Starting phenix.real_space_refine on Fri Aug 7 13:42:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpk_60347/08_2026/8zpk_60347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpk_60347/08_2026/8zpk_60347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zpk_60347/08_2026/8zpk_60347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpk_60347/08_2026/8zpk_60347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zpk_60347/08_2026/8zpk_60347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpk_60347/08_2026/8zpk_60347.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.048 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 86 5.49 5 Mg 3 5.21 5 S 93 5.16 5 C 13885 2.51 5 N 3689 2.21 5 O 4277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22033 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3015 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 357} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3697 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 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: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 769 Classifications: {'DNA': 38} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 37} Chain: "H" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 826 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} 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: 4818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4818 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 566} Chain breaks: 1 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: 3.79, per 1000 atoms: 0.17 Number of scatterers: 22033 At special positions: 0 Unit cell: (114.4, 133.1, 185.9, 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 86 15.00 Mg 3 11.99 O 4277 8.00 N 3689 7.00 C 13885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 887.4 milliseconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4834 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 12 sheets defined 60.6% alpha, 6.3% beta 9 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'B' and resid 241 through 249 removed outlier: 3.593A pdb=" N TYR B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.534A pdb=" N PHE B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.507A pdb=" N ARG B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 310 removed outlier: 3.506A pdb=" N GLN B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) 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 384 Processing helix chain 'B' and resid 389 through 394 removed outlier: 4.223A pdb=" N LYS B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 434 through 445 Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 468 through 474 removed outlier: 3.620A pdb=" N ASN B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 removed outlier: 4.137A pdb=" N PHE B 492 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 506 through 515 removed outlier: 4.153A pdb=" N ALA B 510 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 540 Processing helix chain 'B' and resid 549 through 553 Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.541A pdb=" N ALA B 565 " --> pdb=" O HIS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 585 removed outlier: 3.771A pdb=" N ARG B 580 " --> pdb=" O ARG B 576 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLU B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 4.279A 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 11 through 22 Processing helix chain 'E' and resid 43 through 54 Processing helix chain 'E' and resid 70 through 89 removed outlier: 3.835A 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 119 removed outlier: 4.008A pdb=" N GLN E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR E 119 " --> pdb=" O ILE E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 138 removed outlier: 4.009A 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 145 through 152 removed outlier: 3.856A pdb=" N LYS E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 removed outlier: 3.512A pdb=" N SER E 180 " --> pdb=" O GLN E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 205 removed outlier: 3.648A pdb=" N VAL E 197 " --> pdb=" O ASN E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 211 removed outlier: 3.984A pdb=" N MET E 210 " --> pdb=" O CYS E 206 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 206 through 211' Processing helix chain 'E' and resid 212 through 221 removed outlier: 3.686A pdb=" N ARG E 216 " --> pdb=" O ASP E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 252 removed outlier: 5.815A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.540A pdb=" N LEU E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP E 263 " --> pdb=" O ASN E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 273 removed outlier: 3.755A pdb=" N TYR E 269 " --> pdb=" O LYS E 265 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER E 271 " --> pdb=" O PRO E 267 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 273 " --> pdb=" O TYR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 278 Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'E' and resid 289 through 293 removed outlier: 3.531A pdb=" N PHE E 292 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 293 " --> pdb=" O LYS E 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 289 through 293' Processing helix chain 'E' and resid 325 through 340 removed outlier: 3.561A pdb=" N ILE E 333 " --> pdb=" O LYS E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 345 Processing helix chain 'E' and resid 346 through 351 removed outlier: 3.533A pdb=" N PHE E 350 " --> pdb=" O ASP E 346 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 346 through 351' Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 382 through 394 Processing helix chain 'E' and resid 417 through 430 removed outlier: 3.658A pdb=" N PHE E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 465 Processing helix chain 'E' and resid 470 through 476 removed outlier: 3.699A pdb=" N PHE E 474 " --> pdb=" O ILE E 470 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP E 476 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 3.575A pdb=" N ILE F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 310 removed outlier: 3.722A pdb=" N ILE F 308 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 332 removed outlier: 3.749A pdb=" N LEU F 319 " --> pdb=" O CYS F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 339 Processing helix chain 'F' and resid 341 through 354 removed outlier: 4.018A pdb=" N PHE F 345 " --> pdb=" O ARG F 341 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET F 350 " --> pdb=" O ILE F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 373 removed outlier: 3.567A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 373 " --> pdb=" O VAL F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 387 Processing helix chain 'F' and resid 393 through 403 removed outlier: 3.522A pdb=" N ILE F 398 " --> pdb=" O TYR F 394 " (cutoff:3.500A) removed outlier: 4.531A 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 381 through 385 Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.000A pdb=" N GLY A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 407 removed outlier: 4.006A pdb=" N PHE A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 429 removed outlier: 4.170A pdb=" N LYS A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 484 through 502 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.514A pdb=" N THR A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.788A pdb=" N VAL A 553 " --> pdb=" O TYR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 removed outlier: 4.057A pdb=" N LYS A 558 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.615A pdb=" N ARG A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 630 through 640 Processing helix chain 'A' and resid 685 through 700 removed outlier: 3.711A pdb=" N VAL A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 726 Processing helix chain 'A' and resid 774 through 787 removed outlier: 3.724A pdb=" N VAL A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 798 through 816 Processing helix chain 'A' and resid 822 through 836 removed outlier: 3.552A pdb=" N ASN A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 851 removed outlier: 3.572A pdb=" N ALA A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 876 removed outlier: 3.768A pdb=" N VAL A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 909 through 914 Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'C' and resid 50 through 92 removed outlier: 3.650A pdb=" N VAL C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 139 through 159 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 207 through 211 removed outlier: 3.564A pdb=" N ILE C 211 " --> pdb=" O VAL C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 224 removed outlier: 3.586A pdb=" N LEU C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 removed outlier: 4.334A pdb=" N LYS C 228 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 through 229' Processing helix chain 'C' and resid 243 through 251 removed outlier: 4.314A pdb=" N ILE C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 removed outlier: 3.650A pdb=" N ILE C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 295 through 307 Processing helix chain 'C' and resid 313 through 332 Processing helix chain 'C' and resid 334 through 344 removed outlier: 3.818A pdb=" N ASP C 339 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Proline residue: C 340 - end of helix removed outlier: 3.521A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 355 Processing helix chain 'C' and resid 357 through 371 Processing helix chain 'C' and resid 374 through 381 removed outlier: 3.766A pdb=" N LEU C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 395 removed outlier: 4.062A pdb=" N LEU C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 415 Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 435 through 441 Processing helix chain 'C' and resid 442 through 444 No H-bonds generated for 'chain 'C' and resid 442 through 444' Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.634A pdb=" N LEU C 465 " --> pdb=" O PHE C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 479 removed outlier: 3.592A pdb=" N ILE C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 494 through 497 Processing helix chain 'C' and resid 510 through 517 Processing helix chain 'C' and resid 519 through 531 removed outlier: 3.578A pdb=" N LYS C 526 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 548 removed outlier: 3.536A pdb=" N LEU C 548 " --> pdb=" O PHE C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 560 removed outlier: 4.287A pdb=" N ASP C 560 " --> pdb=" O PHE C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 571 removed outlier: 3.746A pdb=" N GLU C 571 " --> pdb=" O LEU C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 595 removed outlier: 3.686A pdb=" N LYS C 578 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.774A pdb=" N LYS D 69 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 91 Processing helix chain 'D' and resid 108 through 120 Processing helix chain 'D' and resid 140 through 158 removed outlier: 4.029A 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 218 through 222 Processing helix chain 'D' and resid 229 through 240 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 301 through 314 removed outlier: 3.723A pdb=" N GLU D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 310 " --> pdb=" O ASN D 306 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 331 Processing helix chain 'D' and resid 333 through 348 removed outlier: 3.754A pdb=" N LEU D 337 " --> pdb=" O SER D 333 " (cutoff:3.500A) Proline residue: D 343 - end of helix removed outlier: 4.030A 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: 4.232A pdb=" N ASP D 365 " --> pdb=" O CYS D 361 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE D 366 " --> pdb=" O SER D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 380 removed outlier: 3.952A pdb=" N LEU D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 401 removed outlier: 3.648A pdb=" N ARG D 400 " --> pdb=" O ARG D 396 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 Processing helix chain 'D' and resid 452 through 466 removed outlier: 4.212A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 488 removed outlier: 3.519A pdb=" N ALA D 484 " --> pdb=" O ASN D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.768A pdb=" N ARG D 502 " --> pdb=" O PHE D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 517 Processing helix chain 'D' and resid 523 through 527 Processing sheet with id=AA1, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.086A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N HIS B 478 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU B 315 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 314 " --> pdb=" O ILE B 452 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 454 " --> pdb=" O LEU B 314 " (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: 6.899A pdb=" N HIS E 58 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE E 131 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL E 60 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASP E 133 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU E 62 " --> pdb=" O ASP E 133 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR E 169 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU E 35 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE E 34 " --> pdb=" O VAL E 187 " (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 508 through 511 removed outlier: 6.771A pdb=" N LEU A 509 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE A 561 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE A 596 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 563 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N VAL A 598 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 657 through 659 removed outlier: 3.929A pdb=" N SER A 646 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 682 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N GLN A 771 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG A 681 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL A 773 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ARG A 683 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 820 through 821 Processing sheet with id=AA8, first strand: chain 'C' and resid 236 through 240 removed outlier: 6.670A pdb=" N THR C 104 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU C 266 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE C 106 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 128 through 131 Processing sheet with id=AB1, first strand: chain 'C' and resid 534 through 536 removed outlier: 4.697A pdb=" N LEU C 607 " --> pdb=" O GLN C 600 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 133 removed outlier: 8.384A pdb=" N ILE D 273 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE D 99 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 469 through 471 956 hydrogen bonds defined for protein. 2721 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 38 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6931 1.36 - 1.50: 6395 1.50 - 1.64: 9149 1.64 - 1.79: 10 1.79 - 1.93: 143 Bond restraints: 22628 Sorted by residual: bond pdb=" O2G AGS A2001 " pdb=" PG AGS A2001 " ideal model delta sigma weight residual 1.604 1.490 0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" O2G AGS E2001 " pdb=" PG AGS E2001 " ideal model delta sigma weight residual 1.604 1.493 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" O2G AGS D2001 " pdb=" PG AGS D2001 " ideal model delta sigma weight residual 1.604 1.500 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O3B AGS D2001 " pdb=" PB AGS D2001 " ideal model delta sigma weight residual 1.673 1.589 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" O3B AGS E2001 " pdb=" PB AGS E2001 " ideal model delta sigma weight residual 1.673 1.590 0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 22623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 30175 1.55 - 3.09: 648 3.09 - 4.64: 82 4.64 - 6.18: 19 6.18 - 7.73: 6 Bond angle restraints: 30930 Sorted by residual: angle pdb=" N3 DT H 69 " pdb=" C4 DT H 69 " pdb=" O4 DT H 69 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT G 20 " pdb=" C4 DT G 20 " pdb=" O4 DT G 20 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT H 33 " pdb=" C4 DT H 33 " pdb=" O4 DT H 33 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT G 34 " pdb=" C4 DT G 34 " pdb=" O4 DT G 34 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT G 25 " pdb=" C4 DT G 25 " pdb=" O4 DT G 25 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 ... (remaining 30925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 13044 35.97 - 71.95: 530 71.95 - 107.92: 21 107.92 - 143.89: 2 143.89 - 179.87: 1 Dihedral angle restraints: 13598 sinusoidal: 6184 harmonic: 7414 Sorted by residual: dihedral pdb=" O1B AGS E2001 " pdb=" O3B AGS E2001 " pdb=" PB AGS E2001 " pdb=" PG AGS E2001 " ideal model delta sinusoidal sigma weight residual 138.55 -41.32 179.87 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA THR F 281 " pdb=" C THR F 281 " pdb=" N THR F 282 " pdb=" CA THR F 282 " ideal model delta harmonic sigma weight residual -180.00 -158.03 -21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" O1A AGS E2001 " pdb=" O3A AGS E2001 " pdb=" PA AGS E2001 " pdb=" PB AGS E2001 " ideal model delta sinusoidal sigma weight residual 82.37 -52.84 135.21 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 13595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3220 0.073 - 0.147: 280 0.147 - 0.220: 5 0.220 - 0.293: 2 0.293 - 0.367: 1 Chirality restraints: 3508 Sorted by residual: chirality pdb=" C3' AGS D2001 " pdb=" C2' AGS D2001 " pdb=" C4' AGS D2001 " pdb=" O3' AGS D2001 " both_signs ideal model delta sigma weight residual False -2.37 -2.74 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C3' AGS A2001 " pdb=" C2' AGS A2001 " pdb=" C4' AGS A2001 " pdb=" O3' AGS A2001 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C3' AGS E2001 " pdb=" C2' AGS E2001 " pdb=" C4' AGS E2001 " pdb=" O3' AGS E2001 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 3505 not shown) Planarity restraints: 3621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 339 " 0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO F 340 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO F 340 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 340 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 480 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO A 481 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.026 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO C 373 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.023 5.00e-02 4.00e+02 ... (remaining 3618 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 84 2.53 - 3.13: 16216 3.13 - 3.72: 31823 3.72 - 4.31: 43563 4.31 - 4.90: 74370 Nonbonded interactions: 166056 Sorted by model distance: nonbonded pdb=" O3G AGS E2001 " pdb="MG MG E2002 " model vdw 1.942 2.170 nonbonded pdb=" O2G AGS D2001 " pdb="MG MG D2002 " model vdw 2.045 2.170 nonbonded pdb=" OG1 THR D 109 " pdb="MG MG D2002 " model vdw 2.048 2.170 nonbonded pdb=" O2B AGS A2001 " pdb="MG MG A2002 " model vdw 2.114 2.170 nonbonded pdb=" O HIS B 425 " pdb=" OG SER B 455 " model vdw 2.210 3.040 ... (remaining 166051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.740 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 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 : 0.004 0.114 22628 Z= 0.244 Angle : 0.547 7.729 30930 Z= 0.358 Chirality : 0.042 0.367 3508 Planarity : 0.003 0.061 3621 Dihedral : 17.249 179.867 8764 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.18), residues: 2460 helix: 1.46 (0.15), residues: 1294 sheet: -0.18 (0.38), residues: 200 loop : -1.51 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 607 TYR 0.015 0.001 TYR B 473 PHE 0.026 0.001 PHE F 329 TRP 0.013 0.001 TRP C 58 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.24 (22628) covalent geometry : angle 0.54743 / 0.36 (30930) hydrogen bonds : bond 0.16889 / 10.85 ( 977) hydrogen bonds : angle 5.32964 / 3.78 ( 2759) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 307 ASN cc_start: 0.9712 (m110) cc_final: 0.9506 (m-40) REVERT: F 327 CYS cc_start: 0.9303 (m) cc_final: 0.8823 (m) REVERT: C 371 HIS cc_start: 0.8965 (m90) cc_final: 0.8614 (m-70) REVERT: C 533 MET cc_start: 0.8920 (tmm) cc_final: 0.8615 (tmm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1358 time to fit residues: 22.8684 Evaluate side-chains 82 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 261 HIS E 36 GLN E 82 GLN ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN F 318 GLN F 417 GLN A 882 GLN C 138 ASN C 246 ASN C 383 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.042269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.028629 restraints weight = 131737.481| |-----------------------------------------------------------------------------| r_work (start): 0.2488 rms_B_bonded: 4.29 r_work: 0.2342 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22628 Z= 0.191 Angle : 0.572 8.882 30930 Z= 0.306 Chirality : 0.042 0.198 3508 Planarity : 0.004 0.046 3621 Dihedral : 18.189 173.997 3699 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.53 % Allowed : 5.69 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 2460 helix: 1.67 (0.15), residues: 1329 sheet: -0.05 (0.38), residues: 201 loop : -1.37 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 336 TYR 0.016 0.001 TYR F 300 PHE 0.019 0.001 PHE F 345 TRP 0.009 0.001 TRP C 58 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (22628) covalent geometry : angle 0.57187 / 0.31 (30930) hydrogen bonds : bond 0.04830 / 3.09 ( 977) hydrogen bonds : angle 4.15162 / 2.93 ( 2759) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.664 Fit side-chains REVERT: E 188 MET cc_start: 0.9005 (mtm) cc_final: 0.8736 (mtm) REVERT: F 307 ASN cc_start: 0.9510 (m110) cc_final: 0.9241 (m-40) REVERT: F 327 CYS cc_start: 0.9069 (m) cc_final: 0.8797 (m) REVERT: F 354 MET cc_start: 0.8872 (tpp) cc_final: 0.8145 (tpp) REVERT: C 488 GLU cc_start: 0.9539 (mm-30) cc_final: 0.9279 (mt-10) REVERT: C 533 MET cc_start: 0.9138 (tmm) cc_final: 0.8690 (tmm) outliers start: 12 outliers final: 3 residues processed: 87 average time/residue: 0.1146 time to fit residues: 17.3778 Evaluate side-chains 81 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain C residue 446 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 101 optimal weight: 30.0000 chunk 231 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 251 optimal weight: 0.0570 chunk 146 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 82 GLN F 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.042458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.029061 restraints weight = 131469.921| |-----------------------------------------------------------------------------| r_work (start): 0.2501 rms_B_bonded: 4.27 r_work: 0.2357 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22628 Z= 0.130 Angle : 0.496 8.407 30930 Z= 0.271 Chirality : 0.040 0.151 3508 Planarity : 0.003 0.091 3621 Dihedral : 18.006 178.072 3699 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.61 % Allowed : 7.44 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.18), residues: 2460 helix: 1.78 (0.15), residues: 1338 sheet: 0.14 (0.38), residues: 201 loop : -1.40 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 425 TYR 0.015 0.001 TYR F 418 PHE 0.018 0.001 PHE F 345 TRP 0.009 0.001 TRP C 58 HIS 0.011 0.001 HIS C 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (22628) covalent geometry : angle 0.49558 / 0.27 (30930) hydrogen bonds : bond 0.04228 / 2.70 ( 977) hydrogen bonds : angle 3.82982 / 2.71 ( 2759) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: E 188 MET cc_start: 0.9122 (mtm) cc_final: 0.8868 (mtm) REVERT: E 291 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8144 (pp) REVERT: F 307 ASN cc_start: 0.9451 (m110) cc_final: 0.9196 (m110) REVERT: F 327 CYS cc_start: 0.9069 (m) cc_final: 0.8816 (m) REVERT: F 354 MET cc_start: 0.8895 (tpp) cc_final: 0.8677 (tpp) REVERT: A 887 ASP cc_start: 0.9533 (t0) cc_final: 0.9241 (t0) REVERT: C 385 ASN cc_start: 0.9743 (p0) cc_final: 0.9451 (m-40) REVERT: C 488 GLU cc_start: 0.9545 (mm-30) cc_final: 0.9277 (mt-10) REVERT: C 533 MET cc_start: 0.9101 (tmm) cc_final: 0.8561 (tmm) REVERT: D 522 MET cc_start: 0.9430 (ppp) cc_final: 0.9209 (ppp) outliers start: 14 outliers final: 5 residues processed: 87 average time/residue: 0.1221 time to fit residues: 18.2742 Evaluate side-chains 86 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 499 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 159 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 131 optimal weight: 0.3980 chunk 137 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 146 optimal weight: 0.2980 chunk 144 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 82 GLN E 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.042138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.028977 restraints weight = 131638.955| |-----------------------------------------------------------------------------| r_work (start): 0.2506 rms_B_bonded: 4.08 r_work: 0.2359 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22628 Z= 0.136 Angle : 0.480 7.492 30930 Z= 0.261 Chirality : 0.039 0.160 3508 Planarity : 0.003 0.042 3621 Dihedral : 17.773 177.085 3699 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.48 % Allowed : 9.06 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.18), residues: 2460 helix: 1.93 (0.15), residues: 1338 sheet: 0.27 (0.38), residues: 195 loop : -1.37 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 336 TYR 0.011 0.001 TYR F 300 PHE 0.018 0.001 PHE F 345 TRP 0.008 0.001 TRP C 58 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (22628) covalent geometry : angle 0.48023 / 0.26 (30930) hydrogen bonds : bond 0.03840 / 2.45 ( 977) hydrogen bonds : angle 3.70938 / 2.63 ( 2759) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.033 Fit side-chains REVERT: E 188 MET cc_start: 0.9179 (mtm) cc_final: 0.8819 (mtm) REVERT: E 291 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8115 (pp) REVERT: F 307 ASN cc_start: 0.9425 (m110) cc_final: 0.9177 (m110) REVERT: F 327 CYS cc_start: 0.9055 (m) cc_final: 0.8783 (m) REVERT: A 887 ASP cc_start: 0.9569 (t0) cc_final: 0.9240 (t0) REVERT: C 488 GLU cc_start: 0.9545 (mm-30) cc_final: 0.9260 (mt-10) REVERT: C 533 MET cc_start: 0.9111 (tmm) cc_final: 0.8520 (tmm) outliers start: 11 outliers final: 6 residues processed: 87 average time/residue: 0.1318 time to fit residues: 19.9385 Evaluate side-chains 86 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 499 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 47 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 247 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 221 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.041587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.027975 restraints weight = 132302.811| |-----------------------------------------------------------------------------| r_work (start): 0.2477 rms_B_bonded: 4.27 r_work: 0.2330 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22628 Z= 0.197 Angle : 0.513 8.069 30930 Z= 0.276 Chirality : 0.040 0.168 3508 Planarity : 0.003 0.043 3621 Dihedral : 17.661 172.871 3699 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.88 % Allowed : 9.54 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 2460 helix: 1.98 (0.15), residues: 1345 sheet: 0.28 (0.38), residues: 195 loop : -1.36 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 478 TYR 0.010 0.001 TYR C 61 PHE 0.017 0.001 PHE F 345 TRP 0.008 0.001 TRP B 465 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (22628) covalent geometry : angle 0.51289 / 0.28 (30930) hydrogen bonds : bond 0.04069 / 2.59 ( 977) hydrogen bonds : angle 3.77888 / 2.67 ( 2759) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.840 Fit side-chains REVERT: E 188 MET cc_start: 0.9232 (mtm) cc_final: 0.8849 (mtm) REVERT: E 291 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8218 (pp) REVERT: F 307 ASN cc_start: 0.9445 (m110) cc_final: 0.9176 (m110) REVERT: F 327 CYS cc_start: 0.9131 (m) cc_final: 0.8841 (m) REVERT: F 354 MET cc_start: 0.8763 (tpp) cc_final: 0.8163 (tpp) REVERT: A 887 ASP cc_start: 0.9604 (t0) cc_final: 0.9317 (t0) REVERT: C 385 ASN cc_start: 0.9770 (p0) cc_final: 0.9485 (m-40) REVERT: C 488 GLU cc_start: 0.9551 (mm-30) cc_final: 0.9275 (mt-10) REVERT: C 533 MET cc_start: 0.9205 (tmm) cc_final: 0.8546 (tmm) REVERT: D 522 MET cc_start: 0.9428 (ppp) cc_final: 0.9224 (ppp) outliers start: 20 outliers final: 12 residues processed: 94 average time/residue: 0.1323 time to fit residues: 21.5422 Evaluate side-chains 91 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 499 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 98 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 214 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.041440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.027859 restraints weight = 133398.110| |-----------------------------------------------------------------------------| r_work (start): 0.2473 rms_B_bonded: 4.33 r_work: 0.2327 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22628 Z= 0.177 Angle : 0.495 8.324 30930 Z= 0.269 Chirality : 0.039 0.144 3508 Planarity : 0.003 0.043 3621 Dihedral : 17.499 165.281 3699 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.92 % Allowed : 10.16 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.18), residues: 2460 helix: 2.07 (0.15), residues: 1342 sheet: 0.34 (0.38), residues: 195 loop : -1.33 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 145 TYR 0.010 0.001 TYR A 580 PHE 0.018 0.001 PHE F 345 TRP 0.007 0.001 TRP B 465 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (22628) covalent geometry : angle 0.49549 / 0.27 (30930) hydrogen bonds : bond 0.03968 / 2.53 ( 977) hydrogen bonds : angle 3.72346 / 2.63 ( 2759) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.815 Fit side-chains REVERT: E 188 MET cc_start: 0.9263 (mtm) cc_final: 0.8846 (mtm) REVERT: E 291 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8241 (pp) REVERT: F 280 MET cc_start: 0.8250 (mmt) cc_final: 0.7993 (mmm) REVERT: F 307 ASN cc_start: 0.9456 (m110) cc_final: 0.9188 (m110) REVERT: F 327 CYS cc_start: 0.9076 (m) cc_final: 0.8789 (m) REVERT: A 516 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9382 (mt) REVERT: A 623 MET cc_start: 0.9000 (tpp) cc_final: 0.8791 (tpp) REVERT: A 887 ASP cc_start: 0.9626 (t0) cc_final: 0.9334 (t0) REVERT: C 385 ASN cc_start: 0.9742 (p0) cc_final: 0.9450 (m-40) REVERT: C 488 GLU cc_start: 0.9551 (mm-30) cc_final: 0.9277 (mt-10) REVERT: C 533 MET cc_start: 0.9254 (tmm) cc_final: 0.8552 (tmm) REVERT: D 522 MET cc_start: 0.9426 (ppp) cc_final: 0.9195 (ppp) outliers start: 21 outliers final: 12 residues processed: 95 average time/residue: 0.1175 time to fit residues: 19.6741 Evaluate side-chains 92 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 499 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 89 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 184 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 175 optimal weight: 0.0870 chunk 113 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.040873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.027251 restraints weight = 133701.066| |-----------------------------------------------------------------------------| r_work (start): 0.2451 rms_B_bonded: 4.30 r_work: 0.2304 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 22628 Z= 0.235 Angle : 0.548 8.783 30930 Z= 0.291 Chirality : 0.040 0.149 3508 Planarity : 0.003 0.047 3621 Dihedral : 17.470 156.543 3699 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.23 % Allowed : 10.60 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.18), residues: 2460 helix: 2.08 (0.15), residues: 1344 sheet: 0.36 (0.38), residues: 195 loop : -1.36 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 425 TYR 0.011 0.001 TYR E 38 PHE 0.017 0.001 PHE F 345 TRP 0.010 0.001 TRP B 465 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (22628) covalent geometry : angle 0.54821 / 0.29 (30930) hydrogen bonds : bond 0.04347 / 2.77 ( 977) hydrogen bonds : angle 3.86447 / 2.73 ( 2759) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.828 Fit side-chains REVERT: B 265 MET cc_start: 0.9426 (ptp) cc_final: 0.8757 (pmm) REVERT: E 188 MET cc_start: 0.9320 (mtm) cc_final: 0.8869 (mtm) REVERT: E 291 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8239 (pp) REVERT: E 414 MET cc_start: 0.8676 (tpp) cc_final: 0.8437 (tpp) REVERT: F 307 ASN cc_start: 0.9469 (m110) cc_final: 0.9218 (m110) REVERT: F 327 CYS cc_start: 0.9140 (m) cc_final: 0.8874 (m) REVERT: A 623 MET cc_start: 0.9003 (tpp) cc_final: 0.8761 (tpp) REVERT: A 887 ASP cc_start: 0.9643 (t0) cc_final: 0.9397 (t0) REVERT: C 385 ASN cc_start: 0.9757 (p0) cc_final: 0.9476 (m-40) REVERT: C 488 GLU cc_start: 0.9568 (mm-30) cc_final: 0.9280 (mt-10) REVERT: C 533 MET cc_start: 0.9293 (tmm) cc_final: 0.8570 (tmm) REVERT: D 522 MET cc_start: 0.9468 (ppp) cc_final: 0.9234 (ppp) outliers start: 28 outliers final: 17 residues processed: 101 average time/residue: 0.1262 time to fit residues: 22.3247 Evaluate side-chains 96 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 499 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 218 optimal weight: 6.9990 chunk 233 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 438 GLN E 82 GLN D 370 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.041805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.028266 restraints weight = 130354.299| |-----------------------------------------------------------------------------| r_work (start): 0.2494 rms_B_bonded: 4.28 r_work: 0.2348 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22628 Z= 0.101 Angle : 0.465 7.657 30930 Z= 0.254 Chirality : 0.038 0.144 3508 Planarity : 0.003 0.042 3621 Dihedral : 17.320 152.939 3699 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.74 % Allowed : 11.21 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.18), residues: 2460 helix: 2.13 (0.15), residues: 1348 sheet: 0.51 (0.37), residues: 195 loop : -1.25 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 145 TYR 0.009 0.001 TYR A 580 PHE 0.018 0.001 PHE F 345 TRP 0.010 0.001 TRP C 58 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (22628) covalent geometry : angle 0.46487 / 0.25 (30930) hydrogen bonds : bond 0.03510 / 2.25 ( 977) hydrogen bonds : angle 3.54129 / 2.51 ( 2759) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.876 Fit side-chains REVERT: E 188 MET cc_start: 0.9316 (mtm) cc_final: 0.8818 (mtm) REVERT: E 291 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8137 (pp) REVERT: E 426 GLU cc_start: 0.9616 (tp30) cc_final: 0.9389 (tp30) REVERT: F 307 ASN cc_start: 0.9465 (m110) cc_final: 0.9212 (m110) REVERT: F 327 CYS cc_start: 0.9095 (m) cc_final: 0.8819 (m) REVERT: F 354 MET cc_start: 0.8600 (tpp) cc_final: 0.8297 (tpt) REVERT: A 887 ASP cc_start: 0.9637 (t0) cc_final: 0.9391 (t0) REVERT: C 385 ASN cc_start: 0.9764 (p0) cc_final: 0.9483 (m-40) REVERT: C 488 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9260 (mt-10) REVERT: C 533 MET cc_start: 0.9247 (tmm) cc_final: 0.8554 (tmm) outliers start: 17 outliers final: 12 residues processed: 94 average time/residue: 0.1269 time to fit residues: 20.7240 Evaluate side-chains 92 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 499 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 251 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 224 optimal weight: 9.9990 chunk 204 optimal weight: 0.0970 chunk 70 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 148 optimal weight: 0.0170 chunk 234 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.041956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.028496 restraints weight = 130617.960| |-----------------------------------------------------------------------------| r_work (start): 0.2506 rms_B_bonded: 4.25 r_work: 0.2360 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22628 Z= 0.099 Angle : 0.476 12.852 30930 Z= 0.254 Chirality : 0.038 0.230 3508 Planarity : 0.003 0.042 3621 Dihedral : 17.279 150.472 3699 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.79 % Allowed : 11.30 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.18), residues: 2460 helix: 2.15 (0.15), residues: 1350 sheet: 0.69 (0.37), residues: 199 loop : -1.22 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 621 TYR 0.009 0.001 TYR A 580 PHE 0.017 0.001 PHE F 345 TRP 0.009 0.001 TRP C 58 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (22628) covalent geometry : angle 0.47561 / 0.25 (30930) hydrogen bonds : bond 0.03360 / 2.15 ( 977) hydrogen bonds : angle 3.46902 / 2.45 ( 2759) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.854 Fit side-chains REVERT: B 265 MET cc_start: 0.9383 (ptp) cc_final: 0.8761 (pmm) REVERT: E 188 MET cc_start: 0.9289 (mtm) cc_final: 0.8816 (mtm) REVERT: E 291 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8197 (pp) REVERT: E 426 GLU cc_start: 0.9602 (tp30) cc_final: 0.9395 (tp30) REVERT: F 307 ASN cc_start: 0.9472 (m110) cc_final: 0.9221 (m110) REVERT: F 327 CYS cc_start: 0.9133 (m) cc_final: 0.8852 (m) REVERT: F 354 MET cc_start: 0.8653 (tpp) cc_final: 0.8376 (tpt) REVERT: A 887 ASP cc_start: 0.9620 (t0) cc_final: 0.9369 (t0) REVERT: C 385 ASN cc_start: 0.9740 (p0) cc_final: 0.9458 (m-40) REVERT: C 488 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9267 (mt-10) REVERT: C 533 MET cc_start: 0.9247 (tmm) cc_final: 0.8569 (tmm) outliers start: 18 outliers final: 14 residues processed: 94 average time/residue: 0.1328 time to fit residues: 21.7359 Evaluate side-chains 94 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 499 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 82 optimal weight: 30.0000 chunk 12 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 200 optimal weight: 0.2980 chunk 224 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.041696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.028236 restraints weight = 131982.371| |-----------------------------------------------------------------------------| r_work (start): 0.2494 rms_B_bonded: 4.29 r_work: 0.2347 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22628 Z= 0.136 Angle : 0.479 9.913 30930 Z= 0.257 Chirality : 0.039 0.217 3508 Planarity : 0.003 0.042 3621 Dihedral : 17.296 149.653 3699 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.79 % Allowed : 11.34 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.18), residues: 2460 helix: 2.20 (0.15), residues: 1351 sheet: 0.62 (0.37), residues: 201 loop : -1.19 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 478 TYR 0.011 0.001 TYR D 523 PHE 0.017 0.001 PHE F 345 TRP 0.009 0.001 TRP F 421 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (22628) covalent geometry : angle 0.47946 / 0.26 (30930) hydrogen bonds : bond 0.03489 / 2.23 ( 977) hydrogen bonds : angle 3.50554 / 2.47 ( 2759) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.852 Fit side-chains REVERT: B 265 MET cc_start: 0.9422 (ptp) cc_final: 0.8761 (pmm) REVERT: E 188 MET cc_start: 0.9298 (mtm) cc_final: 0.8770 (mtm) REVERT: E 291 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8130 (pp) REVERT: E 414 MET cc_start: 0.8609 (tpp) cc_final: 0.8400 (tpp) REVERT: E 426 GLU cc_start: 0.9615 (tp30) cc_final: 0.9397 (tp30) REVERT: F 307 ASN cc_start: 0.9467 (m110) cc_final: 0.9223 (m110) REVERT: F 327 CYS cc_start: 0.9132 (m) cc_final: 0.8854 (m) REVERT: F 354 MET cc_start: 0.8620 (tpp) cc_final: 0.8386 (tpt) REVERT: A 887 ASP cc_start: 0.9653 (t0) cc_final: 0.9327 (t0) REVERT: C 385 ASN cc_start: 0.9754 (p0) cc_final: 0.9476 (m-40) REVERT: C 488 GLU cc_start: 0.9540 (mm-30) cc_final: 0.9265 (mt-10) REVERT: C 533 MET cc_start: 0.9242 (tmm) cc_final: 0.8547 (tmm) REVERT: D 418 MET cc_start: 0.9427 (ttm) cc_final: 0.8975 (tpp) outliers start: 18 outliers final: 15 residues processed: 92 average time/residue: 0.1355 time to fit residues: 21.6877 Evaluate side-chains 95 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 499 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 231 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 210 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.041230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.027823 restraints weight = 132878.517| |-----------------------------------------------------------------------------| r_work (start): 0.2479 rms_B_bonded: 4.26 r_work: 0.2331 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22628 Z= 0.180 Angle : 0.518 13.006 30930 Z= 0.272 Chirality : 0.039 0.196 3508 Planarity : 0.003 0.042 3621 Dihedral : 17.324 150.100 3699 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.79 % Allowed : 11.38 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.18), residues: 2460 helix: 2.24 (0.15), residues: 1350 sheet: 0.50 (0.38), residues: 195 loop : -1.21 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 478 TYR 0.009 0.001 TYR A 580 PHE 0.017 0.001 PHE F 345 TRP 0.009 0.001 TRP F 421 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (22628) covalent geometry : angle 0.51792 / 0.27 (30930) hydrogen bonds : bond 0.03779 / 2.41 ( 977) hydrogen bonds : angle 3.60393 / 2.54 ( 2759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4530.42 seconds wall clock time: 78 minutes 33.77 seconds (4713.77 seconds total)