Starting phenix.real_space_refine on Sat Jun 21 07:43:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjj_25927/06_2025/7tjj_25927.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjj_25927/06_2025/7tjj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tjj_25927/06_2025/7tjj_25927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjj_25927/06_2025/7tjj_25927.map" model { file = "/net/cci-nas-00/data/ceres_data/7tjj_25927/06_2025/7tjj_25927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjj_25927/06_2025/7tjj_25927.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.15, per 1000 atoms: 0.57 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: 6.12 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 8.89 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: 11.52 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3844 1.31 - 1.44: 7026 1.44 - 1.57: 13990 1.57 - 1.70: 183 1.70 - 1.83: 172 Bond restraints: 25215 Sorted by residual: bond pdb=" C PHE F 98 " pdb=" N ARG F 99 " ideal model delta sigma weight residual 1.334 1.455 -0.120 1.33e-02 5.65e+03 8.18e+01 bond pdb=" C ARG F 99 " pdb=" N GLN F 100 " ideal model delta sigma weight residual 1.335 1.219 0.116 1.38e-02 5.25e+03 7.03e+01 bond pdb=" C ILE I 407 " pdb=" N ALA I 408 " ideal model delta sigma weight residual 1.334 1.242 0.092 1.49e-02 4.50e+03 3.81e+01 bond pdb=" CA ALA A 599 " pdb=" CB ALA A 599 " ideal model delta sigma weight residual 1.534 1.466 0.068 1.60e-02 3.91e+03 1.83e+01 bond pdb=" C THR D 527 " pdb=" O THR D 527 " ideal model delta sigma weight residual 1.235 1.181 0.054 1.33e-02 5.65e+03 1.67e+01 ... (remaining 25210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 34029 3.55 - 7.10: 344 7.10 - 10.65: 43 10.65 - 14.20: 3 14.20 - 17.75: 2 Bond angle restraints: 34421 Sorted by residual: angle pdb=" PA ATP I1001 " pdb=" O3A ATP I1001 " pdb=" PB ATP I1001 " ideal model delta sigma weight residual 136.83 130.02 6.81 1.00e+00 1.00e+00 4.64e+01 angle pdb=" N ARG I 227 " pdb=" CA ARG I 227 " pdb=" C ARG I 227 " ideal model delta sigma weight residual 112.93 106.46 6.47 1.12e+00 7.97e-01 3.33e+01 angle pdb=" N LEU F 29 " pdb=" CA LEU F 29 " pdb=" C LEU F 29 " ideal model delta sigma weight residual 111.82 105.36 6.46 1.16e+00 7.43e-01 3.10e+01 angle pdb=" CA THR A 601 " pdb=" C THR A 601 " pdb=" O THR A 601 " ideal model delta sigma weight residual 121.44 115.22 6.22 1.17e+00 7.31e-01 2.83e+01 angle pdb=" N MET I 225 " pdb=" CA MET I 225 " pdb=" C MET I 225 " ideal model delta sigma weight residual 112.54 106.24 6.30 1.22e+00 6.72e-01 2.67e+01 ... (remaining 34416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 13114 17.90 - 35.79: 1426 35.79 - 53.69: 505 53.69 - 71.59: 123 71.59 - 89.48: 28 Dihedral angle restraints: 15196 sinusoidal: 6910 harmonic: 8286 Sorted by residual: dihedral pdb=" CA ASP C 111 " pdb=" C ASP C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta harmonic sigma weight residual -180.00 -150.55 -29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA PHE B 475 " pdb=" C PHE B 475 " pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta harmonic sigma weight residual 180.00 155.32 24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA LYS E 431 " pdb=" C LYS E 431 " pdb=" N LEU E 432 " pdb=" CA LEU E 432 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 15193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3413 0.080 - 0.161: 458 0.161 - 0.241: 43 0.241 - 0.322: 4 0.322 - 0.402: 1 Chirality restraints: 3919 Sorted by residual: chirality pdb=" CB ILE A 422 " pdb=" CA ILE A 422 " pdb=" CG1 ILE A 422 " pdb=" CG2 ILE A 422 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CA TYR D 524 " pdb=" N TYR D 524 " pdb=" C TYR D 524 " pdb=" CB TYR D 524 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB ILE E 326 " pdb=" CA ILE E 326 " pdb=" CG1 ILE E 326 " pdb=" CG2 ILE E 326 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3916 not shown) Planarity restraints: 4023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 222 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C LEU I 222 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU I 222 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP I 223 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 473 " -0.013 2.00e-02 2.50e+03 2.25e-02 1.01e+01 pdb=" CG TYR B 473 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 473 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR B 473 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 473 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR B 473 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 473 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 473 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 526 " 0.015 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C TRP D 526 " -0.054 2.00e-02 2.50e+03 pdb=" O TRP D 526 " 0.020 2.00e-02 2.50e+03 pdb=" N THR D 527 " 0.019 2.00e-02 2.50e+03 ... (remaining 4020 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 233 2.58 - 3.16: 18862 3.16 - 3.74: 40924 3.74 - 4.32: 57680 4.32 - 4.90: 90236 Nonbonded interactions: 207935 Sorted by model distance: nonbonded pdb=" O3G ATP I1001 " pdb="MG MG I1002 " model vdw 2.003 2.170 nonbonded pdb=" OG1 THR D 109 " pdb="MG MG D1002 " model vdw 2.070 2.170 nonbonded pdb=" O3G ATP D1001 " pdb="MG MG D1002 " model vdw 2.079 2.170 nonbonded pdb="MG MG A1002 " pdb=" O HOH A1124 " model vdw 2.080 2.170 nonbonded pdb=" OG1 THR I 115 " pdb="MG MG I1002 " model vdw 2.084 2.170 ... (remaining 207930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.040 Extract box with map and model: 0.880 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 62.770 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:86.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 25215 Z= 0.282 Angle : 0.942 17.750 34421 Z= 0.522 Chirality : 0.055 0.402 3919 Planarity : 0.007 0.117 4023 Dihedral : 17.517 89.483 9782 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.47 % Allowed : 0.62 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.025 0.003 TRP C 494 HIS 0.016 0.001 HIS C 74 PHE 0.044 0.003 PHE B 437 TYR 0.047 0.003 TYR B 473 ARG 0.021 0.001 ARG A 705 Details of bonding type rmsd hydrogen bonds : bond 0.15191 ( 1236) hydrogen bonds : angle 6.42351 ( 3457) covalent geometry : bond 0.00560 (25215) covalent geometry : angle 0.94243 (34421) *********************** 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 : 3.571 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: 1.7578 time to fit residues: 1101.6989 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 : 2.791 ------------------------------------------------------------------------------- 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 240 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 145 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 258 optimal weight: 0.6980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 774 HIS C 69 HIS C 190 ASN C 418 ASN D 76 GLN D 491 GLN E 248 HIS F 5 GLN F 45 ASN F 51 GLN F 100 GLN F 333 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.076057 restraints weight = 41706.894| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.13 r_work: 0.2850 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25215 Z= 0.181 Angle : 0.601 11.825 34421 Z= 0.324 Chirality : 0.042 0.147 3919 Planarity : 0.005 0.062 4023 Dihedral : 17.720 89.708 4085 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.99 % Allowed : 11.22 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.15), residues: 2731 helix: 0.39 (0.13), residues: 1526 sheet: 0.37 (0.29), residues: 260 loop : -0.66 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 305 HIS 0.007 0.001 HIS F 8 PHE 0.018 0.001 PHE F 98 TYR 0.021 0.002 TYR A 721 ARG 0.010 0.001 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 1236) hydrogen bonds : angle 4.42500 ( 3457) covalent geometry : bond 0.00425 (25215) covalent geometry : angle 0.60062 (34421) *********************** 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 368 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 317 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 SER cc_start: 0.9017 (m) cc_final: 0.8485 (t) REVERT: A 603 ASP cc_start: 0.8439 (p0) cc_final: 0.8075 (p0) REVERT: A 656 ASN cc_start: 0.8694 (t0) cc_final: 0.8438 (t0) REVERT: A 687 ASP cc_start: 0.8350 (m-30) cc_final: 0.8137 (m-30) REVERT: A 705 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8367 (mmm160) REVERT: C 361 MET cc_start: 0.5375 (mmm) cc_final: 0.4828 (mmm) REVERT: C 448 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8156 (pt0) REVERT: C 559 LYS cc_start: 0.7720 (tttm) cc_final: 0.7099 (tttt) REVERT: D 124 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8733 (ttpp) REVERT: D 151 GLU cc_start: 0.8834 (tp30) cc_final: 0.8308 (mm-30) REVERT: E 139 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: E 177 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8572 (tp40) REVERT: E 346 ASP cc_start: 0.7695 (m-30) cc_final: 0.7492 (m-30) REVERT: E 439 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8306 (pttt) REVERT: E 461 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6609 (tm-30) REVERT: F 51 GLN cc_start: 0.8584 (tt0) cc_final: 0.8382 (tt0) REVERT: F 67 GLN cc_start: 0.8419 (mt0) cc_final: 0.8140 (mt0) REVERT: F 74 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7326 (ptp) REVERT: F 100 GLN cc_start: 0.8780 (mt0) cc_final: 0.8454 (mt0) REVERT: F 104 ASN cc_start: 0.8904 (m-40) cc_final: 0.8268 (t0) REVERT: F 287 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7334 (pmt170) REVERT: F 307 ASN cc_start: 0.8767 (m110) cc_final: 0.8419 (m-40) REVERT: F 344 HIS cc_start: 0.6774 (m90) cc_final: 0.6570 (m90) REVERT: F 358 LYS cc_start: 0.7688 (mtmm) cc_final: 0.7395 (mtpp) REVERT: F 396 GLU cc_start: 0.8195 (mp0) cc_final: 0.7542 (mp0) REVERT: I 86 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: I 150 GLN cc_start: 0.8407 (mt0) cc_final: 0.7981 (mt0) REVERT: I 503 THR cc_start: 0.9258 (m) cc_final: 0.9045 (p) outliers start: 51 outliers final: 15 residues processed: 348 average time/residue: 1.6138 time to fit residues: 635.7030 Evaluate side-chains 281 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 258 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 457 ASP 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 D residue 86 ILE Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 439 LYS Chi-restraints excluded: chain E residue 461 GLU Chi-restraints excluded: chain F residue 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 I residue 86 GLU Chi-restraints excluded: chain I residue 449 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 227 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 270 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN C 53 ASN C 418 ASN F 8 HIS F 41 ASN F 318 GLN I 171 ASN I 183 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.077306 restraints weight = 41419.213| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.12 r_work: 0.2878 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2515 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= 0.120 Angle : 0.532 11.716 34421 Z= 0.285 Chirality : 0.040 0.138 3919 Planarity : 0.004 0.060 4023 Dihedral : 17.521 88.830 4080 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.99 % Allowed : 12.55 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2731 helix: 1.01 (0.13), residues: 1532 sheet: 0.32 (0.29), residues: 256 loop : -0.49 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 539 HIS 0.012 0.001 HIS F 8 PHE 0.021 0.001 PHE F 111 TYR 0.017 0.001 TYR A 721 ARG 0.008 0.001 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 1236) hydrogen bonds : angle 4.05657 ( 3457) covalent geometry : bond 0.00269 (25215) covalent geometry : angle 0.53165 (34421) *********************** 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: 51 poor density : 290 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 SER cc_start: 0.9054 (m) cc_final: 0.8563 (t) REVERT: A 503 ARG cc_start: 0.8654 (mtm-85) cc_final: 0.8391 (mpp80) REVERT: A 603 ASP cc_start: 0.8456 (p0) cc_final: 0.7998 (p0) REVERT: A 702 ASP cc_start: 0.8323 (t0) cc_final: 0.8028 (t0) REVERT: A 705 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.8339 (mmm160) REVERT: A 867 ASP cc_start: 0.8671 (p0) cc_final: 0.8441 (OUTLIER) REVERT: A 875 ASP cc_start: 0.8681 (m-30) cc_final: 0.8449 (m-30) REVERT: C 361 MET cc_start: 0.5195 (mmm) cc_final: 0.4688 (mmm) REVERT: C 392 PHE cc_start: 0.8615 (t80) cc_final: 0.8106 (t80) REVERT: C 448 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: C 559 LYS cc_start: 0.7673 (tttm) cc_final: 0.7068 (tttt) REVERT: D 124 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8735 (ttpp) REVERT: D 140 GLN cc_start: 0.8959 (mp10) cc_final: 0.8723 (mp10) REVERT: D 151 GLU cc_start: 0.8826 (tp30) cc_final: 0.8551 (mm-30) REVERT: D 155 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: E 139 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8026 (mp10) REVERT: E 170 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8819 (mtt) REVERT: E 177 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8673 (tp40) REVERT: E 346 ASP cc_start: 0.7755 (m-30) cc_final: 0.7548 (m-30) REVERT: F 77 LEU cc_start: 0.8363 (tp) cc_final: 0.7961 (pp) REVERT: F 104 ASN cc_start: 0.8890 (m-40) cc_final: 0.8293 (t0) REVERT: F 283 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7390 (tp30) REVERT: F 287 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7197 (pmt170) REVERT: F 332 PHE cc_start: 0.7683 (m-10) cc_final: 0.7469 (m-10) REVERT: F 358 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7437 (mmmm) REVERT: F 396 GLU cc_start: 0.8301 (mp0) cc_final: 0.7681 (mp0) REVERT: I 94 LYS cc_start: 0.8756 (mmpt) cc_final: 0.8434 (mmpt) REVERT: I 96 ILE cc_start: 0.8929 (mp) cc_final: 0.8724 (mp) REVERT: I 100 ARG cc_start: 0.7489 (ttp-110) cc_final: 0.6765 (tmm160) REVERT: I 150 GLN cc_start: 0.8428 (mt0) cc_final: 0.7962 (mt0) REVERT: I 261 MET cc_start: 0.8997 (mtm) cc_final: 0.8510 (mtm) REVERT: I 503 THR cc_start: 0.9262 (m) cc_final: 0.9054 (p) outliers start: 51 outliers final: 12 residues processed: 322 average time/residue: 1.6296 time to fit residues: 598.8712 Evaluate side-chains 271 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 254 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 274 VAL Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 409 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 37 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 243 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 242 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 270 GLN D 375 ASN F 8 HIS F 407 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.106564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.072910 restraints weight = 42051.160| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.13 r_work: 0.2792 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 25215 Z= 0.246 Angle : 0.609 12.766 34421 Z= 0.324 Chirality : 0.044 0.151 3919 Planarity : 0.004 0.062 4023 Dihedral : 17.713 89.263 4077 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.30 % Allowed : 13.95 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2731 helix: 1.14 (0.13), residues: 1530 sheet: 0.31 (0.30), residues: 250 loop : -0.48 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 443 HIS 0.013 0.001 HIS F 8 PHE 0.033 0.002 PHE F 329 TYR 0.021 0.002 TYR C 483 ARG 0.009 0.001 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 1236) hydrogen bonds : angle 4.13623 ( 3457) covalent geometry : bond 0.00585 (25215) covalent geometry : angle 0.60925 (34421) *********************** 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 318 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 259 time to evaluate : 2.609 Fit side-chains revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8729 (mppt) cc_final: 0.8284 (mmpt) REVERT: A 420 GLU cc_start: 0.7550 (mp0) cc_final: 0.7186 (pm20) REVERT: A 432 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8637 (t) REVERT: A 603 ASP cc_start: 0.8522 (p0) cc_final: 0.8171 (p0) REVERT: A 705 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8439 (mmm160) REVERT: A 844 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: C 286 ASP cc_start: 0.8343 (t0) cc_final: 0.8016 (t0) REVERT: C 361 MET cc_start: 0.5302 (mmm) cc_final: 0.4817 (mmm) REVERT: C 392 PHE cc_start: 0.8570 (t80) cc_final: 0.7992 (t80) REVERT: C 448 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: C 559 LYS cc_start: 0.7781 (tttm) cc_final: 0.7153 (tttt) REVERT: D 124 LYS cc_start: 0.8977 (ttmm) cc_final: 0.8774 (ttpt) REVERT: D 140 GLN cc_start: 0.8977 (mp10) cc_final: 0.8741 (mp10) REVERT: D 151 GLU cc_start: 0.8825 (tp30) cc_final: 0.8296 (mm-30) REVERT: E 139 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8005 (mp10) REVERT: E 177 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8760 (tp40) REVERT: E 346 ASP cc_start: 0.7889 (m-30) cc_final: 0.7677 (m-30) REVERT: E 461 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6655 (tm-30) REVERT: F 77 LEU cc_start: 0.8332 (tp) cc_final: 0.7981 (pp) REVERT: F 104 ASN cc_start: 0.8855 (m-40) cc_final: 0.8313 (t0) REVERT: F 283 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7402 (tp30) REVERT: F 287 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7278 (pmt170) REVERT: F 329 PHE cc_start: 0.8991 (m-80) cc_final: 0.8627 (m-10) REVERT: F 358 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7370 (mmmt) REVERT: F 396 GLU cc_start: 0.8403 (mp0) cc_final: 0.7800 (mp0) REVERT: I 96 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8712 (mp) REVERT: I 100 ARG cc_start: 0.7530 (ttp-110) cc_final: 0.7068 (ttp80) REVERT: I 488 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7847 (mtpp) outliers start: 59 outliers final: 24 residues processed: 297 average time/residue: 1.5881 time to fit residues: 534.9524 Evaluate side-chains 271 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain 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 177 GLN Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 461 GLU 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 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 96 ILE Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 478 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 95 optimal weight: 0.0050 chunk 132 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 210 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 ASN D 270 GLN E 238 ASN F 318 GLN I 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.076409 restraints weight = 41919.180| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.11 r_work: 0.2862 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25215 Z= 0.111 Angle : 0.523 11.506 34421 Z= 0.281 Chirality : 0.039 0.134 3919 Planarity : 0.003 0.059 4023 Dihedral : 17.409 89.777 4077 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.71 % Allowed : 15.43 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.16), residues: 2731 helix: 1.45 (0.14), residues: 1535 sheet: 0.28 (0.30), residues: 255 loop : -0.35 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 866 HIS 0.025 0.001 HIS F 8 PHE 0.030 0.001 PHE F 329 TYR 0.022 0.001 TYR I 85 ARG 0.011 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 1236) hydrogen bonds : angle 3.86954 ( 3457) covalent geometry : bond 0.00243 (25215) covalent geometry : angle 0.52303 (34421) *********************** 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 313 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 269 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8672 (mppt) cc_final: 0.8278 (mmpt) REVERT: A 420 GLU cc_start: 0.7551 (mp0) cc_final: 0.7190 (pm20) REVERT: A 432 SER cc_start: 0.9016 (m) cc_final: 0.8623 (t) REVERT: A 603 ASP cc_start: 0.8527 (p0) cc_final: 0.8119 (p0) REVERT: A 702 ASP cc_start: 0.8259 (t0) cc_final: 0.8034 (t0) REVERT: A 705 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.8390 (mmm160) REVERT: A 884 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8624 (mmm) REVERT: B 484 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8062 (mt-10) REVERT: C 286 ASP cc_start: 0.8327 (t0) cc_final: 0.7995 (t0) REVERT: C 306 MET cc_start: 0.8701 (mtp) cc_final: 0.8498 (ttt) REVERT: C 361 MET cc_start: 0.5378 (mmm) cc_final: 0.4942 (mmm) REVERT: C 392 PHE cc_start: 0.8507 (t80) cc_final: 0.8082 (t80) REVERT: C 448 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: C 559 LYS cc_start: 0.7744 (tttm) cc_final: 0.7132 (tttt) REVERT: D 140 GLN cc_start: 0.8949 (mp10) cc_final: 0.8700 (mp10) REVERT: D 151 GLU cc_start: 0.8799 (tp30) cc_final: 0.8494 (mm-30) REVERT: D 155 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7756 (mm-40) REVERT: E 139 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: E 346 ASP cc_start: 0.7828 (m-30) cc_final: 0.7608 (m-30) REVERT: E 437 MET cc_start: 0.7859 (tpp) cc_final: 0.7488 (ptm) REVERT: F 77 LEU cc_start: 0.8292 (tp) cc_final: 0.7980 (pp) REVERT: F 104 ASN cc_start: 0.8778 (m-40) cc_final: 0.8329 (t0) REVERT: F 283 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7503 (tp30) REVERT: F 287 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7262 (pmt170) REVERT: F 329 PHE cc_start: 0.9002 (m-80) cc_final: 0.8677 (m-10) REVERT: F 358 LYS cc_start: 0.7638 (mtmm) cc_final: 0.7384 (mmmm) REVERT: F 373 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7950 (tp) REVERT: F 396 GLU cc_start: 0.8417 (mp0) cc_final: 0.7803 (mp0) REVERT: I 94 LYS cc_start: 0.8681 (mmpt) cc_final: 0.8376 (mmpt) REVERT: I 100 ARG cc_start: 0.7514 (ttp-110) cc_final: 0.6822 (tmm160) REVERT: I 227 ARG cc_start: 0.8098 (mmm160) cc_final: 0.7883 (mmm160) outliers start: 44 outliers final: 12 residues processed: 298 average time/residue: 1.6687 time to fit residues: 567.1170 Evaluate side-chains 266 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 248 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain I residue 202 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 117 optimal weight: 2.9990 chunk 230 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 271 optimal weight: 7.9990 chunk 248 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 270 GLN F 8 HIS F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.107967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.075297 restraints weight = 41435.979| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.03 r_work: 0.2840 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25215 Z= 0.151 Angle : 0.541 13.996 34421 Z= 0.288 Chirality : 0.041 0.136 3919 Planarity : 0.003 0.059 4023 Dihedral : 17.426 89.516 4077 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.18 % Allowed : 15.74 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.16), residues: 2731 helix: 1.54 (0.14), residues: 1535 sheet: 0.36 (0.30), residues: 250 loop : -0.32 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 539 HIS 0.011 0.001 HIS F 8 PHE 0.027 0.001 PHE F 345 TYR 0.018 0.001 TYR C 528 ARG 0.006 0.000 ARG F 400 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 1236) hydrogen bonds : angle 3.88209 ( 3457) covalent geometry : bond 0.00355 (25215) covalent geometry : angle 0.54054 (34421) *********************** 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 305 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 249 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7529 (mp0) cc_final: 0.7152 (pm20) REVERT: A 432 SER cc_start: 0.9035 (m) cc_final: 0.8640 (t) REVERT: A 603 ASP cc_start: 0.8538 (p0) cc_final: 0.8194 (p0) REVERT: A 702 ASP cc_start: 0.8398 (t0) cc_final: 0.8098 (t0) REVERT: A 705 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.8327 (mmm160) REVERT: A 844 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: B 484 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8041 (mt-10) REVERT: C 286 ASP cc_start: 0.8316 (t0) cc_final: 0.8106 (t0) REVERT: C 306 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8466 (ttt) REVERT: C 361 MET cc_start: 0.5350 (mmm) cc_final: 0.4844 (mmm) REVERT: C 392 PHE cc_start: 0.8498 (t80) cc_final: 0.8060 (t80) REVERT: C 448 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8238 (pt0) REVERT: C 559 LYS cc_start: 0.7755 (tttm) cc_final: 0.7113 (pttp) REVERT: D 140 GLN cc_start: 0.8958 (mp10) cc_final: 0.8701 (mp10) REVERT: D 151 GLU cc_start: 0.8795 (tp30) cc_final: 0.8592 (mm-30) REVERT: E 139 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: E 230 ASP cc_start: 0.8006 (p0) cc_final: 0.7746 (t0) REVERT: E 346 ASP cc_start: 0.7846 (m-30) cc_final: 0.7618 (m-30) REVERT: E 437 MET cc_start: 0.7880 (tpp) cc_final: 0.7515 (ptt) REVERT: F 77 LEU cc_start: 0.8299 (tp) cc_final: 0.7980 (pp) REVERT: F 104 ASN cc_start: 0.8754 (m-40) cc_final: 0.8320 (t0) REVERT: F 279 LYS cc_start: 0.8160 (mmpt) cc_final: 0.7399 (mmtt) REVERT: F 283 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7507 (tp30) REVERT: F 287 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7282 (pmt170) REVERT: F 329 PHE cc_start: 0.8996 (m-80) cc_final: 0.8646 (m-10) REVERT: F 358 LYS cc_start: 0.7675 (mtmm) cc_final: 0.7367 (mmmm) REVERT: F 373 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7951 (tt) REVERT: F 396 GLU cc_start: 0.8434 (mp0) cc_final: 0.7810 (mp0) REVERT: I 94 LYS cc_start: 0.8696 (mmpt) cc_final: 0.8400 (mmpt) REVERT: I 100 ARG cc_start: 0.7510 (ttp-110) cc_final: 0.6805 (tmm160) REVERT: I 227 ARG cc_start: 0.8069 (mmm160) cc_final: 0.7852 (mmm160) outliers start: 56 outliers final: 23 residues processed: 286 average time/residue: 1.6299 time to fit residues: 530.8785 Evaluate side-chains 277 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 2.653 ------------------------------------------------------------------------------- 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 271 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 478 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 20 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 241 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 270 GLN F 4 GLN F 8 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.108815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.075570 restraints weight = 41885.680| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.11 r_work: 0.2844 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.3068 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= 0.130 Angle : 0.530 13.376 34421 Z= 0.282 Chirality : 0.040 0.133 3919 Planarity : 0.003 0.058 4023 Dihedral : 17.352 89.579 4077 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.83 % Allowed : 16.17 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.16), residues: 2731 helix: 1.60 (0.14), residues: 1538 sheet: 0.31 (0.30), residues: 255 loop : -0.28 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 539 HIS 0.024 0.001 HIS F 8 PHE 0.025 0.001 PHE C 408 TYR 0.019 0.001 TYR C 528 ARG 0.013 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 1236) hydrogen bonds : angle 3.82728 ( 3457) covalent geometry : bond 0.00301 (25215) covalent geometry : angle 0.53006 (34421) *********************** 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 299 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 252 time to evaluate : 3.318 Fit side-chains revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7518 (mp0) cc_final: 0.7130 (pm20) REVERT: A 432 SER cc_start: 0.8993 (m) cc_final: 0.8643 (t) REVERT: A 603 ASP cc_start: 0.8568 (p0) cc_final: 0.8219 (p0) REVERT: A 678 ARG cc_start: 0.8168 (mtp180) cc_final: 0.7584 (ttt180) REVERT: A 702 ASP cc_start: 0.8324 (t0) cc_final: 0.8096 (t0) REVERT: A 705 ARG cc_start: 0.8684 (mmm-85) cc_final: 0.8391 (mmm160) REVERT: A 844 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: B 484 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8079 (mt-10) REVERT: C 55 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: C 306 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8485 (ttt) REVERT: C 361 MET cc_start: 0.5368 (mmm) cc_final: 0.4859 (mmm) REVERT: C 392 PHE cc_start: 0.8523 (t80) cc_final: 0.8132 (t80) REVERT: C 448 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8265 (pt0) REVERT: C 449 TYR cc_start: 0.8205 (m-80) cc_final: 0.7950 (m-80) REVERT: C 559 LYS cc_start: 0.7778 (tttm) cc_final: 0.7157 (pttp) REVERT: D 140 GLN cc_start: 0.8976 (mp10) cc_final: 0.8724 (mp10) REVERT: D 151 GLU cc_start: 0.8809 (tp30) cc_final: 0.8608 (mm-30) REVERT: E 139 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: E 230 ASP cc_start: 0.8033 (p0) cc_final: 0.7688 (t0) REVERT: E 346 ASP cc_start: 0.7857 (m-30) cc_final: 0.7635 (m-30) REVERT: E 368 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7856 (mptt) REVERT: E 437 MET cc_start: 0.8066 (tpp) cc_final: 0.7687 (ptt) REVERT: F 77 LEU cc_start: 0.8294 (tp) cc_final: 0.7938 (pp) REVERT: F 104 ASN cc_start: 0.8720 (m-40) cc_final: 0.8314 (t0) REVERT: F 283 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7491 (tp30) REVERT: F 287 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7282 (pmt170) REVERT: F 329 PHE cc_start: 0.9023 (m-80) cc_final: 0.8654 (m-80) REVERT: F 358 LYS cc_start: 0.7584 (mtmm) cc_final: 0.7249 (mmmm) REVERT: F 373 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7957 (tt) REVERT: F 396 GLU cc_start: 0.8433 (mp0) cc_final: 0.7814 (mp0) REVERT: I 94 LYS cc_start: 0.8740 (mmpt) cc_final: 0.8425 (mmpt) REVERT: I 100 ARG cc_start: 0.7526 (ttp-110) cc_final: 0.6822 (tmm160) REVERT: I 227 ARG cc_start: 0.8054 (mmm160) cc_final: 0.7810 (mmm160) outliers start: 47 outliers final: 20 residues processed: 282 average time/residue: 2.0504 time to fit residues: 658.9463 Evaluate side-chains 279 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 251 time to evaluate : 2.529 ------------------------------------------------------------------------------- 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 880 PHE Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 226 VAL 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 F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 478 CYS Chi-restraints excluded: chain I residue 482 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 271 optimal weight: 8.9990 chunk 139 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 263 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 204 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 270 GLN F 8 HIS F 45 ASN F 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.110013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.076913 restraints weight = 41574.552| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.10 r_work: 0.2875 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25215 Z= 0.110 Angle : 0.519 13.877 34421 Z= 0.276 Chirality : 0.039 0.131 3919 Planarity : 0.003 0.057 4023 Dihedral : 17.133 89.690 4077 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.56 % Allowed : 16.68 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.16), residues: 2731 helix: 1.72 (0.14), residues: 1537 sheet: 0.42 (0.31), residues: 246 loop : -0.24 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 539 HIS 0.015 0.001 HIS F 8 PHE 0.032 0.001 PHE F 345 TYR 0.018 0.001 TYR C 528 ARG 0.014 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 1236) hydrogen bonds : angle 3.74140 ( 3457) covalent geometry : bond 0.00247 (25215) covalent geometry : angle 0.51864 (34421) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8785 (mppt) cc_final: 0.8243 (mmpt) REVERT: A 420 GLU cc_start: 0.7496 (mp0) cc_final: 0.7118 (pm20) REVERT: A 432 SER cc_start: 0.8965 (m) cc_final: 0.8651 (t) REVERT: A 603 ASP cc_start: 0.8587 (p0) cc_final: 0.8199 (p0) REVERT: A 678 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7614 (ttt180) REVERT: A 702 ASP cc_start: 0.8190 (t0) cc_final: 0.7961 (t0) REVERT: A 705 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8402 (mmm160) REVERT: A 844 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: B 484 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8009 (mt-10) REVERT: C 119 LYS cc_start: 0.7764 (mmtm) cc_final: 0.7555 (mmpt) REVERT: C 361 MET cc_start: 0.5271 (mmm) cc_final: 0.4813 (mmm) REVERT: C 392 PHE cc_start: 0.8489 (t80) cc_final: 0.8178 (t80) REVERT: C 448 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: C 449 TYR cc_start: 0.8193 (m-80) cc_final: 0.7936 (m-80) REVERT: C 559 LYS cc_start: 0.7773 (tttm) cc_final: 0.7155 (pttp) REVERT: D 140 GLN cc_start: 0.8955 (mp10) cc_final: 0.8698 (mp10) REVERT: D 151 GLU cc_start: 0.8810 (tp30) cc_final: 0.8397 (mm-30) REVERT: D 155 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7864 (mm-40) REVERT: E 139 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: E 275 LYS cc_start: 0.7210 (mmtt) cc_final: 0.6653 (mmtm) REVERT: E 280 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: E 346 ASP cc_start: 0.7836 (m-30) cc_final: 0.7595 (m-30) REVERT: E 368 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7824 (mptt) REVERT: E 437 MET cc_start: 0.8069 (tpp) cc_final: 0.7704 (ptt) REVERT: F 77 LEU cc_start: 0.8261 (tp) cc_final: 0.7880 (pp) REVERT: F 104 ASN cc_start: 0.8586 (m-40) cc_final: 0.8265 (t0) REVERT: F 279 LYS cc_start: 0.8172 (mmpt) cc_final: 0.7290 (mmtt) REVERT: F 283 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7633 (tp30) REVERT: F 287 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7290 (pmt170) REVERT: F 329 PHE cc_start: 0.8981 (m-80) cc_final: 0.8660 (m-80) REVERT: F 358 LYS cc_start: 0.7584 (mtmm) cc_final: 0.7216 (mmmm) REVERT: F 373 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7844 (tp) REVERT: F 396 GLU cc_start: 0.8443 (mp0) cc_final: 0.7925 (tp30) REVERT: I 94 LYS cc_start: 0.8721 (mmpt) cc_final: 0.8419 (mmpt) REVERT: I 100 ARG cc_start: 0.7590 (ttp-110) cc_final: 0.6922 (tmm160) outliers start: 40 outliers final: 16 residues processed: 291 average time/residue: 1.6865 time to fit residues: 557.0278 Evaluate side-chains 270 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 844 GLU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain I residue 478 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 109 optimal weight: 10.0000 chunk 74 optimal weight: 0.0370 chunk 146 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 271 optimal weight: 0.8980 chunk 213 optimal weight: 0.7980 chunk 269 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN D 270 GLN F 8 HIS F 67 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.110086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.076988 restraints weight = 41924.724| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.10 r_work: 0.2873 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25215 Z= 0.116 Angle : 0.534 14.245 34421 Z= 0.283 Chirality : 0.040 0.163 3919 Planarity : 0.003 0.061 4023 Dihedral : 17.101 89.935 4077 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.29 % Allowed : 17.58 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.16), residues: 2731 helix: 1.76 (0.14), residues: 1542 sheet: 0.48 (0.31), residues: 246 loop : -0.20 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 539 HIS 0.015 0.001 HIS F 8 PHE 0.028 0.001 PHE C 408 TYR 0.019 0.001 TYR C 528 ARG 0.014 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 1236) hydrogen bonds : angle 3.73054 ( 3457) covalent geometry : bond 0.00266 (25215) covalent geometry : angle 0.53407 (34421) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.8778 (mppt) cc_final: 0.8235 (mmpt) REVERT: A 420 GLU cc_start: 0.7491 (mp0) cc_final: 0.7113 (pm20) REVERT: A 432 SER cc_start: 0.8950 (m) cc_final: 0.8646 (t) REVERT: A 503 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.8254 (mpp80) REVERT: A 603 ASP cc_start: 0.8591 (p0) cc_final: 0.8226 (p0) REVERT: A 678 ARG cc_start: 0.8156 (mtp180) cc_final: 0.7575 (ttt180) REVERT: A 702 ASP cc_start: 0.8217 (t0) cc_final: 0.7961 (t0) REVERT: A 705 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8391 (mmm160) REVERT: A 884 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8599 (mmm) REVERT: A 899 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: B 484 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7982 (mt-10) REVERT: C 268 VAL cc_start: 0.9039 (t) cc_final: 0.8786 (m) REVERT: C 361 MET cc_start: 0.5205 (mmm) cc_final: 0.4782 (mmm) REVERT: C 392 PHE cc_start: 0.8500 (t80) cc_final: 0.8215 (t80) REVERT: C 448 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: C 449 TYR cc_start: 0.8173 (m-80) cc_final: 0.7896 (m-80) REVERT: C 559 LYS cc_start: 0.7787 (tttm) cc_final: 0.7170 (pttp) REVERT: D 140 GLN cc_start: 0.8957 (mp10) cc_final: 0.8707 (mp10) REVERT: D 151 GLU cc_start: 0.8817 (tp30) cc_final: 0.8464 (mm-30) REVERT: D 155 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7629 (mm-40) REVERT: E 139 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7967 (mp10) REVERT: E 209 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8472 (mp) REVERT: E 346 ASP cc_start: 0.7869 (m-30) cc_final: 0.7647 (m-30) REVERT: E 368 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7826 (mptt) REVERT: E 437 MET cc_start: 0.8077 (tpp) cc_final: 0.7684 (ptt) REVERT: F 104 ASN cc_start: 0.8605 (m-40) cc_final: 0.8280 (t0) REVERT: F 279 LYS cc_start: 0.8091 (mmpt) cc_final: 0.7385 (mmtt) REVERT: F 283 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7643 (tp30) REVERT: F 287 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7295 (pmt170) REVERT: F 329 PHE cc_start: 0.8966 (m-80) cc_final: 0.8665 (m-80) REVERT: F 358 LYS cc_start: 0.7579 (mtmm) cc_final: 0.7205 (mmmm) REVERT: F 373 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7857 (tp) REVERT: F 396 GLU cc_start: 0.8443 (mp0) cc_final: 0.7931 (tp30) REVERT: I 94 LYS cc_start: 0.8753 (mmpt) cc_final: 0.8452 (mmpt) REVERT: I 100 ARG cc_start: 0.7616 (ttp-110) cc_final: 0.6966 (tmm160) REVERT: I 202 MET cc_start: 0.8530 (ttp) cc_final: 0.8329 (ppp) REVERT: I 343 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8603 (mp0) outliers start: 33 outliers final: 15 residues processed: 272 average time/residue: 1.6126 time to fit residues: 499.2758 Evaluate side-chains 263 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 478 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 151 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 243 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 chunk 182 optimal weight: 3.9990 chunk 247 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN C 250 ASN D 155 GLN D 270 GLN E 238 ASN F 8 HIS F 45 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.106374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.073596 restraints weight = 41686.692| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.02 r_work: 0.2807 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.3217 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 : 0.607 13.857 34421 Z= 0.319 Chirality : 0.043 0.145 3919 Planarity : 0.004 0.065 4023 Dihedral : 17.507 89.041 4077 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.29 % Allowed : 17.77 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 2731 helix: 1.61 (0.13), residues: 1541 sheet: 0.41 (0.30), residues: 250 loop : -0.24 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 443 HIS 0.015 0.001 HIS F 8 PHE 0.034 0.002 PHE F 345 TYR 0.019 0.002 TYR C 483 ARG 0.015 0.001 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 1236) hydrogen bonds : angle 3.94971 ( 3457) covalent geometry : bond 0.00519 (25215) covalent geometry : angle 0.60663 (34421) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5462 Ramachandran restraints generated. 2731 Oldfield, 0 Emsley, 2731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 2.889 Fit side-chains REVERT: A 380 LYS cc_start: 0.8839 (mppt) cc_final: 0.8267 (mmpt) REVERT: A 420 GLU cc_start: 0.7428 (mp0) cc_final: 0.7181 (pm20) REVERT: A 432 SER cc_start: 0.8935 (m) cc_final: 0.8676 (t) REVERT: A 503 ARG cc_start: 0.8603 (mtm-85) cc_final: 0.8264 (mpp80) REVERT: A 603 ASP cc_start: 0.8632 (p0) cc_final: 0.8173 (p0) REVERT: A 678 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7760 (ttp-170) REVERT: A 705 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8433 (mmm160) REVERT: A 884 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8624 (mmm) REVERT: A 899 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: B 484 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7978 (mt-10) REVERT: C 55 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: C 361 MET cc_start: 0.5424 (mmm) cc_final: 0.5025 (mmm) REVERT: C 392 PHE cc_start: 0.8516 (t80) cc_final: 0.8140 (t80) REVERT: C 448 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8467 (pt0) REVERT: C 559 LYS cc_start: 0.7854 (tttm) cc_final: 0.7237 (pttp) REVERT: D 140 GLN cc_start: 0.9009 (mp10) cc_final: 0.8753 (mp10) REVERT: E 139 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: E 209 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8550 (mp) REVERT: E 230 ASP cc_start: 0.8090 (p0) cc_final: 0.7786 (t0) REVERT: E 346 ASP cc_start: 0.7926 (m-30) cc_final: 0.7680 (m-30) REVERT: E 368 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7890 (mptt) REVERT: F 279 LYS cc_start: 0.8162 (mmpt) cc_final: 0.7386 (mmtt) REVERT: F 283 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7653 (tp30) REVERT: F 287 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7292 (pmt170) REVERT: F 329 PHE cc_start: 0.9010 (m-80) cc_final: 0.8635 (m-80) REVERT: F 358 LYS cc_start: 0.7539 (mtmm) cc_final: 0.7153 (mmmm) REVERT: F 373 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7944 (tp) REVERT: F 396 GLU cc_start: 0.8390 (mp0) cc_final: 0.7954 (tp30) REVERT: I 100 ARG cc_start: 0.7554 (ttp-110) cc_final: 0.7126 (ttp80) REVERT: I 202 MET cc_start: 0.8604 (ttp) cc_final: 0.8395 (ppp) REVERT: I 261 MET cc_start: 0.8929 (mtm) cc_final: 0.8501 (mtm) outliers start: 33 outliers final: 16 residues processed: 260 average time/residue: 1.6062 time to fit residues: 474.5487 Evaluate side-chains 253 residues out of total 2566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 880 PHE Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain F residue 8 HIS Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 VAL Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain I residue 478 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 248 optimal weight: 10.0000 chunk 284 optimal weight: 0.9980 chunk 242 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 chunk 186 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 219 optimal weight: 20.0000 chunk 146 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 270 GLN F 8 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.107718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.074405 restraints weight = 41793.411| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.09 r_work: 0.2823 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25215 Z= 0.161 Angle : 0.580 13.619 34421 Z= 0.305 Chirality : 0.042 0.163 3919 Planarity : 0.003 0.064 4023 Dihedral : 17.440 89.066 4077 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.21 % Allowed : 18.04 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.16), residues: 2731 helix: 1.65 (0.13), residues: 1537 sheet: 0.33 (0.30), residues: 246 loop : -0.23 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 443 HIS 0.017 0.001 HIS F 8 PHE 0.031 0.001 PHE C 408 TYR 0.019 0.001 TYR C 528 ARG 0.015 0.001 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 1236) hydrogen bonds : angle 3.88199 ( 3457) covalent geometry : bond 0.00380 (25215) covalent geometry : angle 0.57995 (34421) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22482.92 seconds wall clock time: 391 minutes 32.11 seconds (23492.11 seconds total)