345 (mp0) cc_final: 0.7066 (mp0) REVERT: S 137 MET cc_start: 0.7017 (tmm) cc_final: 0.6341 (tmm) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1170 time to fit residues: 37.2547 Evaluate side-chains 176 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 24 ASN B 99 ASN B 195 ASN M 27 ASN M 148 GLN M 318 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.191073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.147738 restraints weight = 16397.709| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.24 r_work: 0.3559 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14043 Z= 0.131 Angle : 0.552 8.337 19018 Z= 0.291 Chirality : 0.041 0.154 2215 Planarity : 0.004 0.051 2418 Dihedral : 4.534 49.778 1877 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 0.52 % Allowed : 6.71 % Favored : 92.76 % 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: 1.18 (0.20), residues: 1712 helix: 1.57 (0.16), residues: 1003 sheet: 0.71 (0.38), residues: 171 loop : -0.63 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 40 TYR 0.020 0.001 TYR B 70 PHE 0.014 0.001 PHE M 81 TRP 0.019 0.001 TRP A 462 HIS 0.005 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (14043) covalent geometry : angle 0.55203 / 0.29 (19018) hydrogen bonds : bond 0.04036 / 2.64 ( 801) hydrogen bonds : angle 4.56362 / 3.26 ( 2442) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 189 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 371 GLU cc_start: 0.7091 (tp30) cc_final: 0.6711 (tp30) REVERT: B 163 ASP cc_start: 0.7721 (p0) cc_final: 0.7248 (t0) REVERT: B 315 GLU cc_start: 0.8059 (pm20) cc_final: 0.7782 (pm20) REVERT: M 99 GLU cc_start: 0.8306 (pm20) cc_final: 0.8092 (pm20) REVERT: M 173 LEU cc_start: 0.7891 (pt) cc_final: 0.7687 (pt) REVERT: M 185 MET cc_start: 0.6483 (ppp) cc_final: 0.5166 (tpp) REVERT: M 203 LYS cc_start: 0.8034 (mtmm) cc_final: 0.7475 (mtmm) REVERT: M 205 TYR cc_start: 0.7486 (m-80) cc_final: 0.7239 (m-80) REVERT: M 361 MET cc_start: 0.6628 (mtm) cc_final: 0.6324 (mtm) REVERT: M 410 LYS cc_start: 0.8574 (mmtt) cc_final: 0.7953 (tptm) REVERT: S 30 LYS cc_start: 0.7711 (mmtt) cc_final: 0.7505 (tptt) REVERT: S 33 GLU cc_start: 0.8091 (mp0) cc_final: 0.7608 (mp0) outliers start: 8 outliers final: 5 residues processed: 193 average time/residue: 0.1142 time to fit residues: 32.3715 Evaluate side-chains 187 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain M residue 152 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 24 ASN B 173 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.192596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149028 restraints weight = 16755.561| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.45 r_work: 0.3483 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14043 Z= 0.141 Angle : 0.535 7.693 19018 Z= 0.282 Chirality : 0.040 0.142 2215 Planarity : 0.004 0.038 2418 Dihedral : 4.422 45.212 1877 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 0.72 % Allowed : 9.00 % Favored : 90.29 % 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: 1.21 (0.20), residues: 1712 helix: 1.62 (0.16), residues: 1004 sheet: 0.67 (0.38), residues: 171 loop : -0.67 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 344 TYR 0.017 0.001 TYR B 70 PHE 0.011 0.001 PHE M 81 TRP 0.018 0.001 TRP A 462 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (14043) covalent geometry : angle 0.53510 / 0.28 (19018) hydrogen bonds : bond 0.03911 / 2.56 ( 801) hydrogen bonds : angle 4.28551 / 3.07 ( 2442) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 371 GLU cc_start: 0.7094 (tp30) cc_final: 0.6794 (tp30) REVERT: B 163 ASP cc_start: 0.7687 (p0) cc_final: 0.7207 (t0) REVERT: B 315 GLU cc_start: 0.8019 (pm20) cc_final: 0.7660 (pm20) REVERT: B 320 GLU cc_start: 0.7508 (tp30) cc_final: 0.7201 (mm-30) REVERT: M 108 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7735 (mp) REVERT: M 110 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7235 (mm-30) REVERT: M 114 GLU cc_start: 0.7301 (tp30) cc_final: 0.7077 (tp30) REVERT: M 185 MET cc_start: 0.6480 (ppp) cc_final: 0.5207 (tpp) REVERT: M 203 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7523 (mtmm) REVERT: M 308 LYS cc_start: 0.7105 (tppt) cc_final: 0.6766 (tptm) REVERT: M 410 LYS cc_start: 0.8560 (mmtt) cc_final: 0.7914 (tptm) outliers start: 11 outliers final: 5 residues processed: 190 average time/residue: 0.1230 time to fit residues: 34.2477 Evaluate side-chains 178 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 152 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 165 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 89 optimal weight: 0.0970 chunk 123 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 203 ASN M 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.192964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.149838 restraints weight = 16568.073| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.42 r_work: 0.3494 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14043 Z= 0.125 Angle : 0.514 6.962 19018 Z= 0.269 Chirality : 0.040 0.142 2215 Planarity : 0.004 0.038 2418 Dihedral : 4.298 40.456 1877 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 1.17 % Allowed : 10.69 % Favored : 88.14 % 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: 1.29 (0.20), residues: 1712 helix: 1.71 (0.16), residues: 1004 sheet: 0.67 (0.38), residues: 171 loop : -0.68 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 427 TYR 0.017 0.001 TYR B 70 PHE 0.010 0.001 PHE M 81 TRP 0.018 0.001 TRP A 462 HIS 0.004 0.001 HIS M 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (14043) covalent geometry : angle 0.51376 / 0.27 (19018) hydrogen bonds : bond 0.03643 / 2.38 ( 801) hydrogen bonds : angle 4.08863 / 2.92 ( 2442) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 371 GLU cc_start: 0.7127 (tp30) cc_final: 0.6768 (tp30) REVERT: B 83 MET cc_start: 0.8036 (pmm) cc_final: 0.7629 (ptm) REVERT: B 163 ASP cc_start: 0.7775 (p0) cc_final: 0.7260 (t0) REVERT: B 569 SER cc_start: 0.8251 (t) cc_final: 0.7989 (m) REVERT: M 108 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7854 (mp) REVERT: M 158 GLN cc_start: 0.7298 (tm-30) cc_final: 0.6296 (mt0) REVERT: M 185 MET cc_start: 0.6465 (ppp) cc_final: 0.5200 (tpp) REVERT: M 203 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7487 (mtmm) REVERT: M 410 LYS cc_start: 0.8552 (mmtt) cc_final: 0.7920 (tptm) outliers start: 18 outliers final: 9 residues processed: 199 average time/residue: 0.1207 time to fit residues: 35.2675 Evaluate side-chains 187 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 148 GLN Chi-restraints excluded: chain M residue 152 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 132 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 163 optimal weight: 0.0980 chunk 130 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.193347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150020 restraints weight = 16704.046| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.48 r_work: 0.3495 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14043 Z= 0.116 Angle : 0.514 6.693 19018 Z= 0.269 Chirality : 0.039 0.191 2215 Planarity : 0.003 0.038 2418 Dihedral : 4.237 37.122 1877 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 0.91 % Allowed : 11.34 % Favored : 87.74 % 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: 1.36 (0.20), residues: 1712 helix: 1.80 (0.16), residues: 1004 sheet: 0.68 (0.38), residues: 171 loop : -0.73 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 427 TYR 0.019 0.001 TYR B 70 PHE 0.012 0.001 PHE M 394 TRP 0.018 0.001 TRP A 462 HIS 0.006 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (14043) covalent geometry : angle 0.51376 / 0.27 (19018) hydrogen bonds : bond 0.03506 / 2.29 ( 801) hydrogen bonds : angle 4.00577 / 2.86 ( 2442) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 ASP cc_start: 0.7771 (p0) cc_final: 0.7240 (t0) REVERT: B 184 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7792 (mm) REVERT: B 269 LEU cc_start: 0.6459 (pt) cc_final: 0.6028 (pt) REVERT: B 569 SER cc_start: 0.8187 (t) cc_final: 0.7942 (m) REVERT: M 108 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7826 (mp) REVERT: M 158 GLN cc_start: 0.7211 (tm-30) cc_final: 0.6303 (mt0) REVERT: M 185 MET cc_start: 0.6443 (ppp) cc_final: 0.6141 (ppp) REVERT: M 410 LYS cc_start: 0.8463 (mmtt) cc_final: 0.7806 (tptm) outliers start: 14 outliers final: 8 residues processed: 197 average time/residue: 0.1200 time to fit residues: 34.7227 Evaluate side-chains 191 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 152 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 10 HIS ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.190868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.147010 restraints weight = 16526.880| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.47 r_work: 0.3460 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14043 Z= 0.155 Angle : 0.546 6.318 19018 Z= 0.285 Chirality : 0.041 0.152 2215 Planarity : 0.004 0.037 2418 Dihedral : 4.233 33.367 1877 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.96 % Rotamer: Outliers : 1.43 % Allowed : 11.86 % Favored : 86.70 % 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: 1.21 (0.20), residues: 1712 helix: 1.65 (0.16), residues: 1009 sheet: 0.56 (0.39), residues: 174 loop : -0.73 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 42 TYR 0.021 0.001 TYR B 70 PHE 0.012 0.001 PHE A 530 TRP 0.015 0.001 TRP A 462 HIS 0.005 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (14043) covalent geometry : angle 0.54641 / 0.28 (19018) hydrogen bonds : bond 0.03911 / 2.55 ( 801) hydrogen bonds : angle 4.03520 / 2.88 ( 2442) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 MET cc_start: 0.8056 (pmm) cc_final: 0.7504 (ptm) REVERT: B 110 MET cc_start: 0.8046 (ttp) cc_final: 0.7429 (mtp) REVERT: B 155 MET cc_start: 0.2381 (pmm) cc_final: 0.2171 (pmm) REVERT: B 163 ASP cc_start: 0.7732 (p0) cc_final: 0.7231 (t0) REVERT: B 184 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7766 (mm) REVERT: B 202 GLN cc_start: 0.7723 (mp10) cc_final: 0.7500 (mp10) REVERT: B 423 ASN cc_start: 0.8382 (t0) cc_final: 0.8133 (t0) REVERT: B 569 SER cc_start: 0.8211 (t) cc_final: 0.7998 (m) REVERT: M 108 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7864 (mp) REVERT: M 158 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6341 (mt0) REVERT: M 173 LEU cc_start: 0.8266 (pp) cc_final: 0.8056 (pt) REVERT: M 185 MET cc_start: 0.6451 (ppp) cc_final: 0.6127 (ppp) REVERT: M 410 LYS cc_start: 0.8558 (mmtt) cc_final: 0.7922 (tptm) outliers start: 22 outliers final: 13 residues processed: 198 average time/residue: 0.1117 time to fit residues: 32.0931 Evaluate side-chains 184 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 107 optimal weight: 0.1980 chunk 149 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 HIS M 10 HIS M 41 GLN M 100 ASN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 GLN M 318 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.189369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146533 restraints weight = 16593.926| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.41 r_work: 0.3485 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14043 Z= 0.138 Angle : 0.535 7.058 19018 Z= 0.280 Chirality : 0.040 0.164 2215 Planarity : 0.004 0.039 2418 Dihedral : 4.176 33.748 1877 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 1.43 % Allowed : 12.78 % 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 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: 1.25 (0.20), residues: 1712 helix: 1.70 (0.16), residues: 1009 sheet: 0.61 (0.39), residues: 174 loop : -0.76 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 42 TYR 0.022 0.001 TYR B 70 PHE 0.013 0.001 PHE M 394 TRP 0.019 0.001 TRP A 462 HIS 0.004 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (14043) covalent geometry : angle 0.53474 / 0.28 (19018) hydrogen bonds : bond 0.03694 / 2.40 ( 801) hydrogen bonds : angle 3.97304 / 2.84 ( 2442) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.8087 (p0) cc_final: 0.7879 (p0) REVERT: B 110 MET cc_start: 0.8062 (ttp) cc_final: 0.7529 (mtp) REVERT: B 155 MET cc_start: 0.2555 (pmm) cc_final: 0.2335 (pmm) REVERT: B 163 ASP cc_start: 0.7837 (p0) cc_final: 0.7300 (t0) REVERT: B 184 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7920 (mm) REVERT: B 202 GLN cc_start: 0.7761 (mp10) cc_final: 0.7545 (mp10) REVERT: B 423 ASN cc_start: 0.8495 (t0) cc_final: 0.8289 (t0) REVERT: M 108 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8055 (mp) REVERT: M 154 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7638 (pp30) REVERT: M 185 MET cc_start: 0.6502 (ppp) cc_final: 0.6164 (ppp) REVERT: M 319 LYS cc_start: 0.5603 (tptp) cc_final: 0.5244 (tmtt) REVERT: M 410 LYS cc_start: 0.8559 (mmtt) cc_final: 0.7914 (tptm) REVERT: S 61 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7682 (ttt-90) outliers start: 22 outliers final: 12 residues processed: 185 average time/residue: 0.1235 time to fit residues: 33.3981 Evaluate side-chains 180 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 154 GLN Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 61 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 157 optimal weight: 1.9990 chunk 141 optimal weight: 0.0570 chunk 119 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 10 HIS ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.188956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146192 restraints weight = 16631.801| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.43 r_work: 0.3516 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14043 Z= 0.126 Angle : 0.523 6.653 19018 Z= 0.274 Chirality : 0.040 0.142 2215 Planarity : 0.004 0.038 2418 Dihedral : 4.129 33.230 1877 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 1.43 % Allowed : 13.04 % Favored : 85.53 % 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: 1.30 (0.20), residues: 1712 helix: 1.75 (0.16), residues: 1009 sheet: 0.63 (0.39), residues: 174 loop : -0.77 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 42 TYR 0.022 0.001 TYR B 70 PHE 0.013 0.001 PHE M 394 TRP 0.020 0.001 TRP A 462 HIS 0.003 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (14043) covalent geometry : angle 0.52265 / 0.27 (19018) hydrogen bonds : bond 0.03586 / 2.33 ( 801) hydrogen bonds : angle 3.93911 / 2.82 ( 2442) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 GLU cc_start: 0.6946 (tp30) cc_final: 0.6663 (tp30) REVERT: B 74 MET cc_start: 0.5904 (ptp) cc_final: 0.5508 (ptp) REVERT: B 96 GLU cc_start: 0.8125 (mp0) cc_final: 0.7727 (mp0) REVERT: B 110 MET cc_start: 0.7920 (ttp) cc_final: 0.7437 (mtp) REVERT: B 155 MET cc_start: 0.2368 (pmm) cc_final: 0.2168 (pmm) REVERT: B 163 ASP cc_start: 0.7767 (p0) cc_final: 0.7314 (t0) REVERT: B 184 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7823 (mm) REVERT: B 423 ASN cc_start: 0.8365 (t0) cc_final: 0.8111 (t0) REVERT: M 108 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7925 (mp) REVERT: M 154 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7633 (pp30) REVERT: M 185 MET cc_start: 0.6564 (ppp) cc_final: 0.6215 (ppp) REVERT: M 319 LYS cc_start: 0.5528 (tptp) cc_final: 0.5203 (tmtt) REVERT: M 410 LYS cc_start: 0.8453 (mmtt) cc_final: 0.7826 (tptm) REVERT: S 61 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7491 (ttt-90) REVERT: S 139 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7850 (pp30) outliers start: 22 outliers final: 14 residues processed: 187 average time/residue: 0.1266 time to fit residues: 34.2661 Evaluate side-chains 194 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 154 GLN Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 61 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 140 optimal weight: 0.0170 chunk 116 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 81 optimal weight: 0.2980 chunk 152 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 10 HIS ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.189753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.147303 restraints weight = 16510.300| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.33 r_work: 0.3508 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14043 Z= 0.119 Angle : 0.529 7.671 19018 Z= 0.277 Chirality : 0.040 0.141 2215 Planarity : 0.004 0.058 2418 Dihedral : 4.082 32.794 1877 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Rotamer: Outliers : 1.37 % Allowed : 13.36 % Favored : 85.27 % 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: 1.37 (0.20), residues: 1712 helix: 1.82 (0.16), residues: 1009 sheet: 0.67 (0.39), residues: 174 loop : -0.79 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 344 TYR 0.027 0.001 TYR B 72 PHE 0.020 0.001 PHE M 394 TRP 0.021 0.001 TRP A 462 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (14043) covalent geometry : angle 0.52905 / 0.28 (19018) hydrogen bonds : bond 0.03443 / 2.23 ( 801) hydrogen bonds : angle 3.88814 / 2.78 ( 2442) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 GLU cc_start: 0.6979 (tp30) cc_final: 0.6658 (tp30) REVERT: B 96 GLU cc_start: 0.8128 (mp0) cc_final: 0.7765 (mp0) REVERT: B 110 MET cc_start: 0.7964 (ttp) cc_final: 0.7481 (mtp) REVERT: B 163 ASP cc_start: 0.7776 (p0) cc_final: 0.7320 (t0) REVERT: B 184 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7841 (mm) REVERT: B 269 LEU cc_start: 0.6546 (pt) cc_final: 0.5902 (pt) REVERT: B 423 ASN cc_start: 0.8376 (t0) cc_final: 0.8119 (t0) REVERT: M 108 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7932 (mp) REVERT: M 154 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7751 (pp30) REVERT: M 158 GLN cc_start: 0.7117 (tm-30) cc_final: 0.6251 (mt0) REVERT: M 185 MET cc_start: 0.6556 (ppp) cc_final: 0.6206 (ppp) REVERT: M 319 LYS cc_start: 0.5409 (tptp) cc_final: 0.5138 (tmtt) REVERT: M 410 LYS cc_start: 0.8455 (mmtt) cc_final: 0.7845 (tptm) REVERT: S 61 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7491 (ttt-90) outliers start: 21 outliers final: 11 residues processed: 189 average time/residue: 0.1127 time to fit residues: 30.9159 Evaluate side-chains 180 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 154 GLN Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 61 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 48 optimal weight: 0.8980 chunk 84 optimal weight: 0.0870 chunk 3 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 140 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 152 optimal weight: 0.0870 chunk 106 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 307 ASN M 10 HIS ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 GLN M 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.190106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147848 restraints weight = 16488.679| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.31 r_work: 0.3554 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14043 Z= 0.117 Angle : 0.535 8.422 19018 Z= 0.280 Chirality : 0.039 0.141 2215 Planarity : 0.004 0.054 2418 Dihedral : 4.059 32.231 1877 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.25 % Rotamer: Outliers : 1.17 % Allowed : 13.62 % Favored : 85.20 % 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: 1.41 (0.20), residues: 1712 helix: 1.86 (0.16), residues: 1010 sheet: 0.67 (0.39), residues: 174 loop : -0.78 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 344 TYR 0.021 0.001 TYR B 70 PHE 0.025 0.001 PHE M 394 TRP 0.021 0.001 TRP A 462 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14043) covalent geometry : angle 0.53485 / 0.28 (19018) hydrogen bonds : bond 0.03375 / 2.19 ( 801) hydrogen bonds : angle 3.85202 / 2.75 ( 2442) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.8105 (p0) cc_final: 0.7846 (p0) REVERT: A 371 GLU cc_start: 0.7044 (tp30) cc_final: 0.6723 (tp30) REVERT: B 96 GLU cc_start: 0.8186 (mp0) cc_final: 0.7970 (mp0) REVERT: B 110 MET cc_start: 0.8193 (ttp) cc_final: 0.7721 (mtp) REVERT: B 163 ASP cc_start: 0.7865 (p0) cc_final: 0.7375 (t0) REVERT: B 184 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8028 (mm) REVERT: B 269 LEU cc_start: 0.6580 (pt) cc_final: 0.5924 (pt) REVERT: B 423 ASN cc_start: 0.8500 (t0) cc_final: 0.8268 (t0) REVERT: M 108 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8116 (mp) REVERT: M 185 MET cc_start: 0.6544 (ppp) cc_final: 0.6159 (ppp) REVERT: M 319 LYS cc_start: 0.5554 (tptp) cc_final: 0.5313 (tmtt) REVERT: M 394 PHE cc_start: 0.8533 (p90) cc_final: 0.8187 (p90) REVERT: M 410 LYS cc_start: 0.8460 (mmtt) cc_final: 0.7849 (tptm) REVERT: S 61 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7716 (ttt-90) REVERT: S 139 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7967 (pp30) outliers start: 18 outliers final: 13 residues processed: 177 average time/residue: 0.1178 time to fit residues: 30.3863 Evaluate side-chains 180 residues out of total 1541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 48 THR Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 49 PHE Chi-restraints excluded: chain S residue 61 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 132 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 chunk 134 optimal weight: 0.0870 chunk 80 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 10 HIS M 35 ASN ** M 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.189022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.146554 restraints weight = 16524.993| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.31 r_work: 0.3511 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14043 Z= 0.129 Angle : 0.540 8.164 19018 Z= 0.283 Chirality : 0.040 0.140 2215 Planarity : 0.004 0.054 2418 Dihedral : 4.026 30.597 1877 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Rotamer: Outliers : 1.43 % Allowed : 13.49 % Favored : 85.07 % 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: 1.40 (0.20), residues: 1712 helix: 1.83 (0.16), residues: 1011 sheet: 0.66 (0.39), residues: 174 loop : -0.73 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 344 TYR 0.019 0.001 TYR B 70 PHE 0.013 0.001 PHE M 394 TRP 0.019 0.001 TRP A 462 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (14043) covalent geometry : angle 0.54042 / 0.28 (19018) hydrogen bonds : bond 0.03490 / 2.27 ( 801) hydrogen bonds : angle 3.86047 / 2.76 ( 2442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3210.08 seconds wall clock time: 55 minutes 46.64 seconds (3346.64 seconds total)