Starting phenix.real_space_refine on Sun Jul 5 01:05:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tjj_25927/07_2026/7tjj_25927.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjj_25927/07_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_25927/07_2026/7tjj_25927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjj_25927/07_2026/7tjj_25927.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tjj_25927/07_2026/7tjj_25927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjj_25927/07_2026/7tjj_25927.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tjj_25927/07_2026/7tjj_25927.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tjj_25927/07_2026/7tjj_25927.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.93, per 1000 atoms: 0.16 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: 1.72 Conformation dependent library (CDL) restraints added in 998.0 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: 2.72 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: 4.79 Time building geometry restraints manager: 2.40 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: 34022 3.55 - 7.10: 351 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: 13074 17.90 - 35.79: 1399 35.79 - 53.69: 456 53.69 - 71.59: 118 71.59 - 89.48: 25 Dihedral angle restraints: 15072 sinusoidal: 6786 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 15069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3400 0.080 - 0.161: 471 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: 2.290 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 21.590 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 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= 0.351 Angle : 0.962 17.750 34421 Z= 0.580 Chirality : 0.056 0.402 3919 Planarity : 0.007 0.117 4023 Dihedral : 17.156 89.483 9658 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/Z covalent geometry : bond 0.00585 / 0.35 (25215) covalent geometry : angle 0.96224 / 0.58 (34421) hydrogen bonds : bond 0.15191 / 9.87 ( 1236) hydrogen bonds : angle 6.42351 / 4.59 ( 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 : 0.954 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: 0.6855 time to fit residues: 428.4540 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 : 0.895 ------------------------------------------------------------------------------- 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: 30.0000 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... A 608 GLN A 774 HIS C 190 ASN ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN D 76 GLN D 80 GLN D 491 GLN E 238 ASN F 5 GLN F 41 ASN F 51 GLN F 100 GLN F 333 ASN I 171 ASN I 183 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.111905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.079300 restraints weight = 41706.679| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.07 r_work: 0.2911 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25215 Z= 0.134 Angle : 0.619 12.475 34421 Z= 0.334 Chirality : 0.043 0.222 3919 Planarity : 0.005 0.061 4023 Dihedral : 17.398 83.415 3961 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.10 % Allowed : 10.95 % Favored : 86.94 % 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: -0.26 (0.15), residues: 2731 helix: 0.19 (0.13), residues: 1536 sheet: 0.43 (0.30), residues: 238 loop : -0.74 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 683 TYR 0.022 0.001 TYR A 721 PHE 0.021 0.001 PHE F 111 TRP 0.009 0.001 TRP C 58 HIS 0.007 0.001 HIS F 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (25215) covalent geometry : angle 0.61898 / 0.33 (34421) hydrogen bonds : bond 0.04583 / 3.06 ( 1236) hydrogen bonds : angle 4.66782 / 3.30 ( 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 375 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 321 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7553 (pm20) cc_final: 0.7155 (pm20) REVERT: A 432 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8413 (t) REVERT: A 518 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8746 (mmt) REVERT: A 603 ASP cc_start: 0.8331 (p0) cc_final: 0.7996 (p0) REVERT: A 651 ASP cc_start: 0.7938 (t0) cc_final: 0.7704 (t0) REVERT: A 656 ASN cc_start: 0.8620 (t0) cc_final: 0.8376 (t0) REVERT: A 705 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.8264 (mmm160) REVERT: A 844 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: C 361 MET cc_start: 0.5491 (mmm) cc_final: 0.4899 (mmm) REVERT: C 559 LYS cc_start: 0.7688 (tttm) cc_final: 0.7061 (tttt) REVERT: D 124 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8676 (ttpt) REVERT: D 151 GLU cc_start: 0.8829 (tp30) cc_final: 0.8343 (mm-30) REVERT: E 27 ASP cc_start: 0.9103 (m-30) cc_final: 0.8901 (m-30) REVERT: E 139 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: E 275 LYS cc_start: 0.7215 (mmtt) cc_final: 0.6713 (mmtm) REVERT: E 439 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8403 (pttt) REVERT: F 67 GLN cc_start: 0.8529 (mt0) cc_final: 0.8125 (mt0) REVERT: F 77 LEU cc_start: 0.8354 (tp) cc_final: 0.7895 (pp) REVERT: F 95 MET cc_start: 0.8836 (pp-130) cc_final: 0.8343 (tmm) REVERT: F 96 ASN cc_start: 0.8789 (t0) cc_final: 0.8572 (t0) REVERT: F 100 GLN cc_start: 0.8671 (mt0) cc_final: 0.8312 (mt0) REVERT: F 104 ASN cc_start: 0.8909 (m-40) cc_final: 0.8264 (t0) REVERT: F 109 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8169 (mtmm) REVERT: F 287 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6758 (tpp80) REVERT: F 300 TYR cc_start: 0.7769 (m-10) cc_final: 0.7270 (m-10) REVERT: F 332 PHE cc_start: 0.7453 (m-10) cc_final: 0.7237 (m-10) REVERT: F 358 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7403 (mtpp) REVERT: I 86 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: I 100 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7306 (ttp-110) REVERT: I 150 GLN cc_start: 0.8269 (mt0) cc_final: 0.7816 (mt0) REVERT: I 204 HIS cc_start: 0.8455 (m90) cc_final: 0.8170 (m90) REVERT: I 503 THR cc_start: 0.9210 (m) cc_final: 0.8896 (p) outliers start: 54 outliers final: 17 residues processed: 356 average time/residue: 0.6665 time to fit residues: 269.5242 Evaluate side-chains 292 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 266 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain E residue 139 GLN 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 38 ILE Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 345 PHE Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 395 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 100 ARG 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: 3.9990 chunk 224 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 131 optimal weight: 0.0770 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 HIS C 69 HIS ** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN C 555 ASN F 8 HIS F 45 ASN F 51 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.076297 restraints weight = 41681.948| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.05 r_work: 0.2855 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25215 Z= 0.192 Angle : 0.608 11.944 34421 Z= 0.326 Chirality : 0.044 0.206 3919 Planarity : 0.004 0.059 4023 Dihedral : 17.437 76.350 3955 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.18 % Allowed : 12.59 % Favored : 85.23 % 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: 0.30 (0.16), residues: 2731 helix: 0.77 (0.13), residues: 1526 sheet: 0.30 (0.29), residues: 260 loop : -0.64 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 683 TYR 0.019 0.002 TYR A 721 PHE 0.045 0.002 PHE F 345 TRP 0.008 0.001 TRP D 305 HIS 0.011 0.001 HIS F 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (25215) covalent geometry : angle 0.60828 / 0.33 (34421) hydrogen bonds : bond 0.04361 / 2.91 ( 1236) hydrogen bonds : angle 4.35976 / 3.07 ( 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 341 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 285 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7522 (pm20) cc_final: 0.7051 (pm20) REVERT: A 432 SER cc_start: 0.9041 (m) cc_final: 0.8519 (t) REVERT: A 603 ASP cc_start: 0.8401 (p0) cc_final: 0.8057 (p0) REVERT: A 651 ASP cc_start: 0.7973 (t0) cc_final: 0.7751 (t0) REVERT: A 656 ASN cc_start: 0.8643 (t0) cc_final: 0.8250 (t0) REVERT: A 705 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8378 (mmm160) REVERT: C 286 ASP cc_start: 0.7927 (t0) cc_final: 0.7663 (t0) REVERT: C 361 MET cc_start: 0.5411 (mmm) cc_final: 0.4948 (mmm) REVERT: C 448 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8115 (pt0) REVERT: C 559 LYS cc_start: 0.7706 (tttm) cc_final: 0.7107 (tttt) REVERT: D 124 LYS cc_start: 0.8970 (ttmm) cc_final: 0.8747 (ttpp) REVERT: D 151 GLU cc_start: 0.8814 (tp30) cc_final: 0.8557 (mm-30) REVERT: E 139 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: F 12 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8061 (pp20) REVERT: F 67 GLN cc_start: 0.8384 (mt0) cc_final: 0.8067 (mt0) REVERT: F 77 LEU cc_start: 0.8233 (tp) cc_final: 0.7925 (pp) REVERT: F 96 ASN cc_start: 0.8787 (t0) cc_final: 0.8571 (t0) REVERT: F 100 GLN cc_start: 0.8811 (mt0) cc_final: 0.8440 (mt0) REVERT: F 104 ASN cc_start: 0.8957 (m-40) cc_final: 0.8300 (t0) REVERT: F 287 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7684 (pmt-80) REVERT: F 307 ASN cc_start: 0.8771 (m110) cc_final: 0.8423 (m-40) REVERT: F 358 LYS cc_start: 0.7700 (mtmm) cc_final: 0.7406 (mtpp) REVERT: F 396 GLU cc_start: 0.8093 (mp0) cc_final: 0.7388 (mp0) REVERT: I 86 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: I 150 GLN cc_start: 0.8370 (mt0) cc_final: 0.7896 (mt0) REVERT: I 484 ARG cc_start: 0.7386 (mmm-85) cc_final: 0.7105 (mpp80) REVERT: I 503 THR cc_start: 0.9268 (m) cc_final: 0.8984 (p) outliers start: 56 outliers final: 20 residues processed: 320 average time/residue: 0.6795 time to fit residues: 245.7185 Evaluate side-chains 282 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 257 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 493 SER 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 D residue 320 LEU Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain E residue 139 GLN 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 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 362 VAL 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 449 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 33 optimal weight: 3.9990 chunk 106 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 209 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 overall best weight: 1.2480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 HIS B 342 GLN C 418 ASN D 270 GLN F 8 HIS F 41 ASN F 417 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.109977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.077223 restraints weight = 41647.965| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.05 r_work: 0.2872 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.2390 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= 0.125 Angle : 0.552 12.453 34421 Z= 0.295 Chirality : 0.042 0.195 3919 Planarity : 0.004 0.058 4023 Dihedral : 17.407 74.625 3954 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.07 % Allowed : 13.91 % Favored : 84.02 % 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: 0.64 (0.16), residues: 2731 helix: 1.12 (0.13), residues: 1529 sheet: 0.23 (0.29), residues: 256 loop : -0.56 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 683 TYR 0.017 0.001 TYR A 721 PHE 0.020 0.001 PHE F 329 TRP 0.008 0.001 TRP A 539 HIS 0.012 0.001 HIS F 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (25215) covalent geometry : angle 0.55180 / 0.30 (34421) hydrogen bonds : bond 0.03802 / 2.55 ( 1236) hydrogen bonds : angle 4.15296 / 2.93 ( 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 320 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 267 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7480 (pm20) cc_final: 0.7133 (mp0) REVERT: A 432 SER cc_start: 0.9036 (m) cc_final: 0.8535 (t) REVERT: A 603 ASP cc_start: 0.8408 (p0) cc_final: 0.7954 (p0) REVERT: A 656 ASN cc_start: 0.8638 (t0) cc_final: 0.8231 (t0) REVERT: A 705 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8434 (mmm160) REVERT: A 844 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: C 361 MET cc_start: 0.5420 (mmm) cc_final: 0.5010 (mmm) REVERT: C 448 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8113 (pt0) REVERT: C 449 TYR cc_start: 0.8051 (m-80) cc_final: 0.7753 (m-80) REVERT: C 559 LYS cc_start: 0.7690 (tttm) cc_final: 0.7071 (tttt) REVERT: D 124 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8700 (ttpp) REVERT: D 140 GLN cc_start: 0.8963 (mp10) cc_final: 0.8703 (mp10) REVERT: D 151 GLU cc_start: 0.8779 (tp30) cc_final: 0.8475 (mm-30) REVERT: E 139 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: E 234 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8627 (m-40) REVERT: E 275 LYS cc_start: 0.7160 (mmtt) cc_final: 0.6690 (mmtm) REVERT: F 67 GLN cc_start: 0.8335 (mt0) cc_final: 0.8109 (mt0) REVERT: F 74 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7319 (ptp) REVERT: F 95 MET cc_start: 0.8823 (pp-130) cc_final: 0.8394 (tmm) REVERT: F 100 GLN cc_start: 0.8799 (mt0) cc_final: 0.8462 (mt0) REVERT: F 104 ASN cc_start: 0.8904 (m-40) cc_final: 0.8297 (t0) REVERT: F 287 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7259 (pmt170) REVERT: F 329 PHE cc_start: 0.8847 (m-80) cc_final: 0.8625 (m-80) REVERT: F 358 LYS cc_start: 0.7699 (mtmm) cc_final: 0.7399 (mtpp) REVERT: F 396 GLU cc_start: 0.8208 (mp0) cc_final: 0.7489 (mp0) REVERT: I 86 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7856 (mp0) REVERT: I 150 GLN cc_start: 0.8407 (mt0) cc_final: 0.7940 (mt0) REVERT: I 503 THR cc_start: 0.9272 (m) cc_final: 0.9022 (p) outliers start: 53 outliers final: 24 residues processed: 301 average time/residue: 0.7023 time to fit residues: 240.1547 Evaluate side-chains 273 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 252 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 545 ARG Chi-restraints excluded: chain C residue 550 LYS Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 49 LYS 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 368 LYS Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 74 MET 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 362 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 157 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 252 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 644 ASN A 774 HIS C 418 ASN D 155 GLN D 270 GLN D 375 ASN F 8 HIS F 34 ASN F 318 GLN F 417 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.109013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.076181 restraints weight = 41679.695| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.04 r_work: 0.2855 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.2574 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= 0.146 Angle : 0.558 11.018 34421 Z= 0.297 Chirality : 0.042 0.196 3919 Planarity : 0.003 0.059 4023 Dihedral : 17.387 72.448 3954 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.26 % Allowed : 14.34 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.80 (0.16), residues: 2731 helix: 1.27 (0.13), residues: 1531 sheet: 0.21 (0.30), residues: 256 loop : -0.51 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 503 TYR 0.016 0.001 TYR A 721 PHE 0.022 0.001 PHE F 345 TRP 0.008 0.001 TRP A 539 HIS 0.018 0.001 HIS F 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (25215) covalent geometry : angle 0.55776 / 0.30 (34421) hydrogen bonds : bond 0.03793 / 2.55 ( 1236) hydrogen bonds : angle 4.06811 / 2.86 ( 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 323 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 265 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7440 (pm20) cc_final: 0.7127 (mp0) REVERT: A 432 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8582 (t) REVERT: A 603 ASP cc_start: 0.8425 (p0) cc_final: 0.8026 (p0) REVERT: A 656 ASN cc_start: 0.8641 (t0) cc_final: 0.8201 (t0) REVERT: A 705 ARG cc_start: 0.8671 (mmm-85) cc_final: 0.8446 (mmm160) REVERT: A 875 ASP cc_start: 0.8707 (m-30) cc_final: 0.8497 (m-30) REVERT: A 902 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8646 (mttm) REVERT: C 361 MET cc_start: 0.5498 (mmm) cc_final: 0.5074 (mmm) REVERT: C 448 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8085 (pt0) REVERT: C 449 TYR cc_start: 0.8033 (m-80) cc_final: 0.7739 (m-80) REVERT: C 545 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6462 (mtt180) REVERT: C 559 LYS cc_start: 0.7683 (tttm) cc_final: 0.7083 (tttt) REVERT: D 124 LYS cc_start: 0.8974 (ttmm) cc_final: 0.8756 (ttpp) REVERT: D 140 GLN cc_start: 0.8957 (mp10) cc_final: 0.8683 (mp10) REVERT: D 151 GLU cc_start: 0.8791 (tp30) cc_final: 0.8503 (mm-30) REVERT: D 155 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: E 139 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: E 234 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8627 (m-40) REVERT: E 367 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8427 (pttm) REVERT: E 437 MET cc_start: 0.7863 (tpp) cc_final: 0.7501 (ptt) REVERT: F 39 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8934 (mm) REVERT: F 63 TYR cc_start: 0.9128 (t80) cc_final: 0.8893 (t80) REVERT: F 67 GLN cc_start: 0.8349 (mt0) cc_final: 0.7823 (mt0) REVERT: F 100 GLN cc_start: 0.8807 (mt0) cc_final: 0.8530 (mt0) REVERT: F 104 ASN cc_start: 0.8907 (m-40) cc_final: 0.8320 (t0) REVERT: F 287 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7261 (pmt170) REVERT: F 358 LYS cc_start: 0.7623 (mtmm) cc_final: 0.7374 (mmmm) REVERT: F 396 GLU cc_start: 0.8270 (mp0) cc_final: 0.7561 (mp0) REVERT: I 86 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: I 150 GLN cc_start: 0.8429 (mt0) cc_final: 0.7945 (mt0) outliers start: 58 outliers final: 25 residues processed: 301 average time/residue: 0.7537 time to fit residues: 257.8177 Evaluate side-chains 288 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 902 LYS Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 448 GLU 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 C residue 550 LYS Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 49 LYS 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 367 LYS Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 81 ILE 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 362 VAL 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 387 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 103 optimal weight: 10.0000 chunk 250 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 136 optimal weight: 8.9990 chunk 265 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 188 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 629 HIS ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN D 155 GLN D 270 GLN E 248 HIS F 8 HIS F 417 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.107772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.074274 restraints weight = 41729.347| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.09 r_work: 0.2816 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.2710 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= 0.218 Angle : 0.595 10.565 34421 Z= 0.315 Chirality : 0.044 0.208 3919 Planarity : 0.004 0.060 4023 Dihedral : 17.436 72.822 3953 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.14 % Allowed : 14.81 % Favored : 83.05 % 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: 0.82 (0.16), residues: 2731 helix: 1.28 (0.13), residues: 1533 sheet: 0.24 (0.30), residues: 250 loop : -0.48 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 503 TYR 0.020 0.002 TYR C 483 PHE 0.028 0.002 PHE C 408 TRP 0.008 0.001 TRP C 443 HIS 0.010 0.001 HIS F 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (25215) covalent geometry : angle 0.59467 / 0.32 (34421) hydrogen bonds : bond 0.04161 / 2.78 ( 1236) hydrogen bonds : angle 4.11360 / 2.89 ( 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 312 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 257 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8750 (mppt) cc_final: 0.8317 (mmpt) REVERT: A 420 GLU cc_start: 0.7545 (pm20) cc_final: 0.7235 (mp0) REVERT: A 432 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8614 (t) REVERT: A 603 ASP cc_start: 0.8487 (p0) cc_final: 0.8124 (p0) REVERT: A 656 ASN cc_start: 0.8687 (t0) cc_final: 0.8202 (t0) REVERT: A 705 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.8451 (mmm160) REVERT: A 844 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: A 902 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8628 (mptp) REVERT: C 361 MET cc_start: 0.5514 (mmm) cc_final: 0.5063 (mmm) REVERT: C 448 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8158 (pt0) REVERT: C 545 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6496 (mtt180) REVERT: C 559 LYS cc_start: 0.7684 (tttm) cc_final: 0.7086 (tttt) REVERT: D 140 GLN cc_start: 0.8968 (mp10) cc_final: 0.8740 (mp10) REVERT: E 139 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8079 (mp10) REVERT: E 282 LEU cc_start: 0.8962 (mp) cc_final: 0.8544 (mp) REVERT: E 286 LYS cc_start: 0.9149 (mppt) cc_final: 0.8858 (mppt) REVERT: E 367 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8425 (pttm) REVERT: E 437 MET cc_start: 0.7816 (tpp) cc_final: 0.7428 (ptt) REVERT: F 63 TYR cc_start: 0.9175 (t80) cc_final: 0.8922 (t80) REVERT: F 67 GLN cc_start: 0.8392 (mt0) cc_final: 0.7833 (mt0) REVERT: F 100 GLN cc_start: 0.8902 (mt0) cc_final: 0.8615 (mt0) REVERT: F 104 ASN cc_start: 0.8887 (m-40) cc_final: 0.8318 (t0) REVERT: F 287 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7328 (pmt170) REVERT: F 329 PHE cc_start: 0.8860 (m-80) cc_final: 0.8530 (m-10) REVERT: F 358 LYS cc_start: 0.7615 (mtmm) cc_final: 0.7362 (mmmm) REVERT: F 396 GLU cc_start: 0.8332 (mp0) cc_final: 0.7676 (mp0) REVERT: I 85 TYR cc_start: 0.9044 (t80) cc_final: 0.8806 (t80) REVERT: I 86 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: I 150 GLN cc_start: 0.8474 (mt0) cc_final: 0.7984 (mt0) outliers start: 55 outliers final: 30 residues processed: 293 average time/residue: 0.7246 time to fit residues: 240.9519 Evaluate side-chains 281 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 867 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 902 LYS Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 448 GLU 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 C residue 550 LYS Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 169 THR 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 367 LYS Chi-restraints excluded: chain E residue 368 LYS 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 81 ILE Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 362 VAL 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 387 LEU 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: 30.0000 chunk 163 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 262 optimal weight: 3.9990 chunk 271 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 267 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN C 418 ASN D 270 GLN E 2 ASN F 8 HIS F 417 GLN I 151 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.107696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.074217 restraints weight = 41604.705| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.10 r_work: 0.2816 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25215 Z= 0.192 Angle : 0.599 12.514 34421 Z= 0.316 Chirality : 0.044 0.204 3919 Planarity : 0.004 0.062 4023 Dihedral : 17.449 74.370 3953 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.34 % Allowed : 15.39 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.16), residues: 2731 helix: 1.35 (0.13), residues: 1535 sheet: 0.25 (0.30), residues: 250 loop : -0.47 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 683 TYR 0.018 0.002 TYR C 483 PHE 0.028 0.001 PHE C 408 TRP 0.009 0.001 TRP A 539 HIS 0.006 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (25215) covalent geometry : angle 0.59892 / 0.32 (34421) hydrogen bonds : bond 0.04047 / 2.70 ( 1236) hydrogen bonds : angle 4.06254 / 2.86 ( 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 316 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 256 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8728 (mppt) cc_final: 0.8286 (mmpt) REVERT: A 420 GLU cc_start: 0.7531 (pm20) cc_final: 0.7240 (mp0) REVERT: A 432 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8636 (t) REVERT: A 603 ASP cc_start: 0.8489 (p0) cc_final: 0.8077 (p0) REVERT: A 656 ASN cc_start: 0.8673 (t0) cc_final: 0.8207 (t0) REVERT: A 705 ARG cc_start: 0.8708 (mmm-85) cc_final: 0.8442 (mmm160) REVERT: A 844 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: A 902 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8619 (mptp) REVERT: C 361 MET cc_start: 0.5512 (mmm) cc_final: 0.5047 (mmm) REVERT: C 448 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: C 545 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6508 (mtt180) REVERT: C 559 LYS cc_start: 0.7731 (tttm) cc_final: 0.7101 (pttt) REVERT: D 140 GLN cc_start: 0.8956 (mp10) cc_final: 0.8690 (mp10) REVERT: D 151 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8594 (mm-30) REVERT: E 139 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: E 367 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8418 (pttm) REVERT: F 67 GLN cc_start: 0.8442 (mt0) cc_final: 0.7919 (mt0) REVERT: F 100 GLN cc_start: 0.8881 (mt0) cc_final: 0.8635 (mt0) REVERT: F 104 ASN cc_start: 0.8871 (m-40) cc_final: 0.8327 (t0) REVERT: F 287 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7319 (pmt170) REVERT: F 329 PHE cc_start: 0.8952 (m-80) cc_final: 0.8584 (m-10) REVERT: F 358 LYS cc_start: 0.7618 (mtmm) cc_final: 0.7372 (mmmt) REVERT: F 396 GLU cc_start: 0.8373 (mp0) cc_final: 0.7729 (mp0) REVERT: F 414 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7862 (p) REVERT: F 417 GLN cc_start: 0.7805 (mp10) cc_final: 0.7498 (mp-120) REVERT: I 86 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: I 100 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6928 (tmm160) REVERT: I 150 GLN cc_start: 0.8485 (mt0) cc_final: 0.7978 (mt0) outliers start: 60 outliers final: 31 residues processed: 297 average time/residue: 0.7592 time to fit residues: 255.6370 Evaluate side-chains 289 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 867 ASP Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 902 LYS Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 448 GLU 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 C residue 550 LYS Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 169 THR 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 367 LYS Chi-restraints excluded: chain E residue 368 LYS 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 81 ILE 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 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 100 ARG Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 478 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.1491 > 50: distance: 70 - 74: 14.521 distance: 74 - 75: 3.963 distance: 75 - 76: 11.243 distance: 75 - 78: 10.132 distance: 76 - 77: 8.673 distance: 76 - 88: 20.304 distance: 77 - 106: 22.350 distance: 78 - 79: 5.927 distance: 81 - 83: 6.436 distance: 81 - 84: 3.784 distance: 82 - 83: 6.207 distance: 83 - 85: 4.291 distance: 88 - 89: 20.716 distance: 89 - 90: 12.048 distance: 89 - 92: 9.983 distance: 90 - 91: 24.521 distance: 90 - 97: 26.193 distance: 92 - 93: 32.092 distance: 93 - 94: 17.613 distance: 94 - 95: 7.901 distance: 94 - 96: 4.696 distance: 97 - 98: 17.002 distance: 98 - 99: 18.954 distance: 98 - 101: 32.005 distance: 99 - 100: 41.858 distance: 99 - 106: 23.607 distance: 101 - 102: 42.722 distance: 102 - 103: 17.864 distance: 103 - 104: 11.384 distance: 103 - 105: 24.136 distance: 106 - 107: 23.395 distance: 107 - 108: 33.131 distance: 107 - 110: 13.928 distance: 108 - 109: 44.609 distance: 108 - 113: 6.077 distance: 110 - 111: 35.985 distance: 110 - 112: 41.645 distance: 113 - 114: 7.066 distance: 114 - 115: 22.634 distance: 114 - 117: 24.686 distance: 115 - 116: 14.369 distance: 115 - 121: 26.914 distance: 117 - 118: 25.884 distance: 118 - 119: 33.603 distance: 118 - 120: 24.217 distance: 121 - 122: 10.977 distance: 121 - 127: 18.068 distance: 122 - 123: 14.273 distance: 122 - 125: 24.486 distance: 123 - 124: 24.333 distance: 123 - 128: 8.409 distance: 125 - 126: 27.598 distance: 126 - 127: 33.349 distance: 128 - 129: 25.664 distance: 129 - 130: 20.828 distance: 129 - 132: 17.006 distance: 130 - 131: 44.005 distance: 130 - 134: 21.546 distance: 132 - 133: 12.412 distance: 134 - 135: 11.853 distance: 135 - 136: 5.909 distance: 135 - 138: 20.541 distance: 136 - 137: 14.455 distance: 138 - 139: 13.772 distance: 139 - 140: 11.144 distance: 139 - 141: 13.266 distance: 142 - 143: 4.524 distance: 143 - 146: 4.104 distance: 144 - 145: 7.397 distance: 144 - 148: 3.581 distance: 148 - 149: 3.846 distance: 149 - 150: 7.858 distance: 150 - 151: 7.515 distance: 150 - 152: 6.858