Starting phenix.real_space_refine on Thu Mar 5 18:42:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjk_25928/03_2026/7tjk_25928.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjk_25928/03_2026/7tjk_25928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tjk_25928/03_2026/7tjk_25928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjk_25928/03_2026/7tjk_25928.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tjk_25928/03_2026/7tjk_25928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjk_25928/03_2026/7tjk_25928.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 93 5.49 5 Mg 4 5.21 5 S 107 5.16 5 C 15504 2.51 5 N 4101 2.21 5 O 4859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24668 Number of models: 1 Model: "" Number of chains: 21 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: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2057 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} 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: 3588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3588 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 21, 'TRANS': 415} Chain breaks: 3 Chain: "F" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2163 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 7, 'TRANS': 254} 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: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2995 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 14, 'TRANS': 361} Chain breaks: 7 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 5.28, per 1000 atoms: 0.21 Number of scatterers: 24668 At special positions: 0 Unit cell: (116.96, 138.46, 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 107 16.00 P 93 15.00 Mg 4 11.99 O 4859 8.00 N 4101 7.00 C 15504 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: 2.01 Conformation dependent library (CDL) restraints added in 880.4 milliseconds 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5406 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 13 sheets defined 62.3% alpha, 7.8% beta 41 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'A' and resid 374 through 378 removed outlier: 3.513A pdb=" N LYS A 377 " --> pdb=" O PRO A 374 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 378 " --> pdb=" O PHE A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 378' Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.582A pdb=" N LEU A 391 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.927A pdb=" N GLY A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 4.256A pdb=" N LYS A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 484 through 502 removed outlier: 3.520A pdb=" N GLN A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) 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 534 removed outlier: 3.522A pdb=" N GLU A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.693A pdb=" N VAL A 553 " --> pdb=" O TYR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.532A pdb=" N LYS A 558 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 572 removed outlier: 3.529A pdb=" N VAL A 572 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 586 removed outlier: 3.962A pdb=" N THR A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 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 785 removed outlier: 3.567A pdb=" N VAL A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 removed outlier: 4.379A pdb=" N THR A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 815 Processing helix chain 'A' and resid 822 through 836 removed outlier: 3.529A pdb=" N ASN A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 852 removed outlier: 5.100A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 5.080A 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 906 removed outlier: 3.549A pdb=" N ALA A 901 " --> pdb=" O SER A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.916A pdb=" N ASN A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.642A 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: 3.597A pdb=" N LYS B 258 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.718A pdb=" N ARG B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 333 through 342 removed outlier: 3.508A pdb=" N LYS B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 384 Processing helix chain 'B' and resid 389 through 394 removed outlier: 3.953A pdb=" N LYS B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 removed outlier: 3.515A pdb=" N ASP B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 447 removed outlier: 4.004A pdb=" N ILE B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.876A pdb=" N PHE B 492 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 50 through 93 removed outlier: 3.816A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 158 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 196 Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.609A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 229 removed outlier: 3.546A pdb=" N TYR C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 229' Processing helix chain 'C' and resid 243 through 249 removed outlier: 3.988A pdb=" N ILE C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 295 through 308 removed outlier: 3.549A pdb=" N ASN C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 332 removed outlier: 3.679A pdb=" N LEU C 316 " --> pdb=" O HIS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.904A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 338 " --> pdb=" O SER C 335 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP C 339 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Proline residue: C 340 - end of helix removed outlier: 4.080A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 357 through 371 Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 395 through 397 No H-bonds generated for 'chain 'C' and resid 395 through 397' Processing helix chain 'C' and resid 401 through 416 Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 435 through 441 Processing helix chain 'C' and resid 449 through 454 Processing helix chain 'C' and resid 474 through 479 removed outlier: 3.686A pdb=" N ILE C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 512 through 516 removed outlier: 3.561A pdb=" N LYS C 515 " --> pdb=" O ASP C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 530 removed outlier: 3.855A pdb=" N LEU C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 546 Processing helix chain 'C' and resid 549 through 558 Processing helix chain 'C' and resid 563 through 571 Processing helix chain 'C' and resid 574 through 595 removed outlier: 3.856A pdb=" N LEU C 581 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 61 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 90 removed outlier: 3.525A pdb=" N LYS D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.778A pdb=" N GLN D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 4.285A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 157 " --> pdb=" O GLN D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 228 through 241 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.748A 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: 3.640A 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: 3.560A pdb=" N ASP D 365 " --> pdb=" O CYS D 361 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 381 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: 4.628A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 removed outlier: 3.542A pdb=" N ASN D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 removed outlier: 3.520A pdb=" N MET D 496 " --> pdb=" O GLN D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.549A pdb=" N ARG D 502 " --> pdb=" O PHE D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 517 removed outlier: 3.630A pdb=" N ILE D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 3.868A 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: 3.536A pdb=" N ILE E 28 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR E 29 " --> pdb=" O PRO E 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 25 through 29' Processing helix chain 'E' and resid 42 through 54 Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.556A pdb=" N LEU E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 89 removed outlier: 3.739A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 135 through 138 Processing helix chain 'E' and resid 144 through 151 removed outlier: 3.621A pdb=" N LYS E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'E' and resid 172 through 178 removed outlier: 3.548A 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: 5.740A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 221 removed outlier: 3.602A pdb=" N ILE E 219 " --> pdb=" O LEU E 215 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 252 removed outlier: 5.671A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 271 removed outlier: 3.579A pdb=" N LEU E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Proline residue: E 267 - end of helix Processing helix chain 'E' and resid 280 through 288 removed outlier: 3.716A pdb=" N LEU E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 293 removed outlier: 3.814A 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 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 345 through 350 removed outlier: 3.786A pdb=" N ILE E 349 " --> pdb=" O TYR E 345 " (cutoff:3.500A) 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: 3.575A pdb=" N PHE E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 466 removed outlier: 3.610A pdb=" N ILE E 459 " --> pdb=" O PRO E 455 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 15 Processing helix chain 'F' and resid 26 through 47 removed outlier: 4.194A pdb=" N ASN F 45 " --> pdb=" O ASN F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 56 removed outlier: 3.890A pdb=" N VAL F 55 " --> pdb=" O GLN F 51 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 72 removed outlier: 3.779A pdb=" N ILE F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.787A 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 290 removed outlier: 3.563A pdb=" N ILE F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 295 through 309 removed outlier: 3.729A pdb=" N ASN F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 332 removed outlier: 3.594A pdb=" N LEU F 319 " --> pdb=" O CYS F 315 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 339 Processing helix chain 'F' and resid 342 through 352 removed outlier: 3.824A pdb=" N VAL F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER F 348 " --> pdb=" O HIS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 371 removed outlier: 4.313A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 387 Processing helix chain 'F' and resid 393 through 402 removed outlier: 4.042A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 427 Processing helix chain 'I' and resid 54 through 62 Processing helix chain 'I' and resid 81 through 99 removed outlier: 3.601A pdb=" N GLU I 98 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 126 removed outlier: 3.530A 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 188 Processing helix chain 'I' and resid 201 through 210 removed outlier: 4.061A pdb=" N LEU I 205 " --> pdb=" O ASN I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 229 removed outlier: 3.551A pdb=" N LEU I 229 " --> pdb=" O ASP I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 248 removed outlier: 4.604A pdb=" N THR I 241 " --> pdb=" O GLN I 237 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ILE I 242 " --> pdb=" O SER I 238 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU I 244 " --> pdb=" O ARG I 240 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU I 248 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 251 No H-bonds generated for 'chain 'I' and resid 249 through 251' Processing helix chain 'I' and resid 292 through 304 Processing helix chain 'I' and resid 313 through 324 Processing helix chain 'I' and resid 330 through 349 Processing helix chain 'I' and resid 386 through 397 removed outlier: 3.728A pdb=" N ILE I 390 " --> pdb=" O GLY I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 409 Processing helix chain 'I' and resid 411 through 428 removed outlier: 3.800A pdb=" N LEU I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN I 428 " --> pdb=" O SER I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 446 removed outlier: 3.811A pdb=" N LYS I 442 " --> pdb=" O ASP I 438 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS I 446 " --> pdb=" O LYS I 442 " (cutoff:3.500A) Processing helix chain 'I' and resid 454 through 468 Processing helix chain 'I' and resid 494 through 504 removed outlier: 3.580A pdb=" N TYR I 499 " --> pdb=" O MET I 495 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP I 500 " --> pdb=" O ARG I 496 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS I 504 " --> pdb=" O ASP I 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 512 removed outlier: 3.603A pdb=" N LEU I 512 " --> pdb=" O LYS I 509 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 508 through 514 removed outlier: 6.332A pdb=" N LEU A 509 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU A 564 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 511 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASP A 566 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 513 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ILE A 622 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR A 476 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE A 624 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 6.829A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 820 through 821 Processing sheet with id=AA4, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.299A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N HIS B 478 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 315 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 361 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N HIS B 425 " --> pdb=" O LEU B 361 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU B 363 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 124 through 131 removed outlier: 6.479A pdb=" N TYR C 125 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL C 202 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 127 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASN C 204 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE C 129 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASN C 103 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE C 238 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 105 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE C 240 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C 107 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 293 through 294 removed outlier: 6.823A 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 405 through 406 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 62 removed outlier: 4.435A pdb=" N HIS E 58 " --> pdb=" O CYS E 127 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR E 126 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LYS E 165 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU E 128 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE E 167 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU E 130 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR E 169 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU E 132 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU E 33 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N MET E 170 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU E 35 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N VAL E 187 " --> pdb=" O ASN E 32 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE E 34 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N PHE E 189 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.862A 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 154 removed outlier: 8.537A pdb=" N VAL I 219 " --> pdb=" O SER I 164 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA I 166 " --> pdb=" O VAL I 219 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL I 221 " --> pdb=" O ALA I 166 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR I 168 " --> pdb=" O VAL I 221 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASP I 223 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE I 170 " --> pdb=" O ASP I 223 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE I 218 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE I 259 " --> pdb=" O PHE I 218 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL I 220 " --> pdb=" O ILE I 259 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N MET I 261 " --> pdb=" O VAL I 220 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU I 222 " --> pdb=" O MET I 261 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASN I 263 " --> pdb=" O LEU I 222 " (cutoff:3.500A) removed outlier: 3.566A 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 1129 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 2.70 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: 3832 1.31 - 1.44: 7010 1.44 - 1.56: 13980 1.56 - 1.69: 183 1.69 - 1.82: 176 Bond restraints: 25181 Sorted by residual: bond pdb=" N ILE I 170 " pdb=" CA ILE I 170 " ideal model delta sigma weight residual 1.459 1.518 -0.059 1.15e-02 7.56e+03 2.65e+01 bond pdb=" N ASN I 171 " pdb=" CA ASN I 171 " ideal model delta sigma weight residual 1.456 1.518 -0.063 1.22e-02 6.72e+03 2.64e+01 bond pdb=" C LYS B 419 " pdb=" O LYS B 419 " ideal model delta sigma weight residual 1.236 1.183 0.052 1.31e-02 5.83e+03 1.60e+01 bond pdb=" C ASN I 171 " pdb=" O ASN I 171 " ideal model delta sigma weight residual 1.234 1.191 0.043 1.22e-02 6.72e+03 1.26e+01 bond pdb=" C MET A 779 " pdb=" O MET A 779 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.29e-02 6.01e+03 1.21e+01 ... (remaining 25176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 34186 4.23 - 8.45: 175 8.45 - 12.68: 12 12.68 - 16.91: 0 16.91 - 21.13: 1 Bond angle restraints: 34374 Sorted by residual: angle pdb=" PB ATP I1001 " pdb=" O3B ATP I1001 " pdb=" PG ATP I1001 " ideal model delta sigma weight residual 139.87 131.07 8.80 1.00e+00 1.00e+00 7.74e+01 angle pdb=" PA ATP I1001 " pdb=" O3A ATP I1001 " pdb=" PB ATP I1001 " ideal model delta sigma weight residual 136.83 129.57 7.26 1.00e+00 1.00e+00 5.28e+01 angle pdb=" N GLU D 151 " pdb=" CA GLU D 151 " pdb=" CB GLU D 151 " ideal model delta sigma weight residual 110.16 119.19 -9.03 1.48e+00 4.57e-01 3.72e+01 angle pdb=" N ASN I 171 " pdb=" CA ASN I 171 " pdb=" CB ASN I 171 " ideal model delta sigma weight residual 109.97 118.11 -8.14 1.47e+00 4.63e-01 3.07e+01 angle pdb=" C ILE F 81 " pdb=" N ASP F 82 " pdb=" CA ASP F 82 " ideal model delta sigma weight residual 120.38 127.29 -6.91 1.46e+00 4.69e-01 2.24e+01 ... (remaining 34369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13139 17.97 - 35.93: 1383 35.93 - 53.90: 499 53.90 - 71.87: 121 71.87 - 89.84: 29 Dihedral angle restraints: 15171 sinusoidal: 6901 harmonic: 8270 Sorted by residual: dihedral pdb=" CA SER A 854 " pdb=" C SER A 854 " pdb=" N ASP A 855 " pdb=" CA ASP A 855 " ideal model delta harmonic sigma weight residual 180.00 153.55 26.45 0 5.00e+00 4.00e-02 2.80e+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 180.00 156.88 23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA VAL E 8 " pdb=" C VAL E 8 " pdb=" N ALA E 9 " pdb=" CA ALA E 9 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 15168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3159 0.061 - 0.122: 666 0.122 - 0.183: 78 0.183 - 0.245: 9 0.245 - 0.306: 2 Chirality restraints: 3914 Sorted by residual: chirality pdb=" CB VAL B 384 " pdb=" CA VAL B 384 " pdb=" CG1 VAL B 384 " pdb=" CG2 VAL B 384 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ARG I 240 " pdb=" N ARG I 240 " pdb=" C ARG I 240 " pdb=" CB ARG I 240 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA TRP C 494 " pdb=" N TRP C 494 " pdb=" C TRP C 494 " pdb=" CB TRP C 494 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3911 not shown) Planarity restraints: 4013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 26 " 0.081 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO C 27 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO C 27 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO C 27 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 50 " -0.021 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C LYS F 50 " 0.075 2.00e-02 2.50e+03 pdb=" O LYS F 50 " -0.028 2.00e-02 2.50e+03 pdb=" N GLN F 51 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 418 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ILE B 418 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE B 418 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS B 419 " 0.020 2.00e-02 2.50e+03 ... (remaining 4010 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 131 2.49 - 3.09: 15690 3.09 - 3.69: 38873 3.69 - 4.30: 58906 4.30 - 4.90: 92302 Nonbonded interactions: 205902 Sorted by model distance: nonbonded pdb=" OD1 ASP E 136 " pdb=" O HOH E1101 " model vdw 1.886 3.040 nonbonded pdb=" O2B ATP I1001 " pdb="MG MG I1002 " model vdw 2.053 2.170 nonbonded pdb=" OG1 THR D 109 " pdb="MG MG D1002 " model vdw 2.066 2.170 nonbonded pdb=" OG1 THR I 115 " pdb="MG MG I1002 " model vdw 2.082 2.170 nonbonded pdb=" O2G ATP D1001 " pdb="MG MG D1002 " model vdw 2.108 2.170 ... (remaining 205897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.530 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 : 0.005 0.085 25181 Z= 0.255 Angle : 0.885 21.133 34374 Z= 0.509 Chirality : 0.050 0.306 3914 Planarity : 0.007 0.122 4013 Dihedral : 17.378 89.836 9765 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.39 % Allowed : 0.47 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 2721 helix: -1.13 (0.11), residues: 1523 sheet: 0.39 (0.31), residues: 253 loop : -1.05 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 288 TYR 0.026 0.002 TYR F 80 PHE 0.042 0.002 PHE F 329 TRP 0.025 0.002 TRP E 450 HIS 0.012 0.002 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00475 (25181) covalent geometry : angle 0.88509 (34374) hydrogen bonds : bond 0.16543 ( 1221) hydrogen bonds : angle 6.64541 ( 3424) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 519 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8163 (mptp) REVERT: A 544 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7545 (mt-10) REVERT: C 343 VAL cc_start: 0.8379 (m) cc_final: 0.8042 (p) REVERT: C 395 PHE cc_start: 0.6935 (m-80) cc_final: 0.6231 (m-80) REVERT: C 408 PHE cc_start: 0.8881 (t80) cc_final: 0.8631 (t80) REVERT: D 83 ASP cc_start: 0.7777 (t0) cc_final: 0.7537 (t70) REVERT: F 67 GLN cc_start: 0.8279 (tt0) cc_final: 0.7872 (tt0) REVERT: F 100 GLN cc_start: 0.8607 (mt0) cc_final: 0.8404 (mt0) REVERT: F 332 PHE cc_start: 0.7911 (m-10) cc_final: 0.7455 (m-10) REVERT: F 417 GLN cc_start: 0.8649 (tt0) cc_final: 0.7896 (mm-40) REVERT: I 200 LYS cc_start: 0.8458 (ptpp) cc_final: 0.8013 (pptt) REVERT: I 247 LEU cc_start: 0.8453 (tt) cc_final: 0.8174 (mt) REVERT: I 409 LYS cc_start: 0.8950 (mttt) cc_final: 0.8713 (mtpp) REVERT: I 426 LYS cc_start: 0.8288 (mttt) cc_final: 0.7995 (mtmm) outliers start: 10 outliers final: 5 residues processed: 525 average time/residue: 0.7992 time to fit residues: 468.9239 Evaluate side-chains 281 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 276 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 305 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 197 optimal weight: 0.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN A 502 GLN A 810 ASN B 425 HIS C 38 HIS C 477 GLN D 158 HIS E 391 GLN F 7 GLN ** F 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN F 410 ASN I 151 ASN I 203 GLN I 232 ASN I 327 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.111726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076657 restraints weight = 44213.360| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.25 r_work: 0.2916 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25181 Z= 0.221 Angle : 0.622 15.110 34374 Z= 0.333 Chirality : 0.043 0.235 3914 Planarity : 0.005 0.058 4013 Dihedral : 17.808 89.131 4080 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.11 % Allowed : 10.97 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.15), residues: 2721 helix: 0.34 (0.13), residues: 1566 sheet: 0.35 (0.31), residues: 249 loop : -0.68 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 193 TYR 0.024 0.002 TYR C 483 PHE 0.020 0.002 PHE D 363 TRP 0.020 0.002 TRP E 456 HIS 0.007 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00517 (25181) covalent geometry : angle 0.62239 (34374) hydrogen bonds : bond 0.04492 ( 1221) hydrogen bonds : angle 4.53637 ( 3424) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 291 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8575 (mptp) REVERT: A 502 GLN cc_start: 0.8825 (pt0) cc_final: 0.8583 (pt0) REVERT: A 678 ARG cc_start: 0.7740 (mtp180) cc_final: 0.7414 (ttp80) REVERT: A 913 ASN cc_start: 0.8385 (m-40) cc_final: 0.8050 (p0) REVERT: B 268 ASP cc_start: 0.8237 (t70) cc_final: 0.7984 (m-30) REVERT: B 377 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8254 (mppt) REVERT: C 80 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: C 147 MET cc_start: 0.9311 (mmp) cc_final: 0.9070 (mmp) REVERT: C 246 ASN cc_start: 0.8890 (m110) cc_final: 0.8674 (t0) REVERT: C 306 MET cc_start: 0.8760 (ttp) cc_final: 0.8543 (ttm) REVERT: C 391 PHE cc_start: 0.7895 (t80) cc_final: 0.7418 (t80) REVERT: C 395 PHE cc_start: 0.7216 (m-80) cc_final: 0.6939 (m-80) REVERT: C 408 PHE cc_start: 0.9045 (t80) cc_final: 0.8726 (t80) REVERT: C 412 PHE cc_start: 0.8502 (t80) cc_final: 0.8224 (t80) REVERT: C 461 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8026 (tt) REVERT: D 295 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7402 (mpt-90) REVERT: D 467 ASP cc_start: 0.9001 (t0) cc_final: 0.8758 (t0) REVERT: E 170 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.8786 (mmm) REVERT: E 275 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.5853 (mmtm) REVERT: F 5 GLN cc_start: 0.8617 (tp-100) cc_final: 0.8367 (tp40) REVERT: F 100 GLN cc_start: 0.8855 (mt0) cc_final: 0.8535 (mt0) REVERT: F 410 ASN cc_start: 0.7611 (t0) cc_final: 0.7052 (p0) REVERT: F 417 GLN cc_start: 0.8619 (tt0) cc_final: 0.7825 (mm-40) REVERT: I 200 LYS cc_start: 0.8741 (ptpp) cc_final: 0.8235 (pptt) REVERT: I 201 ASN cc_start: 0.6909 (p0) cc_final: 0.6650 (p0) REVERT: I 247 LEU cc_start: 0.8622 (tt) cc_final: 0.8319 (mt) REVERT: I 327 ASN cc_start: 0.8361 (m-40) cc_final: 0.7985 (t0) REVERT: I 409 LYS cc_start: 0.9046 (mttt) cc_final: 0.8805 (mtpp) outliers start: 54 outliers final: 19 residues processed: 322 average time/residue: 0.7335 time to fit residues: 268.1102 Evaluate side-chains 281 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 496 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 3 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 225 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 HIS B 371 ASN E 2 ASN F 7 GLN F 8 HIS F 67 GLN F 318 GLN I 99 HIS I 151 ASN I 454 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.111527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.076730 restraints weight = 44362.860| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.23 r_work: 0.2917 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25181 Z= 0.157 Angle : 0.550 14.168 34374 Z= 0.294 Chirality : 0.041 0.250 3914 Planarity : 0.004 0.049 4013 Dihedral : 17.658 87.855 4075 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.22 % Allowed : 12.84 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 2721 helix: 1.02 (0.13), residues: 1549 sheet: 0.30 (0.31), residues: 254 loop : -0.53 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 317 TYR 0.020 0.001 TYR C 483 PHE 0.016 0.001 PHE D 363 TRP 0.016 0.002 TRP E 456 HIS 0.008 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00364 (25181) covalent geometry : angle 0.55007 (34374) hydrogen bonds : bond 0.03838 ( 1221) hydrogen bonds : angle 4.21653 ( 3424) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 274 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8574 (mptp) REVERT: A 502 GLN cc_start: 0.8837 (pt0) cc_final: 0.8610 (pt0) REVERT: A 678 ARG cc_start: 0.7731 (mtp180) cc_final: 0.7301 (ttp80) REVERT: A 813 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8489 (ttmm) REVERT: A 913 ASN cc_start: 0.8467 (m-40) cc_final: 0.8221 (p0) REVERT: B 268 ASP cc_start: 0.8221 (t70) cc_final: 0.7983 (m-30) REVERT: B 377 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8204 (mppt) REVERT: C 80 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: C 306 MET cc_start: 0.8723 (ttp) cc_final: 0.8508 (ttm) REVERT: C 391 PHE cc_start: 0.7854 (t80) cc_final: 0.7463 (t80) REVERT: C 395 PHE cc_start: 0.7376 (m-80) cc_final: 0.6976 (m-80) REVERT: C 461 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7872 (tt) REVERT: D 139 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: D 258 GLU cc_start: 0.8980 (mp0) cc_final: 0.8736 (mp0) REVERT: D 261 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: D 295 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7396 (mpt180) REVERT: D 467 ASP cc_start: 0.9004 (t0) cc_final: 0.8754 (t0) REVERT: E 170 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.8758 (mmm) REVERT: E 188 MET cc_start: 0.9209 (mpt) cc_final: 0.8926 (mpt) REVERT: E 221 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7709 (mp0) REVERT: E 275 LYS cc_start: 0.6364 (OUTLIER) cc_final: 0.5804 (mmtm) REVERT: E 367 LYS cc_start: 0.8387 (pptt) cc_final: 0.8045 (pttp) REVERT: E 437 MET cc_start: 0.7702 (tpt) cc_final: 0.7478 (tpp) REVERT: F 5 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8397 (tp40) REVERT: F 67 GLN cc_start: 0.8341 (tt0) cc_final: 0.7888 (tt0) REVERT: F 71 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: F 100 GLN cc_start: 0.8781 (mt0) cc_final: 0.8505 (mt0) REVERT: F 277 TYR cc_start: 0.7668 (m-80) cc_final: 0.7395 (m-80) REVERT: F 318 GLN cc_start: 0.6118 (mt0) cc_final: 0.5624 (mt0) REVERT: F 321 CYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7395 (p) REVERT: F 323 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5771 (mp) REVERT: F 410 ASN cc_start: 0.7720 (t0) cc_final: 0.7089 (p0) REVERT: F 417 GLN cc_start: 0.8630 (tt0) cc_final: 0.7863 (mm-40) REVERT: I 57 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8136 (mtm180) REVERT: I 89 MET cc_start: 0.8528 (mmm) cc_final: 0.8315 (mmt) REVERT: I 200 LYS cc_start: 0.8736 (ptpp) cc_final: 0.8242 (pptt) REVERT: I 327 ASN cc_start: 0.8375 (m-40) cc_final: 0.8030 (t0) REVERT: I 502 MET cc_start: 0.8930 (mmt) cc_final: 0.8661 (mmt) outliers start: 57 outliers final: 21 residues processed: 304 average time/residue: 0.7164 time to fit residues: 247.5491 Evaluate side-chains 282 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 78 CYS Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 237 GLN Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 269 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 200 optimal weight: 0.0370 chunk 147 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 chunk 252 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 overall best weight: 2.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 HIS B 342 GLN C 69 HIS C 430 ASN D 152 GLN F 7 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.110287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.074998 restraints weight = 43981.171| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.24 r_work: 0.2871 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 25181 Z= 0.179 Angle : 0.550 14.052 34374 Z= 0.294 Chirality : 0.042 0.260 3914 Planarity : 0.004 0.045 4013 Dihedral : 17.628 85.874 4073 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.85 % Allowed : 13.00 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 2721 helix: 1.29 (0.14), residues: 1556 sheet: 0.18 (0.30), residues: 252 loop : -0.51 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 317 TYR 0.021 0.001 TYR C 483 PHE 0.017 0.001 PHE D 363 TRP 0.015 0.002 TRP A 539 HIS 0.006 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00417 (25181) covalent geometry : angle 0.54973 (34374) hydrogen bonds : bond 0.03839 ( 1221) hydrogen bonds : angle 4.11479 ( 3424) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 265 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 417 GLN cc_start: 0.7969 (tp40) cc_final: 0.7675 (pm20) REVERT: A 420 GLU cc_start: 0.7616 (mp0) cc_final: 0.7291 (mt-10) REVERT: A 502 GLN cc_start: 0.8862 (pt0) cc_final: 0.8579 (pt0) REVERT: A 504 GLU cc_start: 0.8175 (mp0) cc_final: 0.7927 (mp0) REVERT: A 678 ARG cc_start: 0.7662 (mtp180) cc_final: 0.7366 (ttp80) REVERT: A 681 ARG cc_start: 0.8354 (tmm-80) cc_final: 0.8023 (tmm-80) REVERT: A 813 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8503 (ttmm) REVERT: A 908 ASP cc_start: 0.9007 (t0) cc_final: 0.8637 (t70) REVERT: A 913 ASN cc_start: 0.8513 (m-40) cc_final: 0.8248 (p0) REVERT: B 377 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8143 (mppt) REVERT: C 80 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: C 315 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: C 320 MET cc_start: 0.9021 (mtm) cc_final: 0.8816 (mtm) REVERT: C 391 PHE cc_start: 0.7841 (t80) cc_final: 0.7478 (t80) REVERT: C 395 PHE cc_start: 0.7309 (m-80) cc_final: 0.6820 (m-80) REVERT: C 426 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8012 (mm-30) REVERT: C 461 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7778 (tt) REVERT: D 139 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: D 261 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: D 295 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7368 (mpt180) REVERT: D 467 ASP cc_start: 0.9060 (t0) cc_final: 0.8771 (t0) REVERT: E 170 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.8803 (mmm) REVERT: E 188 MET cc_start: 0.9242 (mpt) cc_final: 0.8885 (mpt) REVERT: E 275 LYS cc_start: 0.6361 (OUTLIER) cc_final: 0.5870 (mmtm) REVERT: E 367 LYS cc_start: 0.8421 (pptt) cc_final: 0.8063 (pttp) REVERT: E 449 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7174 (mtp85) REVERT: F 5 GLN cc_start: 0.8608 (tp-100) cc_final: 0.8311 (tp40) REVERT: F 8 HIS cc_start: 0.8778 (t-90) cc_final: 0.8489 (t-170) REVERT: F 67 GLN cc_start: 0.8271 (tt0) cc_final: 0.7842 (tt0) REVERT: F 71 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: F 277 TYR cc_start: 0.7823 (m-80) cc_final: 0.7541 (m-80) REVERT: F 318 GLN cc_start: 0.6212 (mt0) cc_final: 0.5718 (mt0) REVERT: F 321 CYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7310 (p) REVERT: F 323 LEU cc_start: 0.5995 (OUTLIER) cc_final: 0.5653 (mp) REVERT: F 410 ASN cc_start: 0.7785 (t0) cc_final: 0.7081 (p0) REVERT: F 417 GLN cc_start: 0.8576 (tt0) cc_final: 0.7824 (mm-40) REVERT: I 57 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8149 (mtm180) REVERT: I 200 LYS cc_start: 0.8704 (ptpp) cc_final: 0.8133 (pptt) REVERT: I 245 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7980 (mm) REVERT: I 247 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8560 (mt) REVERT: I 327 ASN cc_start: 0.8446 (m-40) cc_final: 0.8072 (t0) REVERT: I 447 THR cc_start: 0.8435 (m) cc_final: 0.8215 (m) REVERT: I 466 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8618 (tp30) REVERT: I 502 MET cc_start: 0.8895 (mmt) cc_final: 0.8689 (mmt) outliers start: 73 outliers final: 28 residues processed: 308 average time/residue: 0.6764 time to fit residues: 237.8418 Evaluate side-chains 286 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 315 GLN Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 237 GLN Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 466 GLU Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 100 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 229 optimal weight: 0.2980 chunk 194 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 GLN I 456 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.111165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.076151 restraints weight = 43748.668| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.24 r_work: 0.2918 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25181 Z= 0.137 Angle : 0.526 13.671 34374 Z= 0.281 Chirality : 0.040 0.264 3914 Planarity : 0.003 0.058 4013 Dihedral : 17.527 86.829 4071 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.81 % Allowed : 13.86 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.16), residues: 2721 helix: 1.46 (0.14), residues: 1555 sheet: 0.15 (0.30), residues: 253 loop : -0.43 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 317 TYR 0.016 0.001 TYR C 449 PHE 0.013 0.001 PHE D 363 TRP 0.016 0.001 TRP I 154 HIS 0.006 0.001 HIS F 8 Details of bonding type rmsd covalent geometry : bond 0.00315 (25181) covalent geometry : angle 0.52602 (34374) hydrogen bonds : bond 0.03495 ( 1221) hydrogen bonds : angle 4.03220 ( 3424) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 257 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7666 (mp0) cc_final: 0.7384 (mt-10) REVERT: A 502 GLN cc_start: 0.8854 (pt0) cc_final: 0.8572 (pt0) REVERT: A 678 ARG cc_start: 0.7735 (mtp180) cc_final: 0.7443 (ttp80) REVERT: A 813 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8497 (ttmm) REVERT: A 908 ASP cc_start: 0.8988 (t0) cc_final: 0.8578 (t70) REVERT: B 377 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8144 (mppt) REVERT: C 80 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: C 391 PHE cc_start: 0.7802 (t80) cc_final: 0.7550 (t80) REVERT: C 395 PHE cc_start: 0.7364 (m-80) cc_final: 0.6908 (m-80) REVERT: C 426 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8018 (tp30) REVERT: C 461 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7895 (tt) REVERT: C 577 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7522 (t70) REVERT: C 585 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6762 (tpt) REVERT: C 606 ASP cc_start: 0.7806 (m-30) cc_final: 0.7331 (p0) REVERT: D 139 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8356 (mm-30) REVERT: D 261 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: D 295 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7353 (mpt180) REVERT: D 467 ASP cc_start: 0.9053 (t0) cc_final: 0.8768 (t0) REVERT: E 170 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.8750 (mmm) REVERT: E 188 MET cc_start: 0.9253 (mpt) cc_final: 0.8933 (mpt) REVERT: E 275 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5960 (mmmm) REVERT: E 367 LYS cc_start: 0.8462 (pptt) cc_final: 0.8067 (pttp) REVERT: E 437 MET cc_start: 0.7634 (tpt) cc_final: 0.7396 (tpp) REVERT: F 5 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8225 (tp40) REVERT: F 287 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7984 (mmp80) REVERT: F 318 GLN cc_start: 0.6335 (mt0) cc_final: 0.5843 (mt0) REVERT: F 321 CYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7430 (p) REVERT: F 323 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5727 (mp) REVERT: F 410 ASN cc_start: 0.7740 (t0) cc_final: 0.7084 (p0) REVERT: F 416 ASP cc_start: 0.8249 (p0) cc_final: 0.7960 (p0) REVERT: F 417 GLN cc_start: 0.8705 (tt0) cc_final: 0.7889 (mm110) REVERT: F 424 ARG cc_start: 0.7317 (mmp80) cc_final: 0.7111 (mmp80) REVERT: I 200 LYS cc_start: 0.8679 (ptpp) cc_final: 0.8108 (pptt) REVERT: I 206 GLN cc_start: 0.9002 (tt0) cc_final: 0.8439 (pt0) REVERT: I 247 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8477 (mt) REVERT: I 327 ASN cc_start: 0.8368 (m-40) cc_final: 0.8079 (t0) REVERT: I 466 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8595 (tp30) REVERT: I 502 MET cc_start: 0.8932 (mmt) cc_final: 0.8692 (mmt) outliers start: 72 outliers final: 26 residues processed: 300 average time/residue: 0.6967 time to fit residues: 237.9802 Evaluate side-chains 292 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 419 GLU Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 237 GLN Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 466 GLU Chi-restraints excluded: chain I residue 472 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 132 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 237 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 ASN C 400 ASN D 323 HIS E 91 ASN F 7 GLN F 67 GLN I 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.109218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.074613 restraints weight = 43822.601| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.20 r_work: 0.2887 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 25181 Z= 0.195 Angle : 0.567 13.858 34374 Z= 0.300 Chirality : 0.042 0.248 3914 Planarity : 0.003 0.059 4013 Dihedral : 17.613 85.900 4071 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.89 % Allowed : 14.21 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.16), residues: 2721 helix: 1.50 (0.14), residues: 1554 sheet: 0.08 (0.31), residues: 247 loop : -0.36 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 317 TYR 0.021 0.001 TYR C 483 PHE 0.017 0.001 PHE D 363 TRP 0.016 0.002 TRP I 154 HIS 0.004 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00458 (25181) covalent geometry : angle 0.56713 (34374) hydrogen bonds : bond 0.03881 ( 1221) hydrogen bonds : angle 4.07931 ( 3424) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 260 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ARG cc_start: 0.6750 (pmm150) cc_final: 0.6476 (pmm150) REVERT: A 502 GLN cc_start: 0.8865 (pt0) cc_final: 0.8587 (pt0) REVERT: A 504 GLU cc_start: 0.8182 (mp0) cc_final: 0.7941 (mp0) REVERT: A 678 ARG cc_start: 0.7742 (mtp180) cc_final: 0.7478 (ttp80) REVERT: A 681 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8063 (tmm-80) REVERT: A 813 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8502 (ttmm) REVERT: A 907 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8460 (mm-30) REVERT: A 908 ASP cc_start: 0.9005 (t0) cc_final: 0.8595 (t70) REVERT: A 913 ASN cc_start: 0.8585 (m-40) cc_final: 0.8294 (p0) REVERT: B 377 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8159 (mppt) REVERT: C 80 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: C 320 MET cc_start: 0.9030 (mtm) cc_final: 0.8706 (mtm) REVERT: C 391 PHE cc_start: 0.7857 (t80) cc_final: 0.7581 (t80) REVERT: C 395 PHE cc_start: 0.7427 (m-80) cc_final: 0.6808 (m-80) REVERT: C 426 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8037 (tp30) REVERT: C 461 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7772 (tt) REVERT: C 577 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7340 (t0) REVERT: C 585 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6857 (tpt) REVERT: C 606 ASP cc_start: 0.7895 (m-30) cc_final: 0.7454 (p0) REVERT: D 139 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8413 (mm-30) REVERT: D 261 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8117 (tt0) REVERT: D 295 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7309 (mpt180) REVERT: D 467 ASP cc_start: 0.9055 (t0) cc_final: 0.8746 (t0) REVERT: E 170 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.8821 (mmm) REVERT: E 188 MET cc_start: 0.9286 (mpt) cc_final: 0.8893 (mpt) REVERT: E 275 LYS cc_start: 0.6323 (OUTLIER) cc_final: 0.4175 (mmtm) REVERT: E 367 LYS cc_start: 0.8512 (pptt) cc_final: 0.8088 (pttp) REVERT: E 437 MET cc_start: 0.7700 (tpt) cc_final: 0.7495 (tpp) REVERT: E 449 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7201 (mtp85) REVERT: F 4 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8725 (tm130) REVERT: F 5 GLN cc_start: 0.8548 (tp-100) cc_final: 0.8218 (tp40) REVERT: F 67 GLN cc_start: 0.8269 (tt0) cc_final: 0.7756 (tt0) REVERT: F 71 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: F 287 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8081 (mmp80) REVERT: F 323 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5715 (mp) REVERT: F 410 ASN cc_start: 0.7756 (t0) cc_final: 0.7033 (p0) REVERT: F 416 ASP cc_start: 0.8239 (p0) cc_final: 0.7949 (p0) REVERT: F 417 GLN cc_start: 0.8642 (tt0) cc_final: 0.7824 (mm110) REVERT: I 57 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8164 (mtm180) REVERT: I 200 LYS cc_start: 0.8708 (ptpp) cc_final: 0.8412 (ptmt) REVERT: I 206 GLN cc_start: 0.9030 (tt0) cc_final: 0.8425 (pt0) REVERT: I 327 ASN cc_start: 0.8420 (m-40) cc_final: 0.8142 (t0) REVERT: I 328 THR cc_start: 0.8565 (m) cc_final: 0.8253 (p) REVERT: I 466 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8596 (tp30) outliers start: 74 outliers final: 32 residues processed: 306 average time/residue: 0.6932 time to fit residues: 241.2133 Evaluate side-chains 301 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 250 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 237 GLN Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 466 GLU Chi-restraints excluded: chain I residue 472 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 269 optimal weight: 0.9990 chunk 260 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 216 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 241 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 GLN F 73 HIS F 318 GLN I 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.109716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.075177 restraints weight = 43749.654| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.20 r_work: 0.2890 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 25181 Z= 0.164 Angle : 0.549 13.660 34374 Z= 0.291 Chirality : 0.041 0.223 3914 Planarity : 0.003 0.067 4013 Dihedral : 17.557 86.311 4071 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.34 % Allowed : 14.87 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.16), residues: 2721 helix: 1.58 (0.14), residues: 1552 sheet: 0.09 (0.31), residues: 247 loop : -0.32 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 317 TYR 0.019 0.001 TYR C 483 PHE 0.015 0.001 PHE D 363 TRP 0.019 0.002 TRP I 154 HIS 0.004 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00385 (25181) covalent geometry : angle 0.54930 (34374) hydrogen bonds : bond 0.03639 ( 1221) hydrogen bonds : angle 4.02575 ( 3424) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 256 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLN cc_start: 0.7994 (tp40) cc_final: 0.7763 (pm20) REVERT: A 420 GLU cc_start: 0.7696 (mp0) cc_final: 0.7383 (mt-10) REVERT: A 502 GLN cc_start: 0.8840 (pt0) cc_final: 0.8564 (pt0) REVERT: A 504 GLU cc_start: 0.8154 (mp0) cc_final: 0.7950 (mp0) REVERT: A 606 GLU cc_start: 0.8734 (mp0) cc_final: 0.8221 (mp0) REVERT: A 678 ARG cc_start: 0.7787 (mtp180) cc_final: 0.7504 (ttp80) REVERT: A 681 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7369 (tmm-80) REVERT: A 683 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7377 (ptp90) REVERT: A 907 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8448 (mm-30) REVERT: A 908 ASP cc_start: 0.8992 (t0) cc_final: 0.8552 (t70) REVERT: A 913 ASN cc_start: 0.8604 (m-40) cc_final: 0.8328 (p0) REVERT: B 377 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8173 (mppt) REVERT: C 80 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: C 391 PHE cc_start: 0.7870 (t80) cc_final: 0.7623 (t80) REVERT: C 395 PHE cc_start: 0.7446 (m-80) cc_final: 0.6761 (m-80) REVERT: C 426 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8019 (tp30) REVERT: C 461 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7861 (tt) REVERT: C 577 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7303 (t0) REVERT: C 585 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6777 (tpt) REVERT: C 606 ASP cc_start: 0.7888 (m-30) cc_final: 0.7446 (p0) REVERT: D 139 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8416 (mm-30) REVERT: D 261 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: D 295 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7290 (mpt180) REVERT: D 467 ASP cc_start: 0.9060 (t0) cc_final: 0.8763 (t0) REVERT: E 170 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.8779 (mmm) REVERT: E 188 MET cc_start: 0.9288 (mpt) cc_final: 0.8958 (mpt) REVERT: E 367 LYS cc_start: 0.8521 (pptt) cc_final: 0.8096 (tmmm) REVERT: E 449 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7154 (mtp85) REVERT: F 5 GLN cc_start: 0.8515 (tp-100) cc_final: 0.8195 (tp40) REVERT: F 67 GLN cc_start: 0.8260 (tt0) cc_final: 0.7737 (tt0) REVERT: F 71 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: F 80 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.6106 (m-80) REVERT: F 100 GLN cc_start: 0.8912 (mt0) cc_final: 0.8704 (mt0) REVERT: F 287 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8101 (mmp80) REVERT: F 323 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5697 (mp) REVERT: F 410 ASN cc_start: 0.7651 (t0) cc_final: 0.6979 (p0) REVERT: F 416 ASP cc_start: 0.8223 (p0) cc_final: 0.7959 (p0) REVERT: F 417 GLN cc_start: 0.8652 (tt0) cc_final: 0.7801 (mm110) REVERT: I 200 LYS cc_start: 0.8717 (ptpp) cc_final: 0.8403 (ptmt) REVERT: I 206 GLN cc_start: 0.9106 (tt0) cc_final: 0.8482 (pt0) REVERT: I 247 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8549 (mt) REVERT: I 327 ASN cc_start: 0.8407 (m-40) cc_final: 0.8158 (t0) REVERT: I 328 THR cc_start: 0.8576 (m) cc_final: 0.8268 (p) REVERT: I 466 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8598 (tp30) outliers start: 60 outliers final: 28 residues processed: 294 average time/residue: 0.7103 time to fit residues: 237.4068 Evaluate side-chains 298 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 683 ARG Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 237 GLN Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 466 GLU Chi-restraints excluded: chain I residue 472 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 92 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 183 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 267 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 242 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 ASN F 7 GLN F 73 HIS F 318 GLN I 263 ASN I 428 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.110331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.075417 restraints weight = 43880.709| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.22 r_work: 0.2906 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25181 Z= 0.153 Angle : 0.551 13.569 34374 Z= 0.291 Chirality : 0.041 0.219 3914 Planarity : 0.003 0.074 4013 Dihedral : 17.504 86.797 4071 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.38 % Allowed : 15.03 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.16), residues: 2721 helix: 1.62 (0.14), residues: 1553 sheet: 0.12 (0.31), residues: 247 loop : -0.32 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 317 TYR 0.018 0.001 TYR C 483 PHE 0.014 0.001 PHE D 363 TRP 0.021 0.002 TRP I 154 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00358 (25181) covalent geometry : angle 0.55136 (34374) hydrogen bonds : bond 0.03534 ( 1221) hydrogen bonds : angle 4.00745 ( 3424) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 GLN cc_start: 0.8869 (pt0) cc_final: 0.8605 (pt0) REVERT: A 504 GLU cc_start: 0.8155 (mp0) cc_final: 0.7946 (mp0) REVERT: A 606 GLU cc_start: 0.8722 (mp0) cc_final: 0.8226 (mp0) REVERT: A 678 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7538 (ttp80) REVERT: A 681 ARG cc_start: 0.8291 (tmm-80) cc_final: 0.7392 (tmm-80) REVERT: A 683 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7395 (ptp90) REVERT: A 907 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8470 (mm-30) REVERT: A 908 ASP cc_start: 0.9000 (t0) cc_final: 0.8572 (t0) REVERT: A 913 ASN cc_start: 0.8602 (m-40) cc_final: 0.8324 (p0) REVERT: B 327 GLU cc_start: 0.8138 (pt0) cc_final: 0.7882 (pp20) REVERT: B 377 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8170 (mppt) REVERT: C 80 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: C 391 PHE cc_start: 0.7854 (t80) cc_final: 0.7630 (t80) REVERT: C 395 PHE cc_start: 0.7461 (m-80) cc_final: 0.6642 (m-80) REVERT: C 411 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8007 (ptt180) REVERT: C 426 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8047 (tp30) REVERT: C 461 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7875 (tt) REVERT: C 577 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7299 (t0) REVERT: C 585 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6807 (tpt) REVERT: D 261 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: D 295 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7298 (mpt180) REVERT: D 467 ASP cc_start: 0.9066 (t0) cc_final: 0.8766 (t0) REVERT: E 170 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.8794 (mmm) REVERT: E 188 MET cc_start: 0.9294 (mpt) cc_final: 0.8981 (mpt) REVERT: E 357 ILE cc_start: 0.7839 (mm) cc_final: 0.7516 (mm) REVERT: E 367 LYS cc_start: 0.8558 (pptt) cc_final: 0.8125 (tmmm) REVERT: E 437 MET cc_start: 0.7654 (tpt) cc_final: 0.7386 (tpp) REVERT: E 449 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7145 (mtp85) REVERT: F 5 GLN cc_start: 0.8533 (tp-100) cc_final: 0.8147 (tp40) REVERT: F 67 GLN cc_start: 0.8270 (tt0) cc_final: 0.7743 (tt0) REVERT: F 71 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: F 80 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6064 (m-80) REVERT: F 92 LYS cc_start: 0.9159 (tptm) cc_final: 0.8865 (tppt) REVERT: F 100 GLN cc_start: 0.8914 (mt0) cc_final: 0.8688 (mt0) REVERT: F 287 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8128 (mmp80) REVERT: F 318 GLN cc_start: 0.6331 (mt0) cc_final: 0.5859 (mt0) REVERT: F 321 CYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7436 (p) REVERT: F 323 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5728 (mp) REVERT: F 410 ASN cc_start: 0.7674 (t0) cc_final: 0.6980 (p0) REVERT: F 416 ASP cc_start: 0.8266 (p0) cc_final: 0.7864 (p0) REVERT: F 417 GLN cc_start: 0.8680 (tt0) cc_final: 0.7876 (mm110) REVERT: I 200 LYS cc_start: 0.8718 (ptpp) cc_final: 0.8413 (ptmt) REVERT: I 206 GLN cc_start: 0.9092 (tt0) cc_final: 0.8465 (pt0) REVERT: I 247 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8562 (mt) REVERT: I 328 THR cc_start: 0.8562 (m) cc_final: 0.8299 (p) REVERT: I 466 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8614 (tp30) outliers start: 61 outliers final: 28 residues processed: 303 average time/residue: 0.7225 time to fit residues: 248.4219 Evaluate side-chains 290 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 244 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 683 ARG Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 455 PHE Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 58 CYS Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 237 GLN Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 466 GLU Chi-restraints excluded: chain I residue 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 205 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 214 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 254 optimal weight: 0.0980 chunk 65 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 240 HIS F 7 GLN F 73 HIS I 263 ASN I 327 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.110992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.076087 restraints weight = 43977.301| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.23 r_work: 0.2915 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25181 Z= 0.138 Angle : 0.554 13.829 34374 Z= 0.291 Chirality : 0.040 0.225 3914 Planarity : 0.003 0.077 4013 Dihedral : 17.429 87.436 4071 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.38 % Allowed : 15.57 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.17), residues: 2721 helix: 1.69 (0.14), residues: 1547 sheet: 0.15 (0.32), residues: 247 loop : -0.27 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG F 424 TYR 0.018 0.001 TYR C 483 PHE 0.013 0.001 PHE D 363 TRP 0.022 0.001 TRP I 154 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00320 (25181) covalent geometry : angle 0.55375 (34374) hydrogen bonds : bond 0.03387 ( 1221) hydrogen bonds : angle 3.97093 ( 3424) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 251 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7622 (mp0) cc_final: 0.7247 (mt-10) REVERT: A 502 GLN cc_start: 0.8899 (pt0) cc_final: 0.8639 (pt0) REVERT: A 504 GLU cc_start: 0.8176 (mp0) cc_final: 0.7959 (mp0) REVERT: A 678 ARG cc_start: 0.7788 (mtp180) cc_final: 0.7538 (ttp80) REVERT: A 681 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7353 (tmm-80) REVERT: A 683 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7358 (ptp90) REVERT: A 813 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8480 (ttmm) REVERT: A 907 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8475 (mm-30) REVERT: A 908 ASP cc_start: 0.8987 (t0) cc_final: 0.8579 (t0) REVERT: A 913 ASN cc_start: 0.8586 (m-40) cc_final: 0.8325 (p0) REVERT: B 377 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8163 (mppt) REVERT: C 80 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: C 391 PHE cc_start: 0.7920 (t80) cc_final: 0.7686 (t80) REVERT: C 395 PHE cc_start: 0.7427 (m-80) cc_final: 0.6592 (m-80) REVERT: C 411 ARG cc_start: 0.8426 (ttp80) cc_final: 0.7992 (ptt180) REVERT: C 426 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8051 (tp30) REVERT: C 454 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.7097 (p-80) REVERT: C 461 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7850 (tt) REVERT: C 577 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7296 (t0) REVERT: D 261 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: D 295 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7293 (mpt180) REVERT: D 467 ASP cc_start: 0.9083 (t0) cc_final: 0.8798 (t0) REVERT: E 170 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.8739 (mmm) REVERT: E 188 MET cc_start: 0.9286 (mpt) cc_final: 0.8980 (mpt) REVERT: E 357 ILE cc_start: 0.7877 (mm) cc_final: 0.7551 (mm) REVERT: E 367 LYS cc_start: 0.8553 (pptt) cc_final: 0.8126 (tmmm) REVERT: E 437 MET cc_start: 0.7677 (tpt) cc_final: 0.7414 (tpp) REVERT: E 449 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7130 (mtp85) REVERT: F 5 GLN cc_start: 0.8532 (tp-100) cc_final: 0.8166 (tp40) REVERT: F 67 GLN cc_start: 0.8304 (tt0) cc_final: 0.7746 (tt0) REVERT: F 71 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: F 80 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6034 (m-80) REVERT: F 318 GLN cc_start: 0.6348 (mt0) cc_final: 0.5872 (mt0) REVERT: F 321 CYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7423 (p) REVERT: F 323 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5660 (mp) REVERT: F 410 ASN cc_start: 0.7697 (t0) cc_final: 0.7000 (p0) REVERT: F 416 ASP cc_start: 0.8265 (p0) cc_final: 0.7881 (p0) REVERT: F 417 GLN cc_start: 0.8710 (tt0) cc_final: 0.7897 (mm110) REVERT: F 424 ARG cc_start: 0.7611 (mmp80) cc_final: 0.7334 (mmp80) REVERT: I 200 LYS cc_start: 0.8702 (ptpp) cc_final: 0.8395 (ptmt) REVERT: I 206 GLN cc_start: 0.9084 (tt0) cc_final: 0.8488 (pt0) REVERT: I 247 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8507 (mt) REVERT: I 466 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8611 (tp30) outliers start: 61 outliers final: 28 residues processed: 290 average time/residue: 0.6933 time to fit residues: 229.3216 Evaluate side-chains 297 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 250 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 683 ARG Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 229 LEU Chi-restraints excluded: chain I residue 237 GLN Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 466 GLU Chi-restraints excluded: chain I residue 472 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 203 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 204 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 276 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 73 HIS I 263 ASN I 327 ASN I 428 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.108561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.074007 restraints weight = 43903.629| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.19 r_work: 0.2849 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25181 Z= 0.219 Angle : 0.607 13.591 34374 Z= 0.317 Chirality : 0.043 0.223 3914 Planarity : 0.004 0.080 4013 Dihedral : 17.588 86.075 4071 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.15 % Allowed : 15.81 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.16), residues: 2721 helix: 1.57 (0.14), residues: 1549 sheet: 0.12 (0.32), residues: 247 loop : -0.33 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 317 TYR 0.022 0.001 TYR C 483 PHE 0.019 0.001 PHE C 455 TRP 0.019 0.002 TRP I 154 HIS 0.004 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00519 (25181) covalent geometry : angle 0.60715 (34374) hydrogen bonds : bond 0.03993 ( 1221) hydrogen bonds : angle 4.10190 ( 3424) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5442 Ramachandran restraints generated. 2721 Oldfield, 0 Emsley, 2721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 248 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLN cc_start: 0.8112 (tp40) cc_final: 0.7826 (pm20) REVERT: A 420 GLU cc_start: 0.7642 (mp0) cc_final: 0.7284 (mt-10) REVERT: A 502 GLN cc_start: 0.8873 (pt0) cc_final: 0.8609 (pt0) REVERT: A 504 GLU cc_start: 0.8174 (mp0) cc_final: 0.7968 (mp0) REVERT: A 606 GLU cc_start: 0.8729 (mp0) cc_final: 0.8265 (mp0) REVERT: A 678 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7560 (ttp80) REVERT: A 681 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7374 (tmm-80) REVERT: A 683 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7384 (ptp90) REVERT: A 813 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8517 (ttmm) REVERT: A 907 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8468 (mm-30) REVERT: A 913 ASN cc_start: 0.8615 (m-40) cc_final: 0.8330 (p0) REVERT: B 377 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8177 (mppt) REVERT: C 80 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: C 391 PHE cc_start: 0.7946 (t80) cc_final: 0.7695 (t80) REVERT: C 395 PHE cc_start: 0.7441 (m-80) cc_final: 0.6554 (m-80) REVERT: C 411 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8014 (ptt180) REVERT: C 426 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8038 (tp30) REVERT: C 454 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.7044 (p-80) REVERT: C 461 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7869 (tt) REVERT: C 577 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7262 (t0) REVERT: D 258 GLU cc_start: 0.8982 (mp0) cc_final: 0.8630 (mt-10) REVERT: D 261 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: D 295 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7268 (mpt180) REVERT: D 467 ASP cc_start: 0.9098 (t0) cc_final: 0.8807 (t0) REVERT: E 170 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.8817 (mmm) REVERT: E 188 MET cc_start: 0.9287 (mpt) cc_final: 0.8886 (mpt) REVERT: E 275 LYS cc_start: 0.5952 (mmtm) cc_final: 0.5047 (mttm) REVERT: E 357 ILE cc_start: 0.7870 (mm) cc_final: 0.7524 (mm) REVERT: E 367 LYS cc_start: 0.8592 (pptt) cc_final: 0.8235 (pttp) REVERT: E 437 MET cc_start: 0.7678 (tpt) cc_final: 0.7402 (tpp) REVERT: E 449 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7241 (mtp85) REVERT: F 5 GLN cc_start: 0.8585 (tp-100) cc_final: 0.8369 (mp10) REVERT: F 12 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8712 (mt-10) REVERT: F 67 GLN cc_start: 0.8338 (tt0) cc_final: 0.7817 (tt0) REVERT: F 71 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: F 80 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: F 279 LYS cc_start: 0.8350 (mptt) cc_final: 0.7633 (tppt) REVERT: F 287 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8142 (mmp80) REVERT: F 323 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5646 (mp) REVERT: F 410 ASN cc_start: 0.7670 (t0) cc_final: 0.6953 (p0) REVERT: I 200 LYS cc_start: 0.8701 (ptpp) cc_final: 0.8394 (ptmt) REVERT: I 206 GLN cc_start: 0.9110 (tt0) cc_final: 0.8469 (pt0) REVERT: I 247 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8553 (mt) REVERT: I 466 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8639 (tp30) outliers start: 55 outliers final: 31 residues processed: 286 average time/residue: 0.7243 time to fit residues: 235.1032 Evaluate side-chains 293 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 683 ARG Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 412 SER Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 323 LEU Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 237 GLN Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 466 GLU Chi-restraints excluded: chain I residue 472 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 207 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 196 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 chunk 267 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 240 HIS F 73 HIS F 110 GLN F 318 GLN I 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.110636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.076251 restraints weight = 43918.399| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.20 r_work: 0.2918 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25181 Z= 0.129 Angle : 0.556 13.597 34374 Z= 0.292 Chirality : 0.040 0.228 3914 Planarity : 0.003 0.080 4013 Dihedral : 17.425 87.727 4071 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.15 % Allowed : 16.24 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.17), residues: 2721 helix: 1.75 (0.14), residues: 1533 sheet: 0.15 (0.32), residues: 247 loop : -0.25 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG D 317 TYR 0.017 0.001 TYR C 483 PHE 0.012 0.001 PHE A 880 TRP 0.027 0.001 TRP I 154 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00297 (25181) covalent geometry : angle 0.55639 (34374) hydrogen bonds : bond 0.03335 ( 1221) hydrogen bonds : angle 3.97358 ( 3424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9956.31 seconds wall clock time: 169 minutes 51.96 seconds (10191.96 seconds total)