Starting phenix.real_space_refine on Wed Jun 18 16:33:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zp5_60327/06_2025/8zp5_60327.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zp5_60327/06_2025/8zp5_60327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zp5_60327/06_2025/8zp5_60327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zp5_60327/06_2025/8zp5_60327.map" model { file = "/net/cci-nas-00/data/ceres_data/8zp5_60327/06_2025/8zp5_60327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zp5_60327/06_2025/8zp5_60327.cif" } resolution = 2.98 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= 0.002 sd= 0.047 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 77 5.49 5 Mg 3 5.21 5 S 93 5.16 5 C 13576 2.51 5 N 3581 2.21 5 O 4152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21482 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 2905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2905 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 13, 'TRANS': 341} Chain breaks: 4 Chain: "E" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3480 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1285 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 152} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 710 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} Chain: "H" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "A" Number of atoms: 3955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3955 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 484} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4778 Classifications: {'peptide': 578} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 561} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3572 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 3 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.19, per 1000 atoms: 0.57 Number of scatterers: 21482 At special positions: 0 Unit cell: (107.06, 135.68, 171.72, 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 93 16.00 P 77 15.00 Mg 3 11.99 O 4152 8.00 N 3581 7.00 C 13576 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: 5.33 Conformation dependent library (CDL) restraints added in 2.7 seconds 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4744 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 14 sheets defined 62.5% alpha, 7.2% beta 13 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 7.29 Creating SS restraints... Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 270 through 283 Processing helix chain 'B' and resid 286 through 298 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 Processing helix chain 'B' and resid 371 through 383 Processing helix chain 'B' and resid 400 through 413 removed outlier: 4.278A pdb=" N ASN B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 447 removed outlier: 3.643A pdb=" N VAL B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 4.294A 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: 3.903A pdb=" N PHE B 492 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 493 " --> pdb=" O SER B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 516 removed outlier: 4.003A pdb=" N SER B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 540 Processing helix chain 'B' and resid 556 through 566 Processing helix chain 'B' and resid 571 through 585 removed outlier: 4.166A pdb=" N GLU B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 616 Processing helix chain 'E' and resid 12 through 22 Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.878A pdb=" N THR E 29 " --> pdb=" O PRO E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 54 Processing helix chain 'E' and resid 69 through 89 removed outlier: 3.556A 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 removed outlier: 3.764A pdb=" N LEU E 138 " --> pdb=" O PHE E 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 144 through 156 removed outlier: 4.769A pdb=" N ASN E 153 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLU E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 178 through 183 removed outlier: 5.223A pdb=" N THR E 181 " --> pdb=" O ARG E 178 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS E 183 " --> pdb=" O SER E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 211 removed outlier: 5.546A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 222 removed outlier: 3.606A pdb=" N ILE E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 252 removed outlier: 6.166A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 272 Proline residue: E 267 - end of helix removed outlier: 3.501A pdb=" N ARG E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 280 removed outlier: 3.528A pdb=" N ILE E 278 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU E 280 " --> pdb=" O GLU E 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 274 through 280' Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'E' and resid 288 through 294 removed outlier: 4.157A pdb=" N PHE E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER E 294 " --> pdb=" O LYS E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 341 Processing helix chain 'E' and resid 372 through 376 removed outlier: 3.729A pdb=" N TYR E 375 " --> pdb=" O ASN E 372 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 376 " --> pdb=" O PRO E 373 " (cutoff:3.500A) No H-bonds generated for '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: 3.658A pdb=" N PHE E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 466 Processing helix chain 'E' and resid 469 through 475 removed outlier: 3.598A pdb=" N TYR E 473 " --> pdb=" O ASN E 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 292 removed outlier: 3.753A pdb=" N ILE F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE F 292 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 309 Processing helix chain 'F' and resid 310 through 313 Processing helix chain 'F' and resid 315 through 332 Processing helix chain 'F' and resid 332 through 339 Processing helix chain 'F' and resid 339 through 351 removed outlier: 4.574A pdb=" N ASP F 343 " --> pdb=" O ASP F 339 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N HIS F 344 " --> pdb=" O PRO F 340 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS F 349 " --> pdb=" O PHE F 345 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET F 350 " --> pdb=" O ILE F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 373 Processing helix chain 'F' and resid 376 through 387 Processing helix chain 'F' and resid 393 through 403 removed outlier: 4.487A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 426 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.668A pdb=" N PHE A 406 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.754A pdb=" N LYS A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 removed outlier: 3.581A pdb=" N SER A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 502 Processing helix chain 'A' and resid 522 through 534 removed outlier: 4.153A pdb=" N GLU A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.908A pdb=" N LYS A 558 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 572 removed outlier: 4.012A pdb=" N MET A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 572' Processing helix chain 'A' and resid 576 through 585 removed outlier: 3.597A pdb=" N TYR A 580 " --> pdb=" O GLN A 576 " (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 removed outlier: 3.940A pdb=" N ALA A 706 " --> pdb=" O ASP A 702 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 787 removed outlier: 3.655A pdb=" N VAL A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 796 removed outlier: 3.551A pdb=" N ARG A 796 " --> pdb=" O THR A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 816 Processing helix chain 'A' and resid 822 through 836 removed outlier: 3.537A pdb=" N ASN A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 851 removed outlier: 5.044A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 876 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.791A pdb=" N ALA A 901 " --> pdb=" O SER A 897 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 914 Processing helix chain 'C' and resid 50 through 92 Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 138 through 159 Processing helix chain 'C' and resid 184 through 190 removed outlier: 4.100A pdb=" N VAL C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 196 Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.604A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 229 removed outlier: 3.668A 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 244 through 251 Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.650A pdb=" N LYS C 275 " --> pdb=" O LYS C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 295 through 308 removed outlier: 3.529A pdb=" N ASN C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 332 Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.999A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 346 removed outlier: 3.539A pdb=" N ASN C 342 " --> pdb=" O ASP C 339 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 346 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 356 removed outlier: 3.897A pdb=" N ARG C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 Processing helix chain 'C' and resid 373 through 381 Processing helix chain 'C' and resid 384 through 395 removed outlier: 3.540A pdb=" N LEU C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 414 removed outlier: 4.563A pdb=" N LYS C 407 " --> pdb=" O ASN C 403 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU C 414 " --> pdb=" O ALA C 410 " (cutoff:3.500A) 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 462 through 465 Processing helix chain 'C' and resid 473 through 480 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 494 through 497 Processing helix chain 'C' and resid 510 through 517 removed outlier: 3.932A pdb=" N LYS C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 531 Processing helix chain 'C' and resid 537 through 548 Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.570A pdb=" N ARG C 558 " --> pdb=" O LEU C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 572 Processing helix chain 'C' and resid 574 through 594 Processing helix chain 'D' and resid 47 through 61 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: 3.636A pdb=" N GLN D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN D 80 " --> pdb=" O GLN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.531A pdb=" N GLN D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 138 through 158 removed outlier: 4.294A pdb=" N ILE D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 229 through 241 Processing helix chain 'D' and resid 255 through 260 removed outlier: 3.605A pdb=" N TYR D 259 " --> pdb=" O ASN D 255 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 260' Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.937A pdb=" N MET D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 removed outlier: 4.082A pdb=" N ASP D 315 " --> pdb=" O LYS D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 331 Processing helix chain 'D' and resid 333 through 348 removed outlier: 3.548A pdb=" N LEU D 337 " --> pdb=" O SER D 333 " (cutoff:3.500A) Proline residue: D 343 - end of helix removed outlier: 3.803A pdb=" N SER D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 361 Processing helix chain 'D' and resid 361 through 372 removed outlier: 3.536A pdb=" N ASP D 365 " --> pdb=" O CYS D 361 " (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 426 removed outlier: 3.573A pdb=" N ILE D 426 " --> pdb=" O ILE D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 466 removed outlier: 4.535A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 490 Processing helix chain 'D' and resid 492 through 497 removed outlier: 3.800A pdb=" N MET D 496 " --> pdb=" O PHE D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 523 through 527 Processing sheet with id=AA1, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.787A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N HIS B 478 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU B 315 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU B 314 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR B 456 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE B 316 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 420 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL B 453 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU B 422 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N SER B 455 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 424 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 554 through 555 Processing sheet with id=AA3, first strand: chain 'E' and resid 58 through 62 removed outlier: 4.397A pdb=" N HIS E 58 " --> pdb=" O CYS E 127 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY E 37 " --> pdb=" O MET E 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 433 through 435 Processing sheet with id=AA5, first strand: chain 'A' and resid 411 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 514 removed outlier: 6.303A pdb=" N ILE A 561 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE A 596 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 563 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 598 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 565 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR A 473 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ALA A 597 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 475 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ALA A 599 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 477 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR A 474 " --> pdb=" O THR A 620 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE A 622 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR A 476 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE A 624 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A 478 " --> pdb=" O PHE A 624 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 657 through 659 Processing sheet with id=AA8, first strand: chain 'A' and resid 820 through 821 Processing sheet with id=AA9, first strand: chain 'C' and resid 128 through 131 removed outlier: 6.510A pdb=" N ILE C 129 " --> pdb=" O ASN C 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 124 through 125 Processing sheet with id=AB2, first strand: chain 'C' and resid 293 through 294 removed outlier: 6.719A pdb=" N ASN C 293 " --> pdb=" O LEU C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 534 through 536 removed outlier: 4.139A pdb=" N LEU C 607 " --> pdb=" O GLN C 600 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 127 through 133 removed outlier: 6.703A pdb=" N HIS D 96 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY D 249 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL D 98 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N THR D 251 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU D 100 " --> pdb=" O THR D 251 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG D 271 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 405 through 406 1019 hydrogen bonds defined for protein. 2946 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 7.90 Time building geometry restraints manager: 6.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 6673 1.35 - 1.50: 6186 1.50 - 1.65: 9038 1.65 - 1.80: 72 1.80 - 1.95: 81 Bond restraints: 22050 Sorted by residual: bond pdb=" C ARG C 145 " pdb=" O ARG C 145 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.26e-02 6.30e+03 9.25e+00 bond pdb=" NE ARG C 145 " pdb=" CZ ARG C 145 " ideal model delta sigma weight residual 1.326 1.304 0.022 1.10e-02 8.26e+03 4.04e+00 bond pdb=" N TYR A 549 " pdb=" CA TYR A 549 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.19e-02 7.06e+03 4.00e+00 bond pdb=" N ARG C 145 " pdb=" CA ARG C 145 " ideal model delta sigma weight residual 1.459 1.478 -0.019 1.28e-02 6.10e+03 2.25e+00 bond pdb=" CZ ARG C 145 " pdb=" NH2 ARG C 145 " ideal model delta sigma weight residual 1.330 1.311 0.019 1.30e-02 5.92e+03 2.07e+00 ... (remaining 22045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 29671 1.72 - 3.43: 375 3.43 - 5.15: 48 5.15 - 6.87: 11 6.87 - 8.59: 5 Bond angle restraints: 30110 Sorted by residual: angle pdb=" CA ARG C 145 " pdb=" C ARG C 145 " pdb=" O ARG C 145 " ideal model delta sigma weight residual 119.97 115.51 4.46 1.15e+00 7.56e-01 1.50e+01 angle pdb=" CA TYR A 549 " pdb=" C TYR A 549 " pdb=" O TYR A 549 " ideal model delta sigma weight residual 120.82 117.31 3.51 1.05e+00 9.07e-01 1.12e+01 angle pdb=" C PHE A 394 " pdb=" N TYR A 395 " pdb=" CA TYR A 395 " ideal model delta sigma weight residual 122.62 116.99 5.63 1.78e+00 3.16e-01 1.00e+01 angle pdb=" N VAL E 466 " pdb=" CA VAL E 466 " pdb=" C VAL E 466 " ideal model delta sigma weight residual 112.29 109.39 2.90 9.40e-01 1.13e+00 9.55e+00 angle pdb=" CG ARG C 145 " pdb=" CD ARG C 145 " pdb=" NE ARG C 145 " ideal model delta sigma weight residual 112.00 105.40 6.60 2.20e+00 2.07e-01 9.01e+00 ... (remaining 30105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.43: 12687 33.43 - 66.86: 489 66.86 - 100.29: 22 100.29 - 133.72: 0 133.72 - 167.16: 1 Dihedral angle restraints: 13199 sinusoidal: 5928 harmonic: 7271 Sorted by residual: dihedral pdb=" O1A AGS A2001 " pdb=" O3A AGS A2001 " pdb=" PA AGS A2001 " pdb=" PB AGS A2001 " ideal model delta sinusoidal sigma weight residual -67.73 99.43 -167.16 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CA PHE A 619 " pdb=" C PHE A 619 " pdb=" N THR A 620 " pdb=" CA THR A 620 " ideal model delta harmonic sigma weight residual 180.00 160.57 19.43 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ASP D 467 " pdb=" C ASP D 467 " pdb=" N PHE D 468 " pdb=" CA PHE D 468 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 13196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2220 0.030 - 0.060: 818 0.060 - 0.090: 240 0.090 - 0.120: 124 0.120 - 0.151: 20 Chirality restraints: 3422 Sorted by residual: chirality pdb=" CB ILE F 374 " pdb=" CA ILE F 374 " pdb=" CG1 ILE F 374 " pdb=" CG2 ILE F 374 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE C 240 " pdb=" N ILE C 240 " pdb=" C ILE C 240 " pdb=" CB ILE C 240 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA VAL B 476 " pdb=" N VAL B 476 " pdb=" C VAL B 476 " pdb=" CB VAL B 476 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 3419 not shown) Planarity restraints: 3544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 475 " -0.013 2.00e-02 2.50e+03 1.25e-02 2.73e+00 pdb=" CG PHE B 475 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 475 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 475 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 475 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 475 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 475 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 505 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO A 506 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 506 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 506 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 345 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.07e+00 pdb=" C PHE F 345 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE F 345 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE F 346 " 0.008 2.00e-02 2.50e+03 ... (remaining 3541 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 159 2.59 - 3.17: 17939 3.17 - 3.75: 33910 3.75 - 4.32: 48492 4.32 - 4.90: 79862 Nonbonded interactions: 180362 Sorted by model distance: nonbonded pdb=" OG1 THR D 109 " pdb="MG MG D2002 " model vdw 2.014 2.170 nonbonded pdb=" O3G AGS A2001 " pdb="MG MG A2002 " model vdw 2.028 2.170 nonbonded pdb=" OG1 THR A 486 " pdb="MG MG A2002 " model vdw 2.036 2.170 nonbonded pdb=" O2G AGS D2001 " pdb="MG MG D2002 " model vdw 2.061 2.170 nonbonded pdb=" O3G AGS E2001 " pdb="MG MG E2002 " model vdw 2.069 2.170 ... (remaining 180357 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 53.180 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 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:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.003 0.038 22050 Z= 0.127 Angle : 0.500 8.587 30110 Z= 0.272 Chirality : 0.038 0.151 3422 Planarity : 0.003 0.038 3544 Dihedral : 16.124 167.155 8455 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.04 % Allowed : 0.22 % Favored : 99.73 % 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: 0.63 (0.17), residues: 2404 helix: 1.18 (0.14), residues: 1346 sheet: -0.05 (0.34), residues: 202 loop : -0.58 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 465 HIS 0.003 0.001 HIS C 65 PHE 0.028 0.001 PHE B 475 TYR 0.015 0.001 TYR A 395 ARG 0.006 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.15222 ( 1047) hydrogen bonds : angle 6.18216 ( 3002) covalent geometry : bond 0.00279 (22050) covalent geometry : angle 0.50014 (30110) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.6920 (mmt) cc_final: 0.5689 (ptt) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 1.4550 time to fit residues: 258.8560 Evaluate side-chains 109 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 ASN C 53 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.082012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.056024 restraints weight = 52861.446| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.77 r_work: 0.2760 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22050 Z= 0.171 Angle : 0.551 6.919 30110 Z= 0.294 Chirality : 0.040 0.199 3422 Planarity : 0.004 0.039 3544 Dihedral : 16.684 158.657 3483 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.80 % Allowed : 6.46 % Favored : 92.74 % 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: 0.91 (0.17), residues: 2404 helix: 1.42 (0.14), residues: 1365 sheet: -0.20 (0.34), residues: 213 loop : -0.45 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 526 HIS 0.009 0.001 HIS C 371 PHE 0.015 0.001 PHE C 345 TYR 0.013 0.001 TYR C 605 ARG 0.006 0.000 ARG A 503 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 1047) hydrogen bonds : angle 4.47061 ( 3002) covalent geometry : bond 0.00397 (22050) covalent geometry : angle 0.55072 (30110) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.7359 (mmt) cc_final: 0.5512 (ptt) REVERT: E 223 GLN cc_start: 0.9272 (mm-40) cc_final: 0.9032 (mm110) REVERT: E 414 MET cc_start: 0.8591 (tpt) cc_final: 0.8378 (tpt) REVERT: F 344 HIS cc_start: 0.9227 (OUTLIER) cc_final: 0.8821 (t70) REVERT: F 419 ASN cc_start: 0.8271 (m-40) cc_final: 0.7962 (m110) REVERT: C 605 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.6398 (p90) outliers start: 18 outliers final: 4 residues processed: 121 average time/residue: 1.8621 time to fit residues: 256.4134 Evaluate side-chains 112 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 4.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 344 HIS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain C residue 605 TYR Chi-restraints excluded: chain D residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 53 optimal weight: 0.0470 chunk 73 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 162 optimal weight: 0.3980 chunk 78 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 ASN ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 490 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.082021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.056070 restraints weight = 52310.348| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.77 r_work: 0.2759 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22050 Z= 0.142 Angle : 0.507 9.475 30110 Z= 0.270 Chirality : 0.039 0.155 3422 Planarity : 0.003 0.040 3544 Dihedral : 16.639 154.254 3483 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.76 % Allowed : 8.73 % Favored : 90.52 % 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: 1.11 (0.17), residues: 2404 helix: 1.57 (0.14), residues: 1369 sheet: -0.20 (0.34), residues: 211 loop : -0.34 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 526 HIS 0.008 0.001 HIS C 371 PHE 0.027 0.001 PHE C 599 TYR 0.017 0.001 TYR C 449 ARG 0.008 0.000 ARG C 452 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1047) hydrogen bonds : angle 4.13753 ( 3002) covalent geometry : bond 0.00328 (22050) covalent geometry : angle 0.50667 (30110) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 498 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6211 (mpt) REVERT: E 1 MET cc_start: 0.7287 (mmt) cc_final: 0.5369 (ptt) REVERT: F 280 MET cc_start: 0.6962 (pmm) cc_final: 0.6683 (pmm) REVERT: F 344 HIS cc_start: 0.9201 (OUTLIER) cc_final: 0.8752 (t70) REVERT: F 419 ASN cc_start: 0.8261 (m-40) cc_final: 0.7930 (m110) REVERT: A 905 MET cc_start: 0.8377 (mpp) cc_final: 0.8162 (mpt) REVERT: D 120 GLN cc_start: 0.8422 (tp-100) cc_final: 0.7762 (tm-30) REVERT: D 317 ARG cc_start: 0.8661 (mtm-85) cc_final: 0.8154 (pmm-80) REVERT: D 496 MET cc_start: 0.8965 (mtm) cc_final: 0.8747 (mtp) outliers start: 17 outliers final: 5 residues processed: 121 average time/residue: 1.3718 time to fit residues: 190.3603 Evaluate side-chains 106 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 344 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain D residue 70 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 131 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 140 optimal weight: 0.8980 chunk 167 optimal weight: 6.9990 chunk 242 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 ASN ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 453 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.081539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.054848 restraints weight = 53213.235| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.78 r_work: 0.2737 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22050 Z= 0.183 Angle : 0.524 9.604 30110 Z= 0.278 Chirality : 0.040 0.158 3422 Planarity : 0.003 0.040 3544 Dihedral : 16.693 152.438 3483 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.98 % Allowed : 10.37 % Favored : 88.65 % 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: 1.16 (0.17), residues: 2404 helix: 1.63 (0.14), residues: 1368 sheet: -0.20 (0.34), residues: 213 loop : -0.34 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 526 HIS 0.006 0.001 HIS C 22 PHE 0.012 0.001 PHE C 362 TYR 0.013 0.001 TYR E 149 ARG 0.008 0.000 ARG D 425 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 1047) hydrogen bonds : angle 4.06662 ( 3002) covalent geometry : bond 0.00432 (22050) covalent geometry : angle 0.52415 (30110) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 498 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6224 (mpt) REVERT: E 1 MET cc_start: 0.7270 (mmt) cc_final: 0.5351 (ptt) REVERT: E 437 MET cc_start: 0.8448 (ppp) cc_final: 0.8140 (tmt) REVERT: F 280 MET cc_start: 0.7012 (pmm) cc_final: 0.6735 (pmm) REVERT: F 309 ASN cc_start: 0.9170 (t0) cc_final: 0.8675 (p0) REVERT: F 344 HIS cc_start: 0.9175 (OUTLIER) cc_final: 0.8704 (t70) REVERT: F 419 ASN cc_start: 0.8282 (m-40) cc_final: 0.7944 (m110) REVERT: A 503 ARG cc_start: 0.8297 (mmm160) cc_final: 0.8048 (mmm160) REVERT: A 722 MET cc_start: 0.9003 (mtm) cc_final: 0.8651 (mtp) REVERT: A 905 MET cc_start: 0.8519 (mpp) cc_final: 0.8199 (mpt) outliers start: 22 outliers final: 7 residues processed: 117 average time/residue: 1.4341 time to fit residues: 195.4647 Evaluate side-chains 108 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 344 HIS Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 70 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 36 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 ASN ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.054161 restraints weight = 53131.911| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.71 r_work: 0.2720 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22050 Z= 0.219 Angle : 0.529 9.089 30110 Z= 0.282 Chirality : 0.040 0.165 3422 Planarity : 0.004 0.072 3544 Dihedral : 16.780 150.297 3483 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.20 % Allowed : 11.18 % Favored : 87.62 % 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: 1.17 (0.17), residues: 2404 helix: 1.64 (0.14), residues: 1367 sheet: -0.25 (0.35), residues: 213 loop : -0.33 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 526 HIS 0.007 0.001 HIS C 22 PHE 0.028 0.001 PHE C 599 TYR 0.014 0.001 TYR E 149 ARG 0.017 0.001 ARG C 452 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 1047) hydrogen bonds : angle 4.05941 ( 3002) covalent geometry : bond 0.00519 (22050) covalent geometry : angle 0.52867 (30110) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 498 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.6214 (mpt) REVERT: E 1 MET cc_start: 0.7267 (mmt) cc_final: 0.5390 (ptt) REVERT: E 437 MET cc_start: 0.8513 (ppp) cc_final: 0.8281 (tmt) REVERT: F 280 MET cc_start: 0.7182 (pmm) cc_final: 0.6696 (pmm) REVERT: F 309 ASN cc_start: 0.9207 (t0) cc_final: 0.8685 (p0) REVERT: F 344 HIS cc_start: 0.9124 (OUTLIER) cc_final: 0.8635 (t70) REVERT: F 419 ASN cc_start: 0.8304 (m-40) cc_final: 0.7978 (m110) REVERT: A 702 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8090 (t0) REVERT: A 722 MET cc_start: 0.8984 (mtm) cc_final: 0.8663 (mtp) REVERT: D 317 ARG cc_start: 0.8681 (mtm-85) cc_final: 0.8095 (pmm-80) outliers start: 27 outliers final: 9 residues processed: 120 average time/residue: 1.3277 time to fit residues: 183.5181 Evaluate side-chains 106 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 344 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 70 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 ASN B 493 GLN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.081190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.054820 restraints weight = 53095.420| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.74 r_work: 0.2733 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22050 Z= 0.172 Angle : 0.516 9.100 30110 Z= 0.274 Chirality : 0.039 0.156 3422 Planarity : 0.003 0.045 3544 Dihedral : 16.702 147.225 3483 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.11 % Allowed : 11.84 % Favored : 87.04 % 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 (0.17), residues: 2404 helix: 1.69 (0.14), residues: 1368 sheet: -0.26 (0.35), residues: 211 loop : -0.33 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 526 HIS 0.008 0.001 HIS C 22 PHE 0.022 0.001 PHE A 619 TYR 0.013 0.001 TYR C 23 ARG 0.010 0.000 ARG A 503 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 1047) hydrogen bonds : angle 4.00248 ( 3002) covalent geometry : bond 0.00405 (22050) covalent geometry : angle 0.51586 (30110) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 498 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6235 (mpt) REVERT: E 1 MET cc_start: 0.7283 (mmt) cc_final: 0.5405 (ptt) REVERT: E 341 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8468 (tt) REVERT: E 437 MET cc_start: 0.8666 (ppp) cc_final: 0.8389 (tmt) REVERT: F 280 MET cc_start: 0.7193 (pmm) cc_final: 0.6763 (pmm) REVERT: F 309 ASN cc_start: 0.9238 (t0) cc_final: 0.8720 (p0) REVERT: F 344 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.8578 (t70) REVERT: F 419 ASN cc_start: 0.8320 (m-40) cc_final: 0.7972 (m110) REVERT: A 503 ARG cc_start: 0.8432 (mmm160) cc_final: 0.8217 (mmm160) REVERT: A 722 MET cc_start: 0.8984 (mtm) cc_final: 0.8638 (mtp) REVERT: C 465 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8406 (mm) REVERT: D 317 ARG cc_start: 0.8686 (mtm-85) cc_final: 0.8098 (pmm-80) outliers start: 25 outliers final: 10 residues processed: 114 average time/residue: 1.3451 time to fit residues: 176.8702 Evaluate side-chains 108 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 344 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 112 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 137 optimal weight: 0.2980 chunk 197 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 178 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 140 optimal weight: 0.5980 chunk 190 optimal weight: 0.7980 chunk 235 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 ASN E 428 HIS ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.082306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.056388 restraints weight = 52758.374| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.71 r_work: 0.2773 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22050 Z= 0.114 Angle : 0.480 9.674 30110 Z= 0.257 Chirality : 0.038 0.147 3422 Planarity : 0.003 0.055 3544 Dihedral : 16.519 141.532 3483 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.29 % Allowed : 12.07 % Favored : 86.64 % 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: 1.32 (0.17), residues: 2404 helix: 1.82 (0.14), residues: 1358 sheet: -0.25 (0.34), residues: 217 loop : -0.33 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 58 HIS 0.007 0.001 HIS C 22 PHE 0.030 0.001 PHE C 599 TYR 0.017 0.001 TYR C 605 ARG 0.008 0.000 ARG C 452 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 1047) hydrogen bonds : angle 3.88254 ( 3002) covalent geometry : bond 0.00259 (22050) covalent geometry : angle 0.47993 (30110) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 498 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.6232 (mpt) REVERT: E 1 MET cc_start: 0.7312 (mmt) cc_final: 0.5362 (ptt) REVERT: F 280 MET cc_start: 0.7081 (pmm) cc_final: 0.6488 (pmm) REVERT: F 309 ASN cc_start: 0.9225 (t0) cc_final: 0.8770 (p0) REVERT: F 344 HIS cc_start: 0.9042 (OUTLIER) cc_final: 0.8478 (t70) REVERT: F 419 ASN cc_start: 0.8288 (m-40) cc_final: 0.7944 (m110) REVERT: A 503 ARG cc_start: 0.8470 (mmm160) cc_final: 0.8223 (mmm160) REVERT: A 722 MET cc_start: 0.9053 (mtm) cc_final: 0.8689 (mtp) REVERT: C 465 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8382 (mm) REVERT: D 317 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8092 (pmm-80) outliers start: 29 outliers final: 12 residues processed: 121 average time/residue: 1.2451 time to fit residues: 177.4536 Evaluate side-chains 110 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 344 HIS Chi-restraints excluded: chain F residue 386 TYR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 206 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.081748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.055530 restraints weight = 53248.761| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.68 r_work: 0.2753 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22050 Z= 0.156 Angle : 0.507 13.911 30110 Z= 0.267 Chirality : 0.039 0.147 3422 Planarity : 0.003 0.041 3544 Dihedral : 16.540 140.777 3483 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.20 % Allowed : 12.56 % Favored : 86.24 % 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: 1.32 (0.17), residues: 2404 helix: 1.82 (0.14), residues: 1358 sheet: -0.26 (0.34), residues: 219 loop : -0.32 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 58 HIS 0.007 0.001 HIS C 22 PHE 0.013 0.001 PHE C 362 TYR 0.017 0.001 TYR F 386 ARG 0.007 0.000 ARG C 452 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 1047) hydrogen bonds : angle 3.88952 ( 3002) covalent geometry : bond 0.00367 (22050) covalent geometry : angle 0.50696 (30110) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 498 MET cc_start: 0.6706 (OUTLIER) cc_final: 0.6194 (mpt) REVERT: E 1 MET cc_start: 0.7307 (mmt) cc_final: 0.5369 (ptt) REVERT: E 437 MET cc_start: 0.8589 (tmt) cc_final: 0.8325 (tmm) REVERT: F 280 MET cc_start: 0.7098 (pmm) cc_final: 0.6539 (pmm) REVERT: F 309 ASN cc_start: 0.9259 (t0) cc_final: 0.8763 (p0) REVERT: F 344 HIS cc_start: 0.9022 (OUTLIER) cc_final: 0.8449 (t70) REVERT: F 419 ASN cc_start: 0.8289 (m-40) cc_final: 0.7956 (m110) REVERT: A 503 ARG cc_start: 0.8453 (mmm160) cc_final: 0.8197 (mmm160) REVERT: A 722 MET cc_start: 0.9067 (mtm) cc_final: 0.8697 (mtp) REVERT: C 465 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8395 (mm) REVERT: D 130 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8999 (mt) REVERT: D 317 ARG cc_start: 0.8652 (mtm-85) cc_final: 0.8089 (pmm-80) outliers start: 27 outliers final: 16 residues processed: 119 average time/residue: 1.2586 time to fit residues: 173.7736 Evaluate side-chains 116 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 344 HIS Chi-restraints excluded: chain F residue 386 TYR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 229 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 145 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 191 optimal weight: 0.0570 chunk 189 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 0.0050 overall best weight: 0.8116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 ASN ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.082356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.056585 restraints weight = 52967.060| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.67 r_work: 0.2772 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22050 Z= 0.121 Angle : 0.500 13.204 30110 Z= 0.262 Chirality : 0.038 0.145 3422 Planarity : 0.003 0.038 3544 Dihedral : 16.509 138.383 3483 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.25 % Allowed : 12.60 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.34 (0.17), residues: 2404 helix: 1.83 (0.14), residues: 1358 sheet: -0.26 (0.34), residues: 219 loop : -0.32 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 58 HIS 0.007 0.001 HIS C 22 PHE 0.019 0.001 PHE C 599 TYR 0.025 0.001 TYR C 449 ARG 0.010 0.000 ARG C 452 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 1047) hydrogen bonds : angle 3.85328 ( 3002) covalent geometry : bond 0.00280 (22050) covalent geometry : angle 0.50014 (30110) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 498 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6225 (mpt) REVERT: E 1 MET cc_start: 0.7302 (mmt) cc_final: 0.5333 (ptt) REVERT: E 437 MET cc_start: 0.8577 (tmt) cc_final: 0.8329 (tmm) REVERT: F 280 MET cc_start: 0.7063 (pmm) cc_final: 0.6578 (pmm) REVERT: F 309 ASN cc_start: 0.9189 (t0) cc_final: 0.8738 (p0) REVERT: F 344 HIS cc_start: 0.8961 (OUTLIER) cc_final: 0.8349 (t70) REVERT: F 419 ASN cc_start: 0.8244 (m-40) cc_final: 0.7919 (m110) REVERT: A 503 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8124 (mmm160) REVERT: A 722 MET cc_start: 0.9079 (mtm) cc_final: 0.8752 (mtp) REVERT: C 465 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8381 (mm) REVERT: C 517 MET cc_start: 0.8707 (ttt) cc_final: 0.8367 (ttt) REVERT: D 130 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8977 (mt) REVERT: D 317 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8085 (pmm-80) REVERT: D 334 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9033 (mm) outliers start: 28 outliers final: 16 residues processed: 123 average time/residue: 1.2063 time to fit residues: 172.7167 Evaluate side-chains 116 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 344 HIS Chi-restraints excluded: chain F residue 386 TYR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 334 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 241 optimal weight: 4.9990 chunk 207 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 123 optimal weight: 0.1980 chunk 133 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.082758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056664 restraints weight = 53268.117| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.70 r_work: 0.2781 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22050 Z= 0.110 Angle : 0.504 15.383 30110 Z= 0.261 Chirality : 0.038 0.142 3422 Planarity : 0.003 0.052 3544 Dihedral : 16.441 136.299 3483 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.98 % Allowed : 12.82 % Favored : 86.20 % 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: 1.38 (0.17), residues: 2404 helix: 1.87 (0.14), residues: 1358 sheet: -0.25 (0.34), residues: 219 loop : -0.31 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 58 HIS 0.007 0.001 HIS C 22 PHE 0.013 0.001 PHE C 362 TYR 0.015 0.001 TYR C 605 ARG 0.013 0.000 ARG C 452 Details of bonding type rmsd hydrogen bonds : bond 0.03039 ( 1047) hydrogen bonds : angle 3.82816 ( 3002) covalent geometry : bond 0.00251 (22050) covalent geometry : angle 0.50391 (30110) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 2.647 Fit side-chains revert: symmetry clash REVERT: B 498 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6256 (mpt) REVERT: E 1 MET cc_start: 0.7286 (mmt) cc_final: 0.5296 (ptt) REVERT: E 437 MET cc_start: 0.8599 (tmt) cc_final: 0.8360 (tmm) REVERT: F 280 MET cc_start: 0.7050 (pmm) cc_final: 0.6670 (pmm) REVERT: F 309 ASN cc_start: 0.9200 (t0) cc_final: 0.8740 (p0) REVERT: F 344 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.8725 (m-70) REVERT: F 386 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.7895 (t80) REVERT: F 419 ASN cc_start: 0.8256 (m-40) cc_final: 0.7964 (m110) REVERT: A 503 ARG cc_start: 0.8507 (mmm160) cc_final: 0.8149 (mmm160) REVERT: A 722 MET cc_start: 0.9085 (mtm) cc_final: 0.8755 (mtp) REVERT: C 465 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8364 (mm) REVERT: C 517 MET cc_start: 0.8730 (ttt) cc_final: 0.8385 (ttt) REVERT: D 130 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8963 (mt) REVERT: D 317 ARG cc_start: 0.8646 (mtm-85) cc_final: 0.8083 (pmm-80) outliers start: 22 outliers final: 13 residues processed: 116 average time/residue: 1.4507 time to fit residues: 197.0118 Evaluate side-chains 114 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 344 HIS Chi-restraints excluded: chain F residue 386 TYR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 229 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 112 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 chunk 23 optimal weight: 0.2980 chunk 188 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 ASN ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.082093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.056281 restraints weight = 53263.671| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.66 r_work: 0.2759 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22050 Z= 0.146 Angle : 0.516 14.054 30110 Z= 0.267 Chirality : 0.038 0.146 3422 Planarity : 0.003 0.038 3544 Dihedral : 16.490 135.930 3483 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.11 % Allowed : 12.73 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.38 (0.17), residues: 2404 helix: 1.88 (0.14), residues: 1358 sheet: -0.27 (0.34), residues: 219 loop : -0.32 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 421 HIS 0.007 0.001 HIS C 22 PHE 0.024 0.001 PHE C 599 TYR 0.024 0.001 TYR C 449 ARG 0.005 0.000 ARG D 425 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 1047) hydrogen bonds : angle 3.82716 ( 3002) covalent geometry : bond 0.00343 (22050) covalent geometry : angle 0.51565 (30110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12335.29 seconds wall clock time: 214 minutes 16.41 seconds (12856.41 seconds total)