Starting phenix.real_space_refine on Thu Mar 5 18:47:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjj_25927/03_2026/7tjj_25927.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjj_25927/03_2026/7tjj_25927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tjj_25927/03_2026/7tjj_25927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjj_25927/03_2026/7tjj_25927.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tjj_25927/03_2026/7tjj_25927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjj_25927/03_2026/7tjj_25927.map" } resolution = 2.7 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 93 5.49 5 Mg 4 5.21 5 S 105 5.16 5 C 15519 2.51 5 N 4112 2.21 5 O 4899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 24732 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3889 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 475} Chain breaks: 4 Chain: "B" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2081 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 1 Chain: "C" Number of atoms: 4504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4504 Classifications: {'peptide': 544} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 528} Chain breaks: 5 Chain: "D" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3536 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 3 Chain: "E" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3596 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 21, 'TRANS': 416} Chain breaks: 3 Chain: "F" Number of atoms: 2141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2141 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 7, 'TRANS': 252} Chain breaks: 2 Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 832 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 846 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "I" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3019 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 5.20, per 1000 atoms: 0.21 Number of scatterers: 24732 At special positions: 0 Unit cell: (117.82, 141.9, 179.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 93 15.00 Mg 4 11.99 O 4899 8.00 N 4112 7.00 C 15519 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: 1.55 Conformation dependent library (CDL) restraints added in 967.7 milliseconds 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5414 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 13 sheets defined 61.3% alpha, 7.7% beta 41 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 423 through 430 Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 484 through 502 Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 522 through 533 removed outlier: 3.521A pdb=" N GLU A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 568 through 572 Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 628 through 640 Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 702 through 726 Processing helix chain 'A' and resid 774 through 784 removed outlier: 3.647A pdb=" N VAL A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 removed outlier: 4.163A pdb=" N THR A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 816 Processing helix chain 'A' and resid 822 through 836 removed outlier: 3.736A pdb=" N ASN A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 852 removed outlier: 5.242A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 876 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.717A pdb=" N ASP A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.553A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 249 Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.718A pdb=" N LYS B 258 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.509A pdb=" N PHE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'B' and resid 300 through 310 removed outlier: 3.561A pdb=" N GLN B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 333 removed outlier: 3.543A pdb=" N LEU B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 371 through 384 Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.582A pdb=" N LYS B 394 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 434 through 447 removed outlier: 3.849A pdb=" N ILE B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.617A pdb=" N TRP B 465 " --> pdb=" O PRO B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 488 through 493 Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 50 through 92 removed outlier: 3.841A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 158 removed outlier: 3.708A pdb=" N GLU C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 196 Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.782A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 229 Processing helix chain 'C' and resid 243 through 249 removed outlier: 4.038A pdb=" N ILE C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 274 through 286 removed outlier: 3.612A pdb=" N ILE C 280 " --> pdb=" O TYR C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 307 Processing helix chain 'C' and resid 313 through 332 Processing helix chain 'C' and resid 333 through 339 removed outlier: 3.860A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 338 " --> pdb=" O SER C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 355 Processing helix chain 'C' and resid 357 through 371 Processing helix chain 'C' and resid 389 through 395 removed outlier: 3.827A pdb=" N PHE C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 414 Processing helix chain 'C' and resid 423 through 433 Processing helix chain 'C' and resid 435 through 441 Processing helix chain 'C' and resid 446 through 450 removed outlier: 3.611A pdb=" N TYR C 449 " --> pdb=" O CYS C 446 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS C 450 " --> pdb=" O LYS C 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 446 through 450' Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 494 through 497 Processing helix chain 'C' and resid 511 through 515 removed outlier: 4.306A pdb=" N LYS C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 511 through 515' Processing helix chain 'C' and resid 519 through 530 removed outlier: 3.948A pdb=" N GLU C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 548 removed outlier: 3.754A pdb=" N THR C 547 " --> pdb=" O ALA C 543 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 548 " --> pdb=" O PHE C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 557 removed outlier: 3.735A pdb=" N ILE C 553 " --> pdb=" O PRO C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 571 removed outlier: 3.711A pdb=" N LEU C 567 " --> pdb=" O ASN C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 595 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 91 removed outlier: 3.597A pdb=" N GLU D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 91 " --> pdb=" O LYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.710A pdb=" N GLN D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 3.890A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 228 through 241 Processing helix chain 'D' and resid 256 through 260 removed outlier: 3.503A pdb=" N LEU D 260 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.852A pdb=" N MET D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 Processing helix chain 'D' and resid 318 through 331 Processing helix chain 'D' and resid 333 through 347 removed outlier: 3.630A pdb=" N SER D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 350 through 361 Processing helix chain 'D' and resid 361 through 372 removed outlier: 3.759A pdb=" N ASP D 365 " --> pdb=" O CYS D 361 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 366 " --> pdb=" O SER D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 382 Processing helix chain 'D' and resid 384 through 401 Processing helix chain 'D' and resid 407 through 424 Processing helix chain 'D' and resid 452 through 466 removed outlier: 3.590A pdb=" N LYS D 457 " --> pdb=" O LYS D 453 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.616A pdb=" N ARG D 502 " --> pdb=" O PHE D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.080A pdb=" N GLN D 528 " --> pdb=" O SER D 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 22 Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.899A pdb=" N THR E 29 " --> pdb=" O PRO E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.789A pdb=" N LEU E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 89 Processing helix chain 'E' and resid 98 through 102 removed outlier: 3.654A pdb=" N GLN E 101 " --> pdb=" O ASP E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'E' and resid 134 through 138 Processing helix chain 'E' and resid 144 through 151 removed outlier: 3.854A pdb=" N LYS E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 removed outlier: 3.671A pdb=" N LEU E 156 " --> pdb=" O ASN E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.617A pdb=" N LEU E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 193 through 211 removed outlier: 5.864A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 222 removed outlier: 3.832A pdb=" N ILE E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 252 removed outlier: 5.808A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 271 Proline residue: E 267 - end of helix Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'E' and resid 289 through 293 removed outlier: 3.703A pdb=" N LEU E 293 " --> pdb=" O LYS E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 341 Processing helix chain 'E' and resid 342 through 346 Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 382 through 394 Processing helix chain 'E' and resid 417 through 430 removed outlier: 3.613A pdb=" N PHE E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 466 removed outlier: 3.666A pdb=" N GLU E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 476 removed outlier: 4.410A pdb=" N ASP E 476 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 15 Processing helix chain 'F' and resid 27 through 47 removed outlier: 3.806A pdb=" N ASN F 45 " --> pdb=" O ASN F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 55 Processing helix chain 'F' and resid 56 through 73 Processing helix chain 'F' and resid 80 through 84 removed outlier: 4.346A pdb=" N SER F 83 " --> pdb=" O TYR F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 281 through 291 removed outlier: 4.118A pdb=" N ILE F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 310 removed outlier: 3.692A pdb=" N ILE F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 315 through 332 removed outlier: 4.074A pdb=" N LEU F 319 " --> pdb=" O CYS F 315 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 339 removed outlier: 3.651A pdb=" N LYS F 338 " --> pdb=" O GLU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 343 Processing helix chain 'F' and resid 347 through 352 removed outlier: 3.596A pdb=" N CYS F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER F 352 " --> pdb=" O SER F 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 347 through 352' Processing helix chain 'F' and resid 359 through 374 removed outlier: 3.792A pdb=" N ILE F 363 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE F 374 " --> pdb=" O LYS F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 386 Processing helix chain 'F' and resid 393 through 402 removed outlier: 3.941A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 426 Processing helix chain 'I' and resid 54 through 62 Processing helix chain 'I' and resid 81 through 97 Processing helix chain 'I' and resid 113 through 126 removed outlier: 3.588A pdb=" N PHE I 126 " --> pdb=" O ILE I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 180 through 190 Processing helix chain 'I' and resid 201 through 209 removed outlier: 3.537A pdb=" N LEU I 205 " --> pdb=" O ASN I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 229 removed outlier: 3.796A pdb=" N LEU I 229 " --> pdb=" O ASP I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 239 removed outlier: 3.639A pdb=" N VAL I 239 " --> pdb=" O GLU I 235 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 249 Processing helix chain 'I' and resid 292 through 305 Processing helix chain 'I' and resid 313 through 324 Processing helix chain 'I' and resid 330 through 348 removed outlier: 3.643A pdb=" N LEU I 334 " --> pdb=" O ASP I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 397 removed outlier: 3.525A pdb=" N ALA I 391 " --> pdb=" O LEU I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 402 through 409 Processing helix chain 'I' and resid 411 through 428 Processing helix chain 'I' and resid 432 through 448 Processing helix chain 'I' and resid 454 through 469 Processing helix chain 'I' and resid 494 through 504 removed outlier: 3.582A pdb=" N PHE I 498 " --> pdb=" O ASP I 494 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS I 504 " --> pdb=" O ASP I 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 512 Processing sheet with id=AA1, first strand: chain 'A' and resid 508 through 514 removed outlier: 6.484A pdb=" N ILE A 561 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE A 596 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 563 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL A 598 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A 565 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR A 473 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA A 597 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE A 475 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA A 599 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL A 477 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N ILE A 622 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR A 476 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N PHE A 624 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA A 478 " --> pdb=" O PHE A 624 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 657 through 659 removed outlier: 3.515A pdb=" N SER A 646 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLN A 771 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG A 681 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 773 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ARG A 683 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 819 through 821 Processing sheet with id=AA4, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.432A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N HIS B 478 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 315 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 124 through 131 removed outlier: 6.356A pdb=" N TYR C 125 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL C 202 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL C 127 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN C 204 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 129 " --> pdb=" O ASN C 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 293 through 294 removed outlier: 7.095A pdb=" N ASN C 293 " --> pdb=" O LEU C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 534 through 536 Processing sheet with id=AA8, first strand: chain 'D' and resid 127 through 133 Processing sheet with id=AA9, first strand: chain 'D' and resid 469 through 471 Processing sheet with id=AB1, first strand: chain 'E' and resid 59 through 62 removed outlier: 6.536A pdb=" N VAL E 60 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU E 33 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N MET E 170 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU E 35 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N VAL E 187 " --> pdb=" O ASN E 32 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE E 34 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE E 189 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN E 36 " --> pdb=" O PHE E 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 433 through 435 Processing sheet with id=AB3, first strand: chain 'I' and resid 152 through 155 removed outlier: 7.052A pdb=" N SER I 164 " --> pdb=" O THR I 217 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL I 219 " --> pdb=" O SER I 164 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA I 166 " --> pdb=" O VAL I 219 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL I 221 " --> pdb=" O ALA I 166 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR I 168 " --> pdb=" O VAL I 221 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASP I 223 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE I 170 " --> pdb=" O ASP I 223 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL I 220 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY I 108 " --> pdb=" O ALA I 262 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 471 through 477 1144 hydrogen bonds defined for protein. 3273 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3844 1.31 - 1.44: 7026 1.44 - 1.57: 13990 1.57 - 1.70: 183 1.70 - 1.83: 172 Bond restraints: 25215 Sorted by residual: bond pdb=" C PHE F 98 " pdb=" N ARG F 99 " ideal model delta sigma weight residual 1.334 1.455 -0.120 1.33e-02 5.65e+03 8.18e+01 bond pdb=" C ARG F 99 " pdb=" N GLN F 100 " ideal model delta sigma weight residual 1.335 1.219 0.116 1.38e-02 5.25e+03 7.03e+01 bond pdb=" C ILE I 407 " pdb=" N ALA I 408 " ideal model delta sigma weight residual 1.334 1.242 0.092 1.49e-02 4.50e+03 3.81e+01 bond pdb=" CA ALA A 599 " pdb=" CB ALA A 599 " ideal model delta sigma weight residual 1.534 1.466 0.068 1.60e-02 3.91e+03 1.83e+01 bond pdb=" C THR D 527 " pdb=" O THR D 527 " ideal model delta sigma weight residual 1.235 1.181 0.054 1.33e-02 5.65e+03 1.67e+01 ... (remaining 25210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 34029 3.55 - 7.10: 344 7.10 - 10.65: 43 10.65 - 14.20: 3 14.20 - 17.75: 2 Bond angle restraints: 34421 Sorted by residual: angle pdb=" PA ATP I1001 " pdb=" O3A ATP I1001 " pdb=" PB ATP I1001 " ideal model delta sigma weight residual 136.83 130.02 6.81 1.00e+00 1.00e+00 4.64e+01 angle pdb=" N ARG I 227 " pdb=" CA ARG I 227 " pdb=" C ARG I 227 " ideal model delta sigma weight residual 112.93 106.46 6.47 1.12e+00 7.97e-01 3.33e+01 angle pdb=" N LEU F 29 " pdb=" CA LEU F 29 " pdb=" C LEU F 29 " ideal model delta sigma weight residual 111.82 105.36 6.46 1.16e+00 7.43e-01 3.10e+01 angle pdb=" CA THR A 601 " pdb=" C THR A 601 " pdb=" O THR A 601 " ideal model delta sigma weight residual 121.44 115.22 6.22 1.17e+00 7.31e-01 2.83e+01 angle pdb=" N MET I 225 " pdb=" CA MET I 225 " pdb=" C MET I 225 " ideal model delta sigma weight residual 112.54 106.24 6.30 1.22e+00 6.72e-01 2.67e+01 ... (remaining 34416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13114 17.90 - 35.79: 1426 35.79 - 53.69: 505 53.69 - 71.59: 123 71.59 - 89.48: 28 Dihedral angle restraints: 15196 sinusoidal: 6910 harmonic: 8286 Sorted by residual: dihedral pdb=" CA ASP C 111 " pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA PHE B 475 " pdb=" C PHE B 475 " pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta harmonic sigma weight residual 180.00 155.32 24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA LYS E 431 " pdb=" C LYS E 431 " pdb=" N LEU E 432 " pdb=" CA LEU E 432 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 15193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3413 0.080 - 0.161: 458 0.161 - 0.241: 43 0.241 - 0.322: 4 0.322 - 0.402: 1 Chirality restraints: 3919 Sorted by residual: chirality pdb=" CB ILE A 422 " pdb=" CA ILE A 422 " pdb=" CG1 ILE A 422 " pdb=" CG2 ILE A 422 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CA TYR D 524 " pdb=" N TYR D 524 " pdb=" C TYR D 524 " pdb=" CB TYR D 524 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB ILE E 326 " pdb=" CA ILE E 326 " pdb=" CG1 ILE E 326 " pdb=" CG2 ILE E 326 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3916 not shown) Planarity restraints: 4023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 222 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C LEU I 222 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU I 222 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP I 223 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 473 " -0.013 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR B 473 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 473 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR B 473 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 473 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR B 473 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 473 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 473 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 526 " 0.015 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C TRP D 526 " -0.054 2.00e-02 2.50e+03 pdb=" O TRP D 526 " 0.020 2.00e-02 2.50e+03 pdb=" N THR D 527 " 0.019 2.00e-02 2.50e+03 ... (remaining 4020 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 233 2.58 - 3.16: 18862 3.16 - 3.74: 40924 3.74 - 4.32: 57680 4.32 - 4.90: 90236 Nonbonded interactions: 207935 Sorted by model distance: nonbonded pdb=" O3G ATP I1001 " pdb="MG MG I1002 " model vdw 2.003 2.170 nonbonded pdb=" OG1 THR D 109 " pdb="MG MG D1002 " model vdw 2.070 2.170 nonbonded pdb=" O3G ATP D1001 " pdb="MG MG D1002 " model vdw 2.079 2.170 nonbonded pdb="MG MG A1002 " pdb=" O HOH A1124 " model vdw 2.080 2.170 nonbonded pdb=" OG1 THR I 115 " pdb="MG MG I1002 " model vdw 2.084 2.170 ... (remaining 207930 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: 1.560 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.780 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.006 0.120 25215 Z= 0.282 Angle : 0.942 17.750 34421 Z= 0.522 Chirality : 0.055 0.402 3919 Planarity : 0.007 0.117 4023 Dihedral : 17.517 89.483 9782 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.47 % Allowed : 0.62 % Favored : 98.91 % 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: -1.54 (0.14), residues: 2731 helix: -1.13 (0.11), residues: 1520 sheet: 0.26 (0.30), residues: 250 loop : -0.88 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 705 TYR 0.047 0.003 TYR B 473 PHE 0.044 0.003 PHE B 437 TRP 0.025 0.003 TRP C 494 HIS 0.016 0.001 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00560 (25215) covalent geometry : angle 0.94243 (34421) hydrogen bonds : bond 0.15191 ( 1236) hydrogen bonds : angle 6.42351 ( 3457) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 544 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 ASP cc_start: 0.7879 (p0) cc_final: 0.7451 (p0) REVERT: C 340 PRO cc_start: 0.7755 (Cg_exo) cc_final: 0.7530 (Cg_endo) REVERT: C 449 TYR cc_start: 0.7853 (m-80) cc_final: 0.7393 (m-80) REVERT: C 559 LYS cc_start: 0.7558 (tttm) cc_final: 0.7131 (tttt) REVERT: F 96 ASN cc_start: 0.8715 (t0) cc_final: 0.8305 (t0) REVERT: F 300 TYR cc_start: 0.7379 (m-10) cc_final: 0.6684 (m-10) REVERT: F 307 ASN cc_start: 0.8661 (m110) cc_final: 0.8405 (m-40) REVERT: F 318 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7599 (mm110) REVERT: F 358 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7555 (mtpp) REVERT: F 416 ASP cc_start: 0.7547 (t0) cc_final: 0.7168 (t0) REVERT: I 159 ASP cc_start: 0.8363 (m-30) cc_final: 0.8095 (p0) REVERT: I 404 ARG cc_start: 0.7817 (mmt180) cc_final: 0.7333 (mmt180) REVERT: I 488 LYS cc_start: 0.7664 (tttp) cc_final: 0.7422 (mtpp) REVERT: I 503 THR cc_start: 0.9152 (m) cc_final: 0.8907 (p) outliers start: 12 outliers final: 5 residues processed: 553 average time/residue: 0.8084 time to fit residues: 501.8458 Evaluate side-chains 302 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 297 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 525 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 774 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN C 69 HIS C 190 ASN C 418 ASN D 76 GLN D 80 GLN D 491 GLN F 5 GLN F 41 ASN F 45 ASN F 51 GLN F 100 GLN F 333 ASN I 183 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.112450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079477 restraints weight = 41910.608| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.11 r_work: 0.2915 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25215 Z= 0.126 Angle : 0.564 11.731 34421 Z= 0.305 Chirality : 0.040 0.147 3919 Planarity : 0.004 0.059 4023 Dihedral : 17.567 89.951 4085 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.75 % Allowed : 10.64 % Favored : 87.61 % 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: -0.06 (0.15), residues: 2731 helix: 0.36 (0.13), residues: 1535 sheet: 0.33 (0.29), residues: 247 loop : -0.62 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 705 TYR 0.021 0.001 TYR A 721 PHE 0.018 0.001 PHE F 98 TRP 0.009 0.001 TRP A 529 HIS 0.007 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00279 (25215) covalent geometry : angle 0.56405 (34421) hydrogen bonds : bond 0.03871 ( 1236) hydrogen bonds : angle 4.38881 ( 3457) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 332 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7508 (pm20) cc_final: 0.7172 (mp0) REVERT: A 432 SER cc_start: 0.8991 (m) cc_final: 0.8420 (t) REVERT: A 503 ARG cc_start: 0.8644 (mtm-85) cc_final: 0.8386 (mpp80) REVERT: A 603 ASP cc_start: 0.8370 (p0) cc_final: 0.8015 (p0) REVERT: A 656 ASN cc_start: 0.8661 (t0) cc_final: 0.8321 (t0) REVERT: A 690 GLU cc_start: 0.9019 (tt0) cc_final: 0.8796 (tt0) REVERT: A 705 ARG cc_start: 0.8565 (mmm-85) cc_final: 0.8272 (mmm160) REVERT: C 286 ASP cc_start: 0.7883 (t0) cc_final: 0.7561 (t0) REVERT: C 361 MET cc_start: 0.5320 (mmm) cc_final: 0.4705 (mmm) REVERT: C 559 LYS cc_start: 0.7711 (tttm) cc_final: 0.7128 (tttt) REVERT: D 124 LYS cc_start: 0.8904 (ttmm) cc_final: 0.8681 (ttpp) REVERT: D 151 GLU cc_start: 0.8837 (tp30) cc_final: 0.8326 (mm-30) REVERT: D 155 GLN cc_start: 0.8160 (mp10) cc_final: 0.7936 (mp10) REVERT: E 27 ASP cc_start: 0.9072 (m-30) cc_final: 0.8851 (m-30) REVERT: E 139 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: E 439 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8281 (pttt) REVERT: E 461 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6561 (tm-30) REVERT: F 12 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8185 (pp20) REVERT: F 51 GLN cc_start: 0.8579 (tt0) cc_final: 0.8353 (tt0) REVERT: F 67 GLN cc_start: 0.8388 (mt0) cc_final: 0.7998 (mt0) REVERT: F 74 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7016 (ptp) REVERT: F 77 LEU cc_start: 0.8306 (tp) cc_final: 0.7913 (pp) REVERT: F 100 GLN cc_start: 0.8691 (mt0) cc_final: 0.8318 (mt0) REVERT: F 104 ASN cc_start: 0.8907 (m-40) cc_final: 0.8258 (t0) REVERT: F 287 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7223 (pmt170) REVERT: F 307 ASN cc_start: 0.8739 (m110) cc_final: 0.8383 (m-40) REVERT: F 344 HIS cc_start: 0.6672 (m90) cc_final: 0.6466 (m90) REVERT: F 358 LYS cc_start: 0.7722 (mtmm) cc_final: 0.7424 (mtpp) REVERT: F 396 GLU cc_start: 0.8187 (mp0) cc_final: 0.7527 (mp0) REVERT: I 86 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: I 150 GLN cc_start: 0.8336 (mt0) cc_final: 0.7882 (mt0) REVERT: I 488 LYS cc_start: 0.7834 (tttp) cc_final: 0.7597 (mtpp) outliers start: 45 outliers final: 10 residues processed: 360 average time/residue: 0.7829 time to fit residues: 317.4489 Evaluate side-chains 287 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 270 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 461 GLU Chi-restraints excluded: chain F residue 12 GLU Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 345 PHE Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 449 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 39 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 224 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS A 774 HIS C 53 ASN C 418 ASN C 555 ASN D 155 GLN E 248 HIS F 8 HIS F 34 ASN F 41 ASN I 171 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.074785 restraints weight = 41850.726| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.12 r_work: 0.2828 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25215 Z= 0.190 Angle : 0.581 11.592 34421 Z= 0.311 Chirality : 0.042 0.143 3919 Planarity : 0.004 0.061 4023 Dihedral : 17.683 87.196 4080 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.10 % Allowed : 12.78 % Favored : 85.11 % 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: 0.49 (0.16), residues: 2731 helix: 0.93 (0.13), residues: 1534 sheet: 0.29 (0.29), residues: 258 loop : -0.53 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 683 TYR 0.019 0.002 TYR C 483 PHE 0.023 0.001 PHE F 329 TRP 0.009 0.001 TRP D 305 HIS 0.012 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00448 (25215) covalent geometry : angle 0.58097 (34421) hydrogen bonds : bond 0.04168 ( 1236) hydrogen bonds : angle 4.15922 ( 3457) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 275 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7501 (pm20) cc_final: 0.7200 (mp0) REVERT: A 432 SER cc_start: 0.9048 (m) cc_final: 0.8564 (t) REVERT: A 603 ASP cc_start: 0.8485 (p0) cc_final: 0.8100 (p0) REVERT: A 651 ASP cc_start: 0.7927 (t0) cc_final: 0.7457 (p0) REVERT: A 656 ASN cc_start: 0.8705 (t0) cc_final: 0.8166 (t0) REVERT: A 705 ARG cc_start: 0.8715 (mmm-85) cc_final: 0.8463 (mmm160) REVERT: C 361 MET cc_start: 0.5306 (mmm) cc_final: 0.4821 (mmm) REVERT: C 392 PHE cc_start: 0.8615 (t80) cc_final: 0.8051 (t80) REVERT: C 448 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8082 (pt0) REVERT: C 449 TYR cc_start: 0.8065 (m-80) cc_final: 0.7820 (m-80) REVERT: C 545 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6551 (mtt180) REVERT: C 559 LYS cc_start: 0.7698 (tttm) cc_final: 0.7086 (tttt) REVERT: D 140 GLN cc_start: 0.8958 (mp10) cc_final: 0.8737 (mp10) REVERT: D 151 GLU cc_start: 0.8832 (tp30) cc_final: 0.8576 (mm-30) REVERT: D 155 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.8005 (mp10) REVERT: E 139 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: E 177 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8746 (tp40) REVERT: E 439 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8369 (pttt) REVERT: F 12 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8156 (pp20) REVERT: F 104 ASN cc_start: 0.8911 (m-40) cc_final: 0.8310 (t0) REVERT: F 287 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7314 (pmt170) REVERT: F 358 LYS cc_start: 0.7615 (mtmm) cc_final: 0.7353 (mmmm) REVERT: F 396 GLU cc_start: 0.8288 (mp0) cc_final: 0.7684 (mp0) REVERT: I 85 TYR cc_start: 0.9028 (t80) cc_final: 0.8793 (t80) REVERT: I 86 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: I 94 LYS cc_start: 0.8727 (mmpt) cc_final: 0.8362 (mmpt) REVERT: I 100 ARG cc_start: 0.7448 (ttp-110) cc_final: 0.6745 (tmm160) REVERT: I 150 GLN cc_start: 0.8435 (mt0) cc_final: 0.7953 (mt0) REVERT: I 261 MET cc_start: 0.9019 (mtm) cc_final: 0.8565 (mtm) REVERT: I 484 ARG cc_start: 0.7440 (mmm-85) cc_final: 0.6904 (mmt-90) outliers start: 54 outliers final: 19 residues processed: 309 average time/residue: 0.8020 time to fit residues: 279.5998 Evaluate side-chains 274 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 545 ARG Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain F residue 12 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 202 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 33 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 140 optimal weight: 0.4980 chunk 209 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN F 8 HIS F 407 GLN I 230 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.106856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.073243 restraints weight = 41988.989| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.12 r_work: 0.2801 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 25215 Z= 0.227 Angle : 0.591 12.916 34421 Z= 0.315 Chirality : 0.043 0.149 3919 Planarity : 0.004 0.062 4023 Dihedral : 17.676 89.688 4077 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.53 % Allowed : 13.87 % Favored : 83.59 % 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: 0.68 (0.16), residues: 2731 helix: 1.13 (0.13), residues: 1531 sheet: 0.27 (0.30), residues: 250 loop : -0.50 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 683 TYR 0.020 0.002 TYR C 483 PHE 0.025 0.002 PHE F 345 TRP 0.010 0.002 TRP A 539 HIS 0.012 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00540 (25215) covalent geometry : angle 0.59149 (34421) hydrogen bonds : bond 0.04248 ( 1236) hydrogen bonds : angle 4.11604 ( 3457) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 261 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8732 (mppt) cc_final: 0.8287 (mmpt) REVERT: A 420 GLU cc_start: 0.7524 (pm20) cc_final: 0.7246 (mp0) REVERT: A 432 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8624 (t) REVERT: A 603 ASP cc_start: 0.8534 (p0) cc_final: 0.8190 (p0) REVERT: A 656 ASN cc_start: 0.8657 (t0) cc_final: 0.8169 (t0) REVERT: A 705 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8455 (mmm160) REVERT: A 844 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: C 286 ASP cc_start: 0.8325 (t0) cc_final: 0.7996 (t0) REVERT: C 306 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8516 (ttt) REVERT: C 361 MET cc_start: 0.5316 (mmm) cc_final: 0.4837 (mmm) REVERT: C 392 PHE cc_start: 0.8579 (t80) cc_final: 0.8014 (t80) REVERT: C 448 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: C 449 TYR cc_start: 0.8058 (m-80) cc_final: 0.7847 (m-80) REVERT: C 545 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6503 (mtt180) REVERT: C 559 LYS cc_start: 0.7765 (tttm) cc_final: 0.7130 (pttt) REVERT: D 140 GLN cc_start: 0.8977 (mp10) cc_final: 0.8746 (mp10) REVERT: D 151 GLU cc_start: 0.8808 (tp30) cc_final: 0.8276 (mm-30) REVERT: D 155 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: E 139 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7975 (mp10) REVERT: E 177 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8813 (tp40) REVERT: E 439 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8414 (pttt) REVERT: F 104 ASN cc_start: 0.8888 (m-40) cc_final: 0.8307 (t0) REVERT: F 287 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7343 (pmt170) REVERT: F 358 LYS cc_start: 0.7621 (mtmm) cc_final: 0.7335 (mmmt) REVERT: F 373 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8141 (tp) REVERT: F 396 GLU cc_start: 0.8398 (mp0) cc_final: 0.7804 (mp0) REVERT: I 85 TYR cc_start: 0.9041 (t80) cc_final: 0.8831 (t80) REVERT: I 86 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: I 100 ARG cc_start: 0.7452 (ttp-110) cc_final: 0.7078 (ttp80) REVERT: I 261 MET cc_start: 0.9009 (mtm) cc_final: 0.8450 (mtm) outliers start: 65 outliers final: 26 residues processed: 304 average time/residue: 0.7959 time to fit residues: 272.3383 Evaluate side-chains 273 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 545 ARG Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 286 LYS Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 478 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 157 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 252 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 chunk 214 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN D 270 GLN E 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.074974 restraints weight = 41704.572| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.04 r_work: 0.2832 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25215 Z= 0.144 Angle : 0.543 12.373 34421 Z= 0.290 Chirality : 0.041 0.136 3919 Planarity : 0.003 0.060 4023 Dihedral : 17.553 89.368 4077 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.18 % Allowed : 15.24 % Favored : 82.58 % 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: 0.92 (0.16), residues: 2731 helix: 1.37 (0.13), residues: 1530 sheet: 0.24 (0.30), residues: 255 loop : -0.43 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 683 TYR 0.015 0.001 TYR A 721 PHE 0.023 0.001 PHE C 408 TRP 0.010 0.001 TRP A 539 HIS 0.018 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00336 (25215) covalent geometry : angle 0.54260 (34421) hydrogen bonds : bond 0.03682 ( 1236) hydrogen bonds : angle 3.96528 ( 3457) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 252 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7454 (pm20) cc_final: 0.7199 (mp0) REVERT: A 432 SER cc_start: 0.9039 (m) cc_final: 0.8679 (t) REVERT: A 603 ASP cc_start: 0.8485 (p0) cc_final: 0.8126 (p0) REVERT: A 656 ASN cc_start: 0.8605 (t0) cc_final: 0.8122 (t0) REVERT: A 705 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.8426 (mmm160) REVERT: C 286 ASP cc_start: 0.8354 (t0) cc_final: 0.8007 (t0) REVERT: C 306 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8469 (ttt) REVERT: C 361 MET cc_start: 0.5259 (mmm) cc_final: 0.4780 (mmm) REVERT: C 392 PHE cc_start: 0.8549 (t80) cc_final: 0.8046 (t80) REVERT: C 448 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: C 449 TYR cc_start: 0.8080 (m-80) cc_final: 0.7842 (m-80) REVERT: C 545 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6494 (mtt180) REVERT: C 559 LYS cc_start: 0.7756 (tttm) cc_final: 0.7119 (pttt) REVERT: D 140 GLN cc_start: 0.8970 (mp10) cc_final: 0.8729 (mp10) REVERT: D 151 GLU cc_start: 0.8809 (tp30) cc_final: 0.8284 (mm-30) REVERT: E 139 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7961 (mp10) REVERT: E 437 MET cc_start: 0.7881 (tpp) cc_final: 0.7481 (ptm) REVERT: F 104 ASN cc_start: 0.8861 (m-40) cc_final: 0.8311 (t0) REVERT: F 287 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7321 (pmt170) REVERT: F 358 LYS cc_start: 0.7575 (mtmm) cc_final: 0.7285 (mmmm) REVERT: F 373 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8017 (tp) REVERT: F 396 GLU cc_start: 0.8381 (mp0) cc_final: 0.7788 (mp0) REVERT: I 85 TYR cc_start: 0.9024 (t80) cc_final: 0.8809 (t80) REVERT: I 100 ARG cc_start: 0.7477 (ttp-110) cc_final: 0.6815 (tmm160) REVERT: I 225 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8581 (mmm) REVERT: I 261 MET cc_start: 0.8979 (mtm) cc_final: 0.8466 (mtm) outliers start: 56 outliers final: 23 residues processed: 291 average time/residue: 0.7989 time to fit residues: 262.3246 Evaluate side-chains 271 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 545 ARG Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 478 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 103 optimal weight: 20.0000 chunk 250 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 323 HIS E 123 GLN F 8 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.105721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.072159 restraints weight = 41854.022| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.11 r_work: 0.2781 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 25215 Z= 0.252 Angle : 0.611 10.921 34421 Z= 0.325 Chirality : 0.044 0.153 3919 Planarity : 0.004 0.063 4023 Dihedral : 17.756 89.478 4077 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.57 % Allowed : 15.55 % Favored : 81.88 % 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: 0.81 (0.16), residues: 2731 helix: 1.27 (0.13), residues: 1532 sheet: 0.20 (0.30), residues: 250 loop : -0.47 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 683 TYR 0.021 0.002 TYR C 483 PHE 0.027 0.002 PHE F 345 TRP 0.012 0.002 TRP C 443 HIS 0.013 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00598 (25215) covalent geometry : angle 0.61060 (34421) hydrogen bonds : bond 0.04450 ( 1236) hydrogen bonds : angle 4.10204 ( 3457) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 247 time to evaluate : 0.977 Fit side-chains REVERT: A 380 LYS cc_start: 0.8756 (mppt) cc_final: 0.8323 (mmpt) REVERT: A 432 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8697 (t) REVERT: A 603 ASP cc_start: 0.8614 (p0) cc_final: 0.8291 (p0) REVERT: A 705 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8534 (mmm160) REVERT: B 497 LYS cc_start: 0.6079 (OUTLIER) cc_final: 0.5863 (pptt) REVERT: C 119 LYS cc_start: 0.7772 (mmtm) cc_final: 0.7441 (mmtm) REVERT: C 306 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8501 (ttt) REVERT: C 361 MET cc_start: 0.5533 (mmm) cc_final: 0.5022 (mmm) REVERT: C 392 PHE cc_start: 0.8553 (t80) cc_final: 0.7976 (t80) REVERT: C 545 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.6586 (mtt180) REVERT: C 559 LYS cc_start: 0.7859 (tttm) cc_final: 0.7243 (pttp) REVERT: D 140 GLN cc_start: 0.9020 (mp10) cc_final: 0.8796 (mp10) REVERT: E 139 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: E 209 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8592 (mp) REVERT: E 230 ASP cc_start: 0.8058 (p0) cc_final: 0.7845 (t0) REVERT: E 414 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7397 (ttt) REVERT: F 104 ASN cc_start: 0.8827 (m-40) cc_final: 0.8301 (t0) REVERT: F 279 LYS cc_start: 0.8083 (mmpt) cc_final: 0.7419 (mmmt) REVERT: F 287 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7291 (pmt170) REVERT: F 329 PHE cc_start: 0.8924 (m-80) cc_final: 0.8502 (m-10) REVERT: F 358 LYS cc_start: 0.7536 (mtmm) cc_final: 0.7189 (mmmm) REVERT: F 396 GLU cc_start: 0.8324 (mp0) cc_final: 0.7953 (tp30) REVERT: I 85 TYR cc_start: 0.8978 (t80) cc_final: 0.8774 (t80) REVERT: I 100 ARG cc_start: 0.7459 (ttp-110) cc_final: 0.7138 (ttp80) REVERT: I 225 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8549 (mmm) REVERT: I 261 MET cc_start: 0.8988 (mtm) cc_final: 0.8462 (mtm) REVERT: I 327 ASN cc_start: 0.7588 (t0) cc_final: 0.7381 (t0) REVERT: I 488 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7679 (mtpt) outliers start: 66 outliers final: 33 residues processed: 294 average time/residue: 0.7393 time to fit residues: 247.0028 Evaluate side-chains 278 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 545 ARG Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 346 ILE Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 478 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 140 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 262 optimal weight: 7.9990 chunk 271 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 267 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 HIS ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.075073 restraints weight = 41534.027| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.07 r_work: 0.2838 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25215 Z= 0.123 Angle : 0.541 11.154 34421 Z= 0.290 Chirality : 0.040 0.133 3919 Planarity : 0.003 0.060 4023 Dihedral : 17.505 89.975 4077 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.87 % Allowed : 16.68 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.09 (0.16), residues: 2731 helix: 1.50 (0.14), residues: 1534 sheet: 0.25 (0.30), residues: 255 loop : -0.35 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 683 TYR 0.019 0.001 TYR C 528 PHE 0.025 0.001 PHE C 408 TRP 0.010 0.001 TRP A 539 HIS 0.029 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00279 (25215) covalent geometry : angle 0.54099 (34421) hydrogen bonds : bond 0.03477 ( 1236) hydrogen bonds : angle 3.89986 ( 3457) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 259 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8717 (mppt) cc_final: 0.8291 (mmpt) REVERT: A 420 GLU cc_start: 0.7393 (pm20) cc_final: 0.7102 (mp0) REVERT: A 432 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8611 (t) REVERT: A 603 ASP cc_start: 0.8542 (p0) cc_final: 0.8180 (p0) REVERT: A 651 ASP cc_start: 0.7827 (t0) cc_final: 0.7310 (p0) REVERT: A 656 ASN cc_start: 0.8736 (t0) cc_final: 0.8206 (t0) REVERT: A 678 ARG cc_start: 0.8083 (mtp180) cc_final: 0.7614 (ttt180) REVERT: A 705 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8429 (mmm160) REVERT: A 844 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: B 484 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8062 (mt-10) REVERT: C 55 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: C 119 LYS cc_start: 0.7704 (mmtm) cc_final: 0.7474 (mmpt) REVERT: C 306 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8461 (ttt) REVERT: C 361 MET cc_start: 0.5423 (mmm) cc_final: 0.5005 (mmm) REVERT: C 392 PHE cc_start: 0.8536 (t80) cc_final: 0.8120 (t80) REVERT: C 545 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6497 (mtt180) REVERT: C 559 LYS cc_start: 0.7824 (tttm) cc_final: 0.7195 (pttp) REVERT: D 140 GLN cc_start: 0.8989 (mp10) cc_final: 0.8751 (mp10) REVERT: D 151 GLU cc_start: 0.8849 (tp30) cc_final: 0.8633 (mm-30) REVERT: E 139 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: E 230 ASP cc_start: 0.8047 (p0) cc_final: 0.7772 (t0) REVERT: E 437 MET cc_start: 0.7907 (tpp) cc_final: 0.7508 (ptm) REVERT: F 95 MET cc_start: 0.8885 (pp-130) cc_final: 0.8637 (ppp) REVERT: F 287 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7336 (pmt170) REVERT: F 329 PHE cc_start: 0.8928 (m-80) cc_final: 0.8531 (m-10) REVERT: F 358 LYS cc_start: 0.7545 (mtmm) cc_final: 0.7179 (mmmm) REVERT: F 396 GLU cc_start: 0.8337 (mp0) cc_final: 0.7927 (tp30) REVERT: I 100 ARG cc_start: 0.7461 (ttp-110) cc_final: 0.6777 (tmm160) REVERT: I 261 MET cc_start: 0.8950 (mtm) cc_final: 0.8409 (mtm) outliers start: 48 outliers final: 22 residues processed: 291 average time/residue: 0.8027 time to fit residues: 263.0797 Evaluate side-chains 272 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 545 ARG Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 202 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 70 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 169 optimal weight: 0.2980 chunk 7 optimal weight: 9.9990 chunk 265 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 184 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 270 GLN F 8 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.108470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.075356 restraints weight = 41647.293| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.10 r_work: 0.2844 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25215 Z= 0.127 Angle : 0.546 10.863 34421 Z= 0.291 Chirality : 0.040 0.158 3919 Planarity : 0.003 0.059 4023 Dihedral : 17.371 89.574 4077 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.83 % Allowed : 17.34 % Favored : 80.83 % 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 (0.16), residues: 2731 helix: 1.62 (0.14), residues: 1539 sheet: 0.34 (0.30), residues: 255 loop : -0.29 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 683 TYR 0.018 0.001 TYR C 528 PHE 0.031 0.001 PHE F 345 TRP 0.009 0.001 TRP A 539 HIS 0.013 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00293 (25215) covalent geometry : angle 0.54576 (34421) hydrogen bonds : bond 0.03359 ( 1236) hydrogen bonds : angle 3.82370 ( 3457) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 258 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8698 (mppt) cc_final: 0.8296 (mmpt) REVERT: A 432 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8634 (t) REVERT: A 603 ASP cc_start: 0.8558 (p0) cc_final: 0.8087 (p0) REVERT: A 623 MET cc_start: 0.8837 (tpt) cc_final: 0.8544 (tpt) REVERT: A 651 ASP cc_start: 0.7850 (t0) cc_final: 0.7307 (p0) REVERT: A 678 ARG cc_start: 0.8137 (mtp180) cc_final: 0.7679 (ttt180) REVERT: A 844 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: A 902 LYS cc_start: 0.8993 (mttt) cc_final: 0.8732 (mmtm) REVERT: B 484 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8053 (mt-10) REVERT: C 55 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: C 119 LYS cc_start: 0.7699 (mmtm) cc_final: 0.7470 (mmpt) REVERT: C 361 MET cc_start: 0.5161 (mmm) cc_final: 0.4759 (mmm) REVERT: C 392 PHE cc_start: 0.8552 (t80) cc_final: 0.8156 (t80) REVERT: C 545 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6512 (mtt180) REVERT: C 559 LYS cc_start: 0.7782 (tttm) cc_final: 0.7200 (pttp) REVERT: D 140 GLN cc_start: 0.8990 (mp10) cc_final: 0.8761 (mp10) REVERT: D 151 GLU cc_start: 0.8855 (tp30) cc_final: 0.8605 (mm-30) REVERT: E 139 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7984 (mp10) REVERT: E 230 ASP cc_start: 0.8051 (p0) cc_final: 0.7731 (t0) REVERT: E 437 MET cc_start: 0.7950 (tpp) cc_final: 0.7613 (ptm) REVERT: F 95 MET cc_start: 0.8869 (pp-130) cc_final: 0.8612 (ppp) REVERT: F 279 LYS cc_start: 0.8196 (mmpt) cc_final: 0.7498 (mmtt) REVERT: F 287 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7310 (pmt170) REVERT: F 329 PHE cc_start: 0.8958 (m-80) cc_final: 0.8595 (m-10) REVERT: F 358 LYS cc_start: 0.7563 (mtmm) cc_final: 0.7162 (mmmm) REVERT: F 396 GLU cc_start: 0.8362 (mp0) cc_final: 0.7955 (tp30) REVERT: I 96 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8803 (mp) REVERT: I 100 ARG cc_start: 0.7525 (ttp-110) cc_final: 0.6855 (tmm160) outliers start: 47 outliers final: 22 residues processed: 288 average time/residue: 0.7939 time to fit residues: 257.3845 Evaluate side-chains 274 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 545 ARG Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 202 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 111 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 14 optimal weight: 0.0370 chunk 252 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN C 250 ASN D 155 GLN D 270 GLN F 8 HIS F 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.106171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.072729 restraints weight = 41888.689| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.11 r_work: 0.2792 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 25215 Z= 0.232 Angle : 0.611 10.038 34421 Z= 0.324 Chirality : 0.044 0.165 3919 Planarity : 0.004 0.062 4023 Dihedral : 17.617 89.418 4077 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.18 % Rotamer: Outliers : 1.79 % Allowed : 17.69 % Favored : 80.51 % 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: 1.11 (0.16), residues: 2731 helix: 1.50 (0.13), residues: 1535 sheet: 0.33 (0.30), residues: 250 loop : -0.32 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 683 TYR 0.021 0.002 TYR C 528 PHE 0.027 0.002 PHE C 408 TRP 0.012 0.002 TRP C 443 HIS 0.006 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00554 (25215) covalent geometry : angle 0.61119 (34421) hydrogen bonds : bond 0.04162 ( 1236) hydrogen bonds : angle 3.99439 ( 3457) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 0.881 Fit side-chains REVERT: A 432 SER cc_start: 0.8952 (m) cc_final: 0.8680 (t) REVERT: A 603 ASP cc_start: 0.8616 (p0) cc_final: 0.8187 (p0) REVERT: A 678 ARG cc_start: 0.8114 (mtp180) cc_final: 0.7710 (ttt180) REVERT: A 844 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: A 899 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: A 902 LYS cc_start: 0.9020 (mttt) cc_final: 0.8698 (mmtm) REVERT: B 265 MET cc_start: 0.7854 (ptp) cc_final: 0.7602 (pmm) REVERT: B 392 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8449 (mt-10) REVERT: B 484 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8015 (mt-10) REVERT: C 55 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: C 119 LYS cc_start: 0.7736 (mmtm) cc_final: 0.7515 (mmpt) REVERT: C 361 MET cc_start: 0.5535 (mmm) cc_final: 0.5086 (mmm) REVERT: C 392 PHE cc_start: 0.8576 (t80) cc_final: 0.8103 (t80) REVERT: C 545 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.6580 (mtt180) REVERT: C 559 LYS cc_start: 0.7876 (tttm) cc_final: 0.7295 (pttp) REVERT: D 140 GLN cc_start: 0.9013 (mp10) cc_final: 0.8791 (mp10) REVERT: D 151 GLU cc_start: 0.8883 (tp30) cc_final: 0.8533 (mm-30) REVERT: E 139 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7989 (mp10) REVERT: E 209 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8576 (mp) REVERT: E 230 ASP cc_start: 0.8107 (p0) cc_final: 0.7838 (t0) REVERT: E 437 MET cc_start: 0.7973 (tpp) cc_final: 0.7531 (ptm) REVERT: F 51 GLN cc_start: 0.8640 (tt0) cc_final: 0.8433 (tt0) REVERT: F 95 MET cc_start: 0.8896 (pp-130) cc_final: 0.8634 (ppp) REVERT: F 100 GLN cc_start: 0.8883 (mt0) cc_final: 0.8562 (mt0) REVERT: F 279 LYS cc_start: 0.8208 (mmpt) cc_final: 0.7473 (mmtt) REVERT: F 287 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7302 (pmt170) REVERT: F 329 PHE cc_start: 0.8964 (m-80) cc_final: 0.8547 (m-10) REVERT: F 358 LYS cc_start: 0.7475 (mtmm) cc_final: 0.7123 (mmmm) REVERT: F 396 GLU cc_start: 0.8353 (mp0) cc_final: 0.7960 (tp30) REVERT: F 417 GLN cc_start: 0.7942 (mp10) cc_final: 0.7663 (mp10) REVERT: I 96 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8810 (mp) REVERT: I 100 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.7069 (ttp80) REVERT: I 488 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7549 (mtpt) outliers start: 46 outliers final: 24 residues processed: 284 average time/residue: 0.7927 time to fit residues: 253.6961 Evaluate side-chains 261 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 545 ARG Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 478 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 43 optimal weight: 0.7980 chunk 206 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 273 optimal weight: 0.2980 chunk 224 optimal weight: 5.9990 chunk 247 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN D 155 GLN D 270 GLN F 5 GLN F 8 HIS F 45 ASN F 318 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.108416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.075235 restraints weight = 41685.495| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.10 r_work: 0.2841 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25215 Z= 0.127 Angle : 0.565 15.207 34421 Z= 0.299 Chirality : 0.040 0.167 3919 Planarity : 0.003 0.062 4023 Dihedral : 17.415 89.797 4077 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.60 % Allowed : 17.93 % Favored : 80.48 % 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: 1.27 (0.16), residues: 2731 helix: 1.62 (0.14), residues: 1539 sheet: 0.38 (0.30), residues: 255 loop : -0.24 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 683 TYR 0.020 0.001 TYR C 528 PHE 0.034 0.001 PHE F 345 TRP 0.010 0.001 TRP A 539 HIS 0.014 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00291 (25215) covalent geometry : angle 0.56516 (34421) hydrogen bonds : bond 0.03399 ( 1236) hydrogen bonds : angle 3.85193 ( 3457) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 407 GLU cc_start: 0.8372 (pm20) cc_final: 0.8128 (pm20) REVERT: A 432 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8621 (t) REVERT: A 503 ARG cc_start: 0.8582 (mtm-85) cc_final: 0.8291 (mpp80) REVERT: A 603 ASP cc_start: 0.8616 (p0) cc_final: 0.8262 (p0) REVERT: A 623 MET cc_start: 0.8753 (tpt) cc_final: 0.8505 (tpt) REVERT: A 651 ASP cc_start: 0.7794 (t0) cc_final: 0.7297 (p0) REVERT: A 678 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7671 (ttt180) REVERT: A 844 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: A 899 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: A 902 LYS cc_start: 0.9029 (mttt) cc_final: 0.8697 (mttm) REVERT: B 265 MET cc_start: 0.7739 (ptp) cc_final: 0.7486 (pmm) REVERT: B 484 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8029 (mt-10) REVERT: C 55 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: C 119 LYS cc_start: 0.7679 (mmtm) cc_final: 0.7472 (mmpt) REVERT: C 361 MET cc_start: 0.5453 (mmm) cc_final: 0.5013 (mmm) REVERT: C 392 PHE cc_start: 0.8551 (t80) cc_final: 0.8116 (t80) REVERT: C 545 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6528 (mtt180) REVERT: C 559 LYS cc_start: 0.7851 (tttm) cc_final: 0.7246 (pttp) REVERT: D 140 GLN cc_start: 0.9011 (mp10) cc_final: 0.8792 (mp10) REVERT: D 151 GLU cc_start: 0.8850 (tp30) cc_final: 0.8622 (mm-30) REVERT: E 139 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: E 230 ASP cc_start: 0.8087 (p0) cc_final: 0.7800 (t0) REVERT: E 437 MET cc_start: 0.8006 (tpp) cc_final: 0.7585 (ptm) REVERT: F 95 MET cc_start: 0.8884 (pp-130) cc_final: 0.8622 (ppp) REVERT: F 275 LYS cc_start: 0.7558 (pttt) cc_final: 0.7316 (tmtp) REVERT: F 279 LYS cc_start: 0.8207 (mmpt) cc_final: 0.7519 (mmtt) REVERT: F 287 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7263 (ppt170) REVERT: F 329 PHE cc_start: 0.8959 (m-80) cc_final: 0.8568 (m-10) REVERT: F 358 LYS cc_start: 0.7491 (mtmm) cc_final: 0.7185 (mmmm) REVERT: F 396 GLU cc_start: 0.8362 (mp0) cc_final: 0.7950 (tp30) REVERT: I 96 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8803 (mp) REVERT: I 100 ARG cc_start: 0.7498 (ttp-110) cc_final: 0.6819 (tmm160) REVERT: I 488 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7490 (tptt) outliers start: 41 outliers final: 21 residues processed: 271 average time/residue: 0.7713 time to fit residues: 236.3726 Evaluate side-chains 268 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 239 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 545 ARG Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 478 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 206 optimal weight: 0.6980 chunk 259 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN D 155 GLN F 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.107425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.074801 restraints weight = 41689.696| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.03 r_work: 0.2833 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25215 Z= 0.148 Angle : 0.572 13.042 34421 Z= 0.303 Chirality : 0.041 0.169 3919 Planarity : 0.004 0.064 4023 Dihedral : 17.412 89.827 4077 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.40 % Allowed : 18.04 % Favored : 80.55 % 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: 1.30 (0.16), residues: 2731 helix: 1.64 (0.13), residues: 1541 sheet: 0.43 (0.30), residues: 250 loop : -0.23 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 683 TYR 0.022 0.001 TYR C 528 PHE 0.031 0.001 PHE C 408 TRP 0.009 0.001 TRP A 539 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00349 (25215) covalent geometry : angle 0.57164 (34421) hydrogen bonds : bond 0.03561 ( 1236) hydrogen bonds : angle 3.86431 ( 3457) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10554.47 seconds wall clock time: 179 minutes 58.74 seconds (10798.74 seconds total)