Starting phenix.real_space_refine on Sat Jun 21 06:58:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tjk_25928/06_2025/7tjk_25928.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tjk_25928/06_2025/7tjk_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tjk_25928/06_2025/7tjk_25928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tjk_25928/06_2025/7tjk_25928.map" model { file = "/net/cci-nas-00/data/ceres_data/7tjk_25928/06_2025/7tjk_25928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tjk_25928/06_2025/7tjk_25928.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 93 5.49 5 Mg 4 5.21 5 S 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.70, per 1000 atoms: 0.60 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: 6.32 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 8.61 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: 10.22 Time building geometry restraints manager: 7.41 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: 1.810 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: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 62.500 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.570 ------------------------------------------------------------------------------- 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 : 3.81 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (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 TRP 0.025 0.002 TRP E 450 HIS 0.012 0.002 HIS C 65 PHE 0.042 0.002 PHE F 329 TYR 0.026 0.002 TYR F 80 ARG 0.005 0.001 ARG B 288 Details of bonding type rmsd hydrogen bonds : bond 0.16543 ( 1221) hydrogen bonds : angle 6.64541 ( 3424) covalent geometry : bond 0.00475 (25181) covalent geometry : angle 0.88509 (34374) *********************** 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 : 2.936 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: 0.8287 (mttt) cc_final: 0.7995 (mtmm) outliers start: 10 outliers final: 5 residues processed: 525 average time/residue: 1.8558 time to fit residues: 1098.8521 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 : 2.841 ------------------------------------------------------------------------------- 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 238 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 810 ASN B 399 HIS C 38 HIS C 477 GLN D 158 HIS ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 HIS F 7 GLN ** F 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN F 410 ASN I 99 HIS I 151 ASN I 203 GLN I 232 ASN I 327 ASN I 454 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.109658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.074518 restraints weight = 44363.984| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.25 r_work: 0.2879 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 25181 Z= 0.287 Angle : 0.668 13.736 34374 Z= 0.356 Chirality : 0.045 0.191 3914 Planarity : 0.005 0.057 4013 Dihedral : 17.965 84.477 4080 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.46 % Allowed : 10.77 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 2721 helix: 0.39 (0.13), residues: 1554 sheet: 0.25 (0.30), residues: 254 loop : -0.67 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 456 HIS 0.008 0.001 HIS F 59 PHE 0.023 0.002 PHE D 363 TYR 0.030 0.002 TYR C 483 ARG 0.011 0.001 ARG C 193 Details of bonding type rmsd hydrogen bonds : bond 0.04859 ( 1221) hydrogen bonds : angle 4.51019 ( 3424) covalent geometry : bond 0.00671 (25181) covalent geometry : angle 0.66757 (34374) *********************** 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 357 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 294 time to evaluate : 3.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 LYS cc_start: 0.8951 (mmtt) cc_final: 0.8585 (mptp) REVERT: A 502 GLN cc_start: 0.8860 (pt0) cc_final: 0.8616 (pt0) REVERT: A 504 GLU cc_start: 0.8248 (mp0) cc_final: 0.8043 (mp0) REVERT: A 678 ARG cc_start: 0.7768 (mtp180) cc_final: 0.7444 (ttp80) REVERT: A 913 ASN cc_start: 0.8500 (m-40) cc_final: 0.8243 (p0) REVERT: B 268 ASP cc_start: 0.8248 (t70) cc_final: 0.8008 (m-30) REVERT: B 377 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8218 (mppt) REVERT: B 387 GLU cc_start: 0.8563 (tp30) cc_final: 0.8253 (pm20) REVERT: C 80 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: C 147 MET cc_start: 0.9317 (mmp) cc_final: 0.9038 (mmp) REVERT: C 246 ASN cc_start: 0.8831 (m110) cc_final: 0.8616 (t0) REVERT: C 346 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7695 (mp) REVERT: C 391 PHE cc_start: 0.7943 (t80) cc_final: 0.7481 (t80) REVERT: C 395 PHE cc_start: 0.7232 (m-80) cc_final: 0.6860 (m-80) REVERT: C 408 PHE cc_start: 0.9109 (t80) cc_final: 0.8787 (t80) REVERT: C 412 PHE cc_start: 0.8536 (t80) cc_final: 0.8252 (t80) REVERT: C 461 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7999 (tt) REVERT: D 295 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7394 (mpt-90) REVERT: D 467 ASP cc_start: 0.9027 (t0) cc_final: 0.8786 (t0) REVERT: E 170 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.8810 (mmm) REVERT: E 188 MET cc_start: 0.9167 (mpt) cc_final: 0.8932 (mpt) REVERT: E 275 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.5849 (mmtm) REVERT: E 367 LYS cc_start: 0.8424 (pptt) cc_final: 0.8049 (pttp) REVERT: F 5 GLN cc_start: 0.8666 (tp-100) cc_final: 0.8405 (tp40) REVERT: F 100 GLN cc_start: 0.8900 (mt0) cc_final: 0.8629 (mt0) REVERT: F 410 ASN cc_start: 0.7655 (t0) cc_final: 0.7051 (p0) REVERT: F 417 GLN cc_start: 0.8597 (tt0) cc_final: 0.7818 (mm-40) REVERT: I 57 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8160 (mtm180) REVERT: I 200 LYS cc_start: 0.8723 (ptpp) cc_final: 0.8210 (pptt) REVERT: I 327 ASN cc_start: 0.8410 (m-40) cc_final: 0.8071 (t0) outliers start: 63 outliers final: 19 residues processed: 332 average time/residue: 1.7786 time to fit residues: 671.8754 Evaluate side-chains 280 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 2.945 ------------------------------------------------------------------------------- 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 346 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 555 ASN 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 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 321 CYS Chi-restraints excluded: chain F residue 371 GLU Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 496 ARG Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 B 371 ASN B 425 HIS C 69 HIS C 430 ASN D 152 GLN E 2 ASN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN F 67 GLN F 318 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.112054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.077054 restraints weight = 43524.094| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.24 r_work: 0.2936 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2738 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= 0.122 Angle : 0.531 14.091 34374 Z= 0.284 Chirality : 0.040 0.266 3914 Planarity : 0.003 0.051 4013 Dihedral : 17.649 87.887 4073 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.03 % Allowed : 13.43 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2721 helix: 1.04 (0.13), residues: 1554 sheet: 0.27 (0.31), residues: 252 loop : -0.54 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 456 HIS 0.005 0.001 HIS F 59 PHE 0.016 0.001 PHE C 455 TYR 0.018 0.001 TYR I 85 ARG 0.011 0.000 ARG D 317 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 1221) hydrogen bonds : angle 4.15872 ( 3424) covalent geometry : bond 0.00273 (25181) covalent geometry : angle 0.53106 (34374) *********************** 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 319 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 267 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7620 (mp0) cc_final: 0.7410 (mp0) REVERT: A 502 GLN cc_start: 0.8898 (pt0) cc_final: 0.8600 (pt0) REVERT: A 504 GLU cc_start: 0.8183 (mp0) cc_final: 0.7969 (mp0) REVERT: A 678 ARG cc_start: 0.7736 (mtp180) cc_final: 0.7261 (ttp80) REVERT: A 681 ARG cc_start: 0.8375 (tmm-80) cc_final: 0.8123 (tmm-80) REVERT: A 908 ASP cc_start: 0.8993 (t0) cc_final: 0.8652 (t70) REVERT: A 913 ASN cc_start: 0.8477 (m-40) cc_final: 0.8227 (p0) REVERT: B 268 ASP cc_start: 0.8193 (t70) cc_final: 0.7936 (m-30) REVERT: B 377 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8178 (mppt) REVERT: B 387 GLU cc_start: 0.8632 (tp30) cc_final: 0.8257 (pm20) REVERT: C 80 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: C 391 PHE cc_start: 0.7877 (t80) cc_final: 0.7534 (t80) REVERT: C 395 PHE cc_start: 0.7326 (m-80) cc_final: 0.6909 (m-80) REVERT: C 408 PHE cc_start: 0.9059 (t80) cc_final: 0.8616 (t80) REVERT: C 411 ARG cc_start: 0.8433 (ttp80) cc_final: 0.8110 (ptt180) REVERT: C 461 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7857 (tt) REVERT: D 295 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7412 (mpt180) REVERT: D 467 ASP cc_start: 0.9031 (t0) cc_final: 0.8787 (t0) REVERT: E 188 MET cc_start: 0.9191 (mpt) cc_final: 0.8946 (mpt) REVERT: E 275 LYS cc_start: 0.6411 (OUTLIER) cc_final: 0.5882 (mmtm) REVERT: E 367 LYS cc_start: 0.8386 (pptt) cc_final: 0.8036 (pttp) REVERT: F 5 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8360 (tp40) REVERT: F 100 GLN cc_start: 0.8751 (mt0) cc_final: 0.8456 (mt0) REVERT: F 277 TYR cc_start: 0.7538 (m-80) cc_final: 0.7299 (m-80) REVERT: F 318 GLN cc_start: 0.6277 (mt0) cc_final: 0.5765 (mt0) REVERT: F 321 CYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7378 (p) REVERT: F 323 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5766 (mp) REVERT: F 410 ASN cc_start: 0.7682 (t0) cc_final: 0.7068 (p0) REVERT: F 417 GLN cc_start: 0.8624 (tt0) cc_final: 0.7870 (mm110) REVERT: I 200 LYS cc_start: 0.8691 (ptpp) cc_final: 0.8132 (pptt) REVERT: I 247 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8494 (mt) REVERT: I 327 ASN cc_start: 0.8406 (m-40) cc_final: 0.8037 (t0) outliers start: 52 outliers final: 18 residues processed: 297 average time/residue: 1.4884 time to fit residues: 505.7590 Evaluate side-chains 264 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 343 LEU 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 461 ILE Chi-restraints excluded: chain D residue 295 ARG Chi-restraints excluded: chain E residue 3 VAL 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 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 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 229 LEU Chi-restraints excluded: chain I residue 247 LEU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 472 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 234 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN A 774 HIS D 58 GLN E 91 ASN E 245 GLN ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 GLN F 67 GLN I 456 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.107895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.073453 restraints weight = 44251.984| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.32 r_work: 0.2852 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 25181 Z= 0.273 Angle : 0.616 13.643 34374 Z= 0.326 Chirality : 0.045 0.267 3914 Planarity : 0.004 0.054 4013 Dihedral : 17.836 86.254 4071 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.93 % Allowed : 13.39 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.16), residues: 2721 helix: 1.16 (0.14), residues: 1554 sheet: 0.12 (0.30), residues: 252 loop : -0.55 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 539 HIS 0.006 0.001 HIS F 59 PHE 0.021 0.002 PHE D 363 TYR 0.025 0.002 TYR C 483 ARG 0.012 0.001 ARG D 317 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 1221) hydrogen bonds : angle 4.28856 ( 3424) covalent geometry : bond 0.00644 (25181) covalent geometry : angle 0.61583 (34374) *********************** 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 335 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 260 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLN cc_start: 0.8008 (tp40) cc_final: 0.7735 (pm20) REVERT: A 420 GLU cc_start: 0.7595 (mp0) cc_final: 0.7296 (mt-10) REVERT: A 502 GLN cc_start: 0.8868 (pt0) cc_final: 0.8576 (pt0) REVERT: A 678 ARG cc_start: 0.7745 (mtp180) cc_final: 0.7470 (ttp80) REVERT: A 913 ASN cc_start: 0.8526 (m-40) cc_final: 0.8261 (p0) REVERT: B 263 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6713 (mmp) REVERT: B 377 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8162 (mppt) REVERT: C 80 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: C 391 PHE cc_start: 0.7849 (t80) cc_final: 0.7541 (t80) REVERT: C 395 PHE cc_start: 0.7398 (m-80) cc_final: 0.6957 (m-80) REVERT: C 400 ASN cc_start: 0.8442 (t0) cc_final: 0.8171 (t0) REVERT: C 408 PHE cc_start: 0.9038 (t80) cc_final: 0.8634 (t80) REVERT: C 411 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8127 (ptt180) REVERT: C 426 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8050 (mm-30) REVERT: C 461 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7732 (tt) REVERT: C 577 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7542 (t70) REVERT: C 585 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6918 (tpt) REVERT: D 242 ARG cc_start: 0.8183 (pmt170) cc_final: 0.7915 (pmt170) REVERT: D 258 GLU cc_start: 0.9015 (mp0) cc_final: 0.8787 (mp0) REVERT: D 295 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7386 (mpt180) REVERT: D 467 ASP cc_start: 0.9071 (t0) cc_final: 0.8774 (t0) REVERT: E 275 LYS cc_start: 0.6364 (OUTLIER) cc_final: 0.5889 (mmmm) REVERT: E 367 LYS cc_start: 0.8439 (pptt) cc_final: 0.8036 (pttp) REVERT: E 414 MET cc_start: 0.8457 (tpt) cc_final: 0.8234 (tpt) REVERT: E 437 MET cc_start: 0.7679 (tpt) cc_final: 0.7465 (tpp) REVERT: E 449 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7221 (mtp85) REVERT: E 462 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6284 (mp) REVERT: F 5 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8298 (tp40) REVERT: F 277 TYR cc_start: 0.7756 (m-80) cc_final: 0.7526 (m-80) REVERT: F 287 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.8050 (mmp80) REVERT: F 323 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5734 (mp) REVERT: F 410 ASN cc_start: 0.7739 (t0) cc_final: 0.7080 (p0) REVERT: F 417 GLN cc_start: 0.8631 (tt0) cc_final: 0.7909 (mm110) REVERT: I 200 LYS cc_start: 0.8706 (ptpp) cc_final: 0.8401 (ptmt) REVERT: I 247 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8631 (mt) REVERT: I 327 ASN cc_start: 0.8512 (m-40) cc_final: 0.8170 (t0) REVERT: I 328 THR cc_start: 0.8609 (m) cc_final: 0.8267 (p) outliers start: 75 outliers final: 30 residues processed: 305 average time/residue: 1.4418 time to fit residues: 504.4738 Evaluate side-chains 284 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain B residue 263 MET 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 572 THR Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 600 GLN 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 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 E residue 462 ILE Chi-restraints excluded: chain F residue 58 CYS 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 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 220 VAL 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 453 LEU 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 242 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 270 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 230 optimal weight: 20.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 323 HIS ** E 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN F 67 GLN F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.108126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.073859 restraints weight = 44140.481| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.31 r_work: 0.2858 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 25181 Z= 0.238 Angle : 0.588 13.402 34374 Z= 0.311 Chirality : 0.044 0.275 3914 Planarity : 0.004 0.053 4013 Dihedral : 17.789 86.231 4071 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.85 % Allowed : 14.17 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 2721 helix: 1.26 (0.14), residues: 1552 sheet: 0.04 (0.31), residues: 247 loop : -0.45 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 539 HIS 0.006 0.001 HIS F 8 PHE 0.018 0.001 PHE D 363 TYR 0.022 0.002 TYR C 483 ARG 0.014 0.000 ARG D 317 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 1221) hydrogen bonds : angle 4.19432 ( 3424) covalent geometry : bond 0.00562 (25181) covalent geometry : angle 0.58800 (34374) *********************** 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: 73 poor density : 256 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLN cc_start: 0.8030 (tp40) cc_final: 0.7824 (pm20) REVERT: A 502 GLN cc_start: 0.8891 (pt0) cc_final: 0.8585 (pt0) REVERT: A 504 GLU cc_start: 0.8255 (mp0) cc_final: 0.7978 (mp0) REVERT: A 678 ARG cc_start: 0.7807 (mtp180) cc_final: 0.7512 (ttp80) REVERT: A 913 ASN cc_start: 0.8533 (m-40) cc_final: 0.8252 (p0) REVERT: B 377 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8196 (mppt) REVERT: C 80 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: C 320 MET cc_start: 0.9032 (mtm) cc_final: 0.8795 (mtm) REVERT: C 355 SER cc_start: 0.9327 (m) cc_final: 0.9006 (p) REVERT: C 391 PHE cc_start: 0.7803 (t80) cc_final: 0.7539 (t80) REVERT: C 395 PHE cc_start: 0.7431 (m-80) cc_final: 0.6744 (m-80) REVERT: C 408 PHE cc_start: 0.9049 (t80) cc_final: 0.8758 (t80) REVERT: C 426 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8028 (mm-30) REVERT: C 461 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7739 (tt) REVERT: C 577 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7431 (t70) REVERT: C 585 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6939 (tpt) REVERT: D 295 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7351 (mpt180) REVERT: D 467 ASP cc_start: 0.9059 (t0) cc_final: 0.8775 (t0) REVERT: E 170 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8962 (mtt) REVERT: E 188 MET cc_start: 0.9287 (mpt) cc_final: 0.8886 (mpt) REVERT: E 275 LYS cc_start: 0.6265 (OUTLIER) cc_final: 0.5712 (mmmm) REVERT: E 357 ILE cc_start: 0.7863 (mm) cc_final: 0.7456 (mm) REVERT: E 367 LYS cc_start: 0.8562 (pptt) cc_final: 0.8238 (pttp) REVERT: E 414 MET cc_start: 0.8416 (tpt) cc_final: 0.8204 (tpt) REVERT: F 5 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8457 (tp40) REVERT: F 67 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: F 71 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: F 100 GLN cc_start: 0.9013 (mt0) cc_final: 0.8676 (mt0) REVERT: F 277 TYR cc_start: 0.7765 (m-80) cc_final: 0.7502 (m-80) REVERT: F 323 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5816 (mp) REVERT: F 410 ASN cc_start: 0.7710 (t0) cc_final: 0.6972 (p0) REVERT: F 417 GLN cc_start: 0.8610 (tt0) cc_final: 0.7912 (mp10) REVERT: I 57 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8166 (mtm180) REVERT: I 200 LYS cc_start: 0.8706 (ptpp) cc_final: 0.8370 (ptmt) REVERT: I 327 ASN cc_start: 0.8462 (m-40) cc_final: 0.8169 (t0) REVERT: I 328 THR cc_start: 0.8595 (m) cc_final: 0.8245 (p) outliers start: 73 outliers final: 30 residues processed: 302 average time/residue: 1.4234 time to fit residues: 492.3821 Evaluate side-chains 285 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 265 MET 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 553 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 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 477 ILE Chi-restraints excluded: chain F residue 67 GLN 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 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 247 LEU Chi-restraints excluded: chain I residue 256 PHE Chi-restraints excluded: chain I residue 429 SER Chi-restraints excluded: chain I residue 453 LEU 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 66 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 214 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 GLN F 7 GLN F 67 GLN F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.109001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.073662 restraints weight = 43721.470| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.25 r_work: 0.2867 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25181 Z= 0.187 Angle : 0.569 13.359 34374 Z= 0.301 Chirality : 0.042 0.286 3914 Planarity : 0.003 0.063 4013 Dihedral : 17.745 86.409 4071 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.62 % Allowed : 15.42 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.16), residues: 2721 helix: 1.38 (0.14), residues: 1551 sheet: 0.02 (0.31), residues: 247 loop : -0.39 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 539 HIS 0.004 0.001 HIS A 629 PHE 0.016 0.001 PHE D 363 TYR 0.019 0.001 TYR C 483 ARG 0.015 0.000 ARG D 317 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 1221) hydrogen bonds : angle 4.13166 ( 3424) covalent geometry : bond 0.00439 (25181) covalent geometry : angle 0.56947 (34374) *********************** 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 316 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 249 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLN cc_start: 0.8101 (tp40) cc_final: 0.7892 (pm20) REVERT: A 420 GLU cc_start: 0.7658 (mp0) cc_final: 0.7347 (mt-10) REVERT: A 502 GLN cc_start: 0.8867 (pt0) cc_final: 0.8568 (pt0) REVERT: A 504 GLU cc_start: 0.8209 (mp0) cc_final: 0.7923 (mp0) REVERT: A 606 GLU cc_start: 0.8715 (mp0) cc_final: 0.8189 (mp0) REVERT: A 678 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7492 (ttp80) REVERT: A 907 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8462 (mm-30) REVERT: A 913 ASN cc_start: 0.8536 (m-40) cc_final: 0.8248 (p0) REVERT: B 377 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8182 (mppt) REVERT: C 80 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: C 355 SER cc_start: 0.9277 (m) cc_final: 0.8913 (p) REVERT: C 391 PHE cc_start: 0.7838 (t80) cc_final: 0.7611 (t80) REVERT: C 395 PHE cc_start: 0.7424 (m-80) cc_final: 0.6606 (m-80) REVERT: C 426 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: C 461 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7737 (tt) REVERT: C 577 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7204 (t0) REVERT: C 585 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.6940 (tpt) REVERT: D 242 ARG cc_start: 0.8019 (pmt170) cc_final: 0.7809 (pmt170) REVERT: D 295 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7288 (mpt180) REVERT: D 467 ASP cc_start: 0.9057 (t0) cc_final: 0.8762 (t0) REVERT: E 170 MET cc_start: 0.9435 (OUTLIER) cc_final: 0.8920 (mtt) REVERT: E 188 MET cc_start: 0.9300 (mpt) cc_final: 0.8958 (mpt) REVERT: E 357 ILE cc_start: 0.7812 (mm) cc_final: 0.7460 (mm) REVERT: E 367 LYS cc_start: 0.8593 (pptt) cc_final: 0.8277 (pttp) REVERT: E 414 MET cc_start: 0.8385 (tpt) cc_final: 0.8160 (tpt) REVERT: E 437 MET cc_start: 0.7664 (tpt) cc_final: 0.7462 (tpp) REVERT: E 449 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7239 (mtp85) REVERT: F 5 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8312 (tp40) REVERT: F 67 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: F 71 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: F 277 TYR cc_start: 0.7760 (m-80) cc_final: 0.7352 (m-80) REVERT: F 279 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7470 (tppt) REVERT: F 323 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5732 (mp) REVERT: F 410 ASN cc_start: 0.7723 (t0) cc_final: 0.6977 (p0) REVERT: F 417 GLN cc_start: 0.8633 (tt0) cc_final: 0.7944 (mp10) REVERT: F 424 ARG cc_start: 0.7350 (mmp80) cc_final: 0.7142 (mmp80) REVERT: I 57 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8134 (mtm180) REVERT: I 200 LYS cc_start: 0.8712 (ptpp) cc_final: 0.8387 (ptmt) REVERT: I 261 MET cc_start: 0.8516 (mtm) cc_final: 0.8277 (mtt) REVERT: I 327 ASN cc_start: 0.8437 (m-40) cc_final: 0.8190 (t0) REVERT: I 328 THR cc_start: 0.8610 (m) cc_final: 0.8270 (p) outliers start: 67 outliers final: 33 residues processed: 292 average time/residue: 1.5257 time to fit residues: 519.8129 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 : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 265 MET 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 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 295 ARG Chi-restraints excluded: chain D residue 416 GLU 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 67 GLN 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 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 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 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 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 19 optimal weight: 3.9990 chunk 166 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 GLN F 67 GLN F 73 HIS F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.110891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.076642 restraints weight = 43939.318| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.21 r_work: 0.2928 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25181 Z= 0.111 Angle : 0.523 13.444 34374 Z= 0.276 Chirality : 0.040 0.273 3914 Planarity : 0.003 0.064 4013 Dihedral : 17.478 87.954 4071 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.16), residues: 2721 helix: 1.61 (0.14), residues: 1541 sheet: 0.03 (0.31), residues: 248 loop : -0.26 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 154 HIS 0.004 0.001 HIS C 69 PHE 0.011 0.001 PHE B 243 TYR 0.016 0.001 TYR C 483 ARG 0.017 0.000 ARG D 317 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 1221) hydrogen bonds : angle 3.96089 ( 3424) covalent geometry : bond 0.00245 (25181) covalent geometry : angle 0.52275 (34374) *********************** 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 325 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 270 time to evaluate : 4.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 GLN cc_start: 0.8859 (pt0) cc_final: 0.8583 (pt0) REVERT: A 504 GLU cc_start: 0.8200 (mp0) cc_final: 0.7950 (mp0) REVERT: A 606 GLU cc_start: 0.8733 (mp0) cc_final: 0.8221 (mp0) REVERT: A 678 ARG cc_start: 0.7769 (mtp180) cc_final: 0.7494 (ttp80) REVERT: A 681 ARG cc_start: 0.8281 (tmm-80) cc_final: 0.8032 (tmm-80) REVERT: A 907 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8424 (mm-30) REVERT: A 913 ASN cc_start: 0.8537 (m-40) cc_final: 0.8255 (p0) REVERT: B 327 GLU cc_start: 0.8156 (pt0) cc_final: 0.7866 (pp20) REVERT: B 377 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8136 (mppt) REVERT: C 80 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: C 355 SER cc_start: 0.9280 (m) cc_final: 0.8954 (p) REVERT: C 395 PHE cc_start: 0.7438 (m-80) cc_final: 0.6577 (m-80) REVERT: C 426 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8070 (tp30) REVERT: C 461 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7746 (tt) REVERT: C 577 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7196 (t0) REVERT: C 606 ASP cc_start: 0.7930 (m-30) cc_final: 0.7345 (p0) REVERT: D 295 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7286 (mpt180) REVERT: D 467 ASP cc_start: 0.9069 (t0) cc_final: 0.8767 (t0) REVERT: E 188 MET cc_start: 0.9286 (mpt) cc_final: 0.8991 (mpt) REVERT: E 367 LYS cc_start: 0.8592 (pptt) cc_final: 0.8254 (pttp) REVERT: E 414 MET cc_start: 0.8393 (tpt) cc_final: 0.8188 (tpt) REVERT: E 449 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7139 (mtp85) REVERT: F 5 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8180 (tp40) REVERT: F 67 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: F 71 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: F 100 GLN cc_start: 0.8932 (mt0) cc_final: 0.8660 (mt0) REVERT: F 277 TYR cc_start: 0.7834 (m-80) cc_final: 0.7370 (m-80) REVERT: F 279 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7592 (tppt) REVERT: F 318 GLN cc_start: 0.6085 (mt0) cc_final: 0.5614 (mt0) REVERT: F 321 CYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7391 (p) REVERT: F 323 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5634 (mp) REVERT: F 410 ASN cc_start: 0.7744 (t0) cc_final: 0.7024 (p0) REVERT: F 417 GLN cc_start: 0.8656 (tt0) cc_final: 0.7855 (mm110) REVERT: F 424 ARG cc_start: 0.7381 (mmp80) cc_final: 0.6988 (mmp80) REVERT: I 200 LYS cc_start: 0.8697 (ptpp) cc_final: 0.8380 (ptmt) REVERT: I 206 GLN cc_start: 0.9084 (tt0) cc_final: 0.8383 (pt0) REVERT: I 247 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8472 (mt) REVERT: I 327 ASN cc_start: 0.8406 (m-40) cc_final: 0.8202 (t0) REVERT: I 328 THR cc_start: 0.8570 (m) cc_final: 0.8295 (p) outliers start: 55 outliers final: 22 residues processed: 309 average time/residue: 2.0501 time to fit residues: 735.7185 Evaluate side-chains 287 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 80 GLU 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 547 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP 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 449 ARG Chi-restraints excluded: chain F residue 67 GLN 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 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 I residue 164 SER 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 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 221 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 250 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 269 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 206 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 ASN ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 ASN F 7 GLN F 67 GLN F 73 HIS I 263 ASN I 428 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.108500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.073502 restraints weight = 43925.402| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.22 r_work: 0.2866 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 25181 Z= 0.238 Angle : 0.612 13.823 34374 Z= 0.318 Chirality : 0.044 0.267 3914 Planarity : 0.004 0.073 4013 Dihedral : 17.676 86.356 4071 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.46 % Allowed : 16.55 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.16), residues: 2721 helix: 1.49 (0.14), residues: 1552 sheet: 0.02 (0.31), residues: 247 loop : -0.30 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 154 HIS 0.004 0.001 HIS A 629 PHE 0.036 0.002 PHE C 391 TYR 0.022 0.001 TYR C 483 ARG 0.017 0.000 ARG D 317 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 1221) hydrogen bonds : angle 4.12223 ( 3424) covalent geometry : bond 0.00565 (25181) covalent geometry : angle 0.61178 (34374) *********************** 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 312 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 249 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7650 (mp0) cc_final: 0.7281 (mt-10) REVERT: A 502 GLN cc_start: 0.8889 (pt0) cc_final: 0.8616 (pt0) REVERT: A 504 GLU cc_start: 0.8205 (mp0) cc_final: 0.7985 (mp0) REVERT: A 606 GLU cc_start: 0.8736 (mp0) cc_final: 0.8251 (mp0) REVERT: A 678 ARG cc_start: 0.7835 (mtp180) cc_final: 0.7579 (ttp80) REVERT: A 907 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8470 (mm-30) REVERT: A 913 ASN cc_start: 0.8518 (m-40) cc_final: 0.8229 (p0) REVERT: B 327 GLU cc_start: 0.8089 (pt0) cc_final: 0.7853 (pp20) REVERT: B 377 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8219 (mppt) REVERT: C 80 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: C 355 SER cc_start: 0.9278 (m) cc_final: 0.8956 (p) REVERT: C 395 PHE cc_start: 0.7498 (m-80) cc_final: 0.6554 (m-80) REVERT: C 426 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: C 461 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7792 (tt) REVERT: C 577 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7254 (t0) REVERT: D 295 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7278 (mpt180) REVERT: D 467 ASP cc_start: 0.9061 (t0) cc_final: 0.8753 (t0) REVERT: E 188 MET cc_start: 0.9309 (mpt) cc_final: 0.8913 (mpt) REVERT: E 357 ILE cc_start: 0.7857 (mm) cc_final: 0.7503 (mm) REVERT: E 367 LYS cc_start: 0.8599 (pptt) cc_final: 0.8244 (pttp) REVERT: E 414 MET cc_start: 0.8426 (tpt) cc_final: 0.8204 (tpt) REVERT: E 449 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7305 (mtp85) REVERT: F 4 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8701 (tm130) REVERT: F 5 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8164 (tp40) REVERT: F 67 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: F 71 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: F 277 TYR cc_start: 0.7790 (m-80) cc_final: 0.7401 (m-80) REVERT: F 279 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7576 (tppt) REVERT: F 287 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7994 (mmp80) REVERT: F 323 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5710 (mp) REVERT: F 410 ASN cc_start: 0.7681 (t0) cc_final: 0.6984 (p0) REVERT: F 417 GLN cc_start: 0.8654 (tt0) cc_final: 0.7961 (mp10) REVERT: F 424 ARG cc_start: 0.7483 (mmp80) cc_final: 0.7199 (tpp-160) REVERT: I 200 LYS cc_start: 0.8688 (ptpp) cc_final: 0.8365 (ptmt) REVERT: I 206 GLN cc_start: 0.9129 (tt0) cc_final: 0.8432 (pt0) REVERT: I 327 ASN cc_start: 0.8436 (m-40) cc_final: 0.8228 (t0) REVERT: I 328 THR cc_start: 0.8606 (m) cc_final: 0.8290 (p) outliers start: 63 outliers final: 30 residues processed: 293 average time/residue: 1.5991 time to fit residues: 538.9115 Evaluate side-chains 285 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 5.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 654 THR 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 461 ILE Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP 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 449 ARG Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 67 GLN 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 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 I residue 164 SER Chi-restraints excluded: chain I residue 173 ILE 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 453 LEU 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 85 optimal weight: 2.9990 chunk 80 optimal weight: 0.0030 chunk 29 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 260 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 GLN F 67 GLN F 73 HIS F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.110525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.076264 restraints weight = 43842.770| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.20 r_work: 0.2919 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 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 0.033 25181 Z= 0.123 Angle : 0.551 14.523 34374 Z= 0.288 Chirality : 0.040 0.297 3914 Planarity : 0.003 0.076 4013 Dihedral : 17.498 88.032 4071 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.68 % Allowed : 17.60 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.17), residues: 2721 helix: 1.66 (0.14), residues: 1542 sheet: 0.06 (0.32), residues: 247 loop : -0.22 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 154 HIS 0.005 0.001 HIS C 69 PHE 0.013 0.001 PHE C 408 TYR 0.016 0.001 TYR C 483 ARG 0.019 0.000 ARG D 317 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 1221) hydrogen bonds : angle 3.97753 ( 3424) covalent geometry : bond 0.00281 (25181) covalent geometry : angle 0.55141 (34374) *********************** 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 303 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 260 time to evaluate : 4.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLN cc_start: 0.8090 (tp40) cc_final: 0.7850 (pm20) REVERT: A 420 GLU cc_start: 0.7694 (mp0) cc_final: 0.7319 (mt-10) REVERT: A 502 GLN cc_start: 0.8870 (pt0) cc_final: 0.8582 (pt0) REVERT: A 504 GLU cc_start: 0.8184 (mp0) cc_final: 0.7861 (mp0) REVERT: A 606 GLU cc_start: 0.8742 (mp0) cc_final: 0.8239 (mp0) REVERT: A 678 ARG cc_start: 0.7791 (mtp180) cc_final: 0.7549 (ttp80) REVERT: A 681 ARG cc_start: 0.8258 (tmm-80) cc_final: 0.8027 (tmm-80) REVERT: A 907 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8439 (mm-30) REVERT: A 913 ASN cc_start: 0.8518 (m-40) cc_final: 0.8212 (p0) REVERT: B 327 GLU cc_start: 0.8153 (pt0) cc_final: 0.7867 (pp20) REVERT: B 377 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8178 (mppt) REVERT: C 80 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: C 355 SER cc_start: 0.9279 (m) cc_final: 0.8977 (p) REVERT: C 391 PHE cc_start: 0.7840 (t80) cc_final: 0.7612 (t80) REVERT: C 395 PHE cc_start: 0.7429 (m-80) cc_final: 0.7207 (m-80) REVERT: C 426 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8098 (tp30) REVERT: C 454 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.7103 (p-80) REVERT: C 461 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7929 (tt) REVERT: C 577 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7238 (t0) REVERT: D 295 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7279 (mpt180) REVERT: D 467 ASP cc_start: 0.9088 (t0) cc_final: 0.8792 (t0) REVERT: E 188 MET cc_start: 0.9312 (mpt) cc_final: 0.9006 (mpt) REVERT: E 357 ILE cc_start: 0.7825 (mm) cc_final: 0.7501 (mm) REVERT: E 367 LYS cc_start: 0.8591 (pptt) cc_final: 0.8242 (pttp) REVERT: E 414 MET cc_start: 0.8441 (tpt) cc_final: 0.8231 (tpt) REVERT: E 449 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7190 (mtp85) REVERT: F 5 GLN cc_start: 0.8597 (tp-100) cc_final: 0.8182 (tp40) REVERT: F 8 HIS cc_start: 0.8803 (t-90) cc_final: 0.8272 (t-170) REVERT: F 67 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: F 71 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: F 80 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6199 (m-80) REVERT: F 277 TYR cc_start: 0.7826 (m-80) cc_final: 0.7569 (m-80) REVERT: F 287 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8049 (mmp80) REVERT: F 318 GLN cc_start: 0.6404 (mt0) cc_final: 0.5954 (mt0) REVERT: F 321 CYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7388 (p) REVERT: F 323 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5685 (mp) REVERT: F 410 ASN cc_start: 0.7732 (t0) cc_final: 0.7026 (p0) REVERT: F 417 GLN cc_start: 0.8649 (tt0) cc_final: 0.7857 (mm-40) REVERT: F 424 ARG cc_start: 0.7498 (mmp80) cc_final: 0.7236 (tpp-160) REVERT: I 200 LYS cc_start: 0.8673 (ptpp) cc_final: 0.8346 (ptmt) REVERT: I 206 GLN cc_start: 0.9106 (tt0) cc_final: 0.8390 (pt0) REVERT: I 247 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8488 (mt) REVERT: I 328 THR cc_start: 0.8570 (m) cc_final: 0.8317 (p) outliers start: 43 outliers final: 25 residues processed: 292 average time/residue: 1.9691 time to fit residues: 671.2186 Evaluate side-chains 284 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 244 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU 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 553 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP 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 341 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 449 ARG Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 67 GLN 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 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 I residue 164 SER 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 472 SER Chi-restraints excluded: chain I residue 506 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 275 optimal weight: 0.0050 chunk 72 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 217 optimal weight: 8.9990 chunk 195 optimal weight: 7.9990 chunk 281 optimal weight: 0.0980 chunk 123 optimal weight: 10.0000 overall best weight: 3.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 GLN F 67 GLN F 73 HIS I 327 ASN I 428 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.108385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.073481 restraints weight = 43906.207| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.21 r_work: 0.2864 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 25181 Z= 0.256 Angle : 0.634 14.428 34374 Z= 0.327 Chirality : 0.044 0.274 3914 Planarity : 0.004 0.080 4013 Dihedral : 17.682 86.380 4071 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.87 % Allowed : 17.53 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.16), residues: 2721 helix: 1.48 (0.14), residues: 1552 sheet: 0.03 (0.32), residues: 247 loop : -0.32 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 154 HIS 0.006 0.001 HIS F 8 PHE 0.020 0.002 PHE C 408 TYR 0.023 0.002 TYR C 483 ARG 0.019 0.001 ARG D 317 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 1221) hydrogen bonds : angle 4.14123 ( 3424) covalent geometry : bond 0.00606 (25181) covalent geometry : angle 0.63428 (34374) ********************** 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 294 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLN cc_start: 0.8171 (tp40) cc_final: 0.7960 (pm20) REVERT: A 420 GLU cc_start: 0.7758 (mp0) cc_final: 0.7401 (mt-10) REVERT: A 502 GLN cc_start: 0.8901 (pt0) cc_final: 0.8625 (pt0) REVERT: A 504 GLU cc_start: 0.8190 (mp0) cc_final: 0.7940 (mp0) REVERT: A 606 GLU cc_start: 0.8723 (mp0) cc_final: 0.8239 (mp0) REVERT: A 678 ARG cc_start: 0.7849 (mtp180) cc_final: 0.7630 (ttp80) REVERT: A 681 ARG cc_start: 0.8364 (tmm-80) cc_final: 0.8129 (tmm-80) REVERT: A 907 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8495 (mm-30) REVERT: A 913 ASN cc_start: 0.8517 (m-40) cc_final: 0.8233 (p0) REVERT: B 377 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8218 (mppt) REVERT: C 80 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: C 355 SER cc_start: 0.9212 (m) cc_final: 0.8886 (p) REVERT: C 391 PHE cc_start: 0.7970 (t80) cc_final: 0.7515 (t80) REVERT: C 395 PHE cc_start: 0.7555 (m-80) cc_final: 0.6818 (m-80) REVERT: C 426 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8069 (tp30) REVERT: C 454 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.7138 (p-80) REVERT: C 461 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7935 (tt) REVERT: C 577 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7319 (t0) REVERT: D 295 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7240 (mpt180) REVERT: D 467 ASP cc_start: 0.9061 (t0) cc_final: 0.8771 (t0) REVERT: E 188 MET cc_start: 0.9319 (mpt) cc_final: 0.8929 (mpt) REVERT: E 357 ILE cc_start: 0.7903 (mm) cc_final: 0.7549 (mm) REVERT: E 367 LYS cc_start: 0.8586 (pptt) cc_final: 0.8215 (pttp) REVERT: E 414 MET cc_start: 0.8475 (tpt) cc_final: 0.8270 (tpt) REVERT: E 449 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7316 (mtp85) REVERT: F 5 GLN cc_start: 0.8590 (tp-100) cc_final: 0.8261 (tp-100) REVERT: F 67 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: F 71 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: F 80 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.6302 (m-80) REVERT: F 277 TYR cc_start: 0.7772 (m-80) cc_final: 0.7499 (m-80) REVERT: F 287 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7981 (mmp80) REVERT: F 318 GLN cc_start: 0.6507 (mt0) cc_final: 0.6053 (mt0) REVERT: F 321 CYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7292 (p) REVERT: F 323 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5686 (mp) REVERT: F 410 ASN cc_start: 0.7707 (t0) cc_final: 0.7048 (p0) REVERT: F 417 GLN cc_start: 0.8664 (tt0) cc_final: 0.7956 (mp10) REVERT: F 424 ARG cc_start: 0.7464 (mmp80) cc_final: 0.7216 (tpp-160) REVERT: I 200 LYS cc_start: 0.8689 (ptpp) cc_final: 0.8349 (ptmt) REVERT: I 206 GLN cc_start: 0.9131 (tt0) cc_final: 0.8446 (pt0) outliers start: 48 outliers final: 26 residues processed: 280 average time/residue: 1.7664 time to fit residues: 567.1441 Evaluate side-chains 280 residues out of total 2562 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 240 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain C residue 80 GLU 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 495 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 577 ASP 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 449 ARG Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain F residue 67 GLN 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 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 I residue 164 SER Chi-restraints excluded: chain I residue 197 LEU 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 472 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 283 random chunks: chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 chunk 250 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 111 optimal weight: 0.0570 chunk 118 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 240 HIS F 67 GLN F 73 HIS I 263 ASN I 428 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.109878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.075599 restraints weight = 43780.258| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.19 r_work: 0.2906 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25181 Z= 0.138 Angle : 0.570 15.056 34374 Z= 0.296 Chirality : 0.041 0.292 3914 Planarity : 0.003 0.080 4013 Dihedral : 17.558 87.638 4071 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.72 % Allowed : 17.72 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2721 helix: 1.62 (0.14), residues: 1547 sheet: 0.06 (0.32), residues: 247 loop : -0.26 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 154 HIS 0.004 0.001 HIS C 69 PHE 0.021 0.001 PHE C 408 TYR 0.017 0.001 TYR C 483 ARG 0.019 0.000 ARG D 317 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 1221) hydrogen bonds : angle 4.01107 ( 3424) covalent geometry : bond 0.00321 (25181) covalent geometry : angle 0.56987 (34374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22343.96 seconds wall clock time: 391 minutes 22.79 seconds (23482.79 seconds total)