Starting phenix.real_space_refine on Sun Aug 24 18:23:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpk_60347/08_2025/8zpk_60347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpk_60347/08_2025/8zpk_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zpk_60347/08_2025/8zpk_60347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpk_60347/08_2025/8zpk_60347.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpk_60347/08_2025/8zpk_60347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpk_60347/08_2025/8zpk_60347.cif" } 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-2.0-5787/lib/python3.9/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: 4.63, per 1000 atoms: 0.21 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: 1.57 Conformation dependent library (CDL) restraints added in 889.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 2.35 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: 3.61 Time building geometry restraints manager: 2.19 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 1.557 1.490 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O2B AGS E2001 " pdb=" PB AGS E2001 " ideal model delta sigma weight residual 1.531 1.478 0.053 1.60e-02 3.91e+03 1.10e+01 bond pdb=" O2B AGS D2001 " pdb=" PB AGS D2001 " ideal model delta sigma weight residual 1.531 1.478 0.053 1.60e-02 3.91e+03 1.10e+01 bond pdb=" O3G AGS A2001 " pdb=" PG AGS A2001 " ideal model delta sigma weight residual 1.558 1.492 0.066 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O2G AGS E2001 " pdb=" PG AGS E2001 " ideal model delta sigma weight residual 1.557 1.493 0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 22623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 30550 1.98 - 3.96: 313 3.96 - 5.94: 45 5.94 - 7.92: 13 7.92 - 9.90: 9 Bond angle restraints: 30930 Sorted by residual: angle pdb=" N ARG A 888 " pdb=" CA ARG A 888 " pdb=" C ARG A 888 " ideal model delta sigma weight residual 114.56 110.04 4.52 1.27e+00 6.20e-01 1.27e+01 angle pdb=" N VAL A 532 " pdb=" CA VAL A 532 " pdb=" C VAL A 532 " ideal model delta sigma weight residual 113.71 110.55 3.16 9.50e-01 1.11e+00 1.10e+01 angle pdb=" O3A AGS E2001 " pdb=" PB AGS E2001 " pdb=" O3B AGS E2001 " ideal model delta sigma weight residual 109.69 99.79 9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C3' AGS A2001 " pdb=" C4' AGS A2001 " pdb=" O4' AGS A2001 " ideal model delta sigma weight residual 105.29 101.26 4.03 1.27e+00 6.22e-01 1.01e+01 angle pdb=" PA AGS D2001 " pdb=" O3A AGS D2001 " pdb=" PB AGS D2001 " ideal model delta sigma weight residual 119.76 128.76 -9.00 3.00e+00 1.11e-01 9.00e+00 ... (remaining 30925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.32: 12661 28.32 - 56.65: 831 56.65 - 84.97: 49 84.97 - 113.29: 2 113.29 - 141.61: 1 Dihedral angle restraints: 13544 sinusoidal: 6130 harmonic: 7414 Sorted by residual: 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 A2001 " pdb=" O3A AGS A2001 " pdb=" PA AGS A2001 " pdb=" PB AGS A2001 " ideal model delta sinusoidal sigma weight residual -67.73 73.88 -141.61 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" O1B AGS E2001 " pdb=" O3B AGS E2001 " pdb=" PB AGS E2001 " pdb=" PG AGS E2001 " ideal model delta sinusoidal sigma weight residual 68.91 -41.32 110.23 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 13541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2287 0.031 - 0.061: 833 0.061 - 0.092: 258 0.092 - 0.123: 107 0.123 - 0.153: 29 Chirality restraints: 3514 Sorted by residual: chirality pdb=" CA ILE B 452 " pdb=" N ILE B 452 " pdb=" C ILE B 452 " pdb=" CB ILE B 452 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CB THR A 413 " pdb=" CA THR A 413 " pdb=" OG1 THR A 413 " pdb=" CG2 THR A 413 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA VAL B 423 " pdb=" N VAL B 423 " pdb=" C VAL B 423 " pdb=" CB VAL B 423 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 3511 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: 1.450 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.020 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22628 Z= 0.143 Angle : 0.540 9.903 30930 Z= 0.282 Chirality : 0.039 0.153 3514 Planarity : 0.003 0.061 3621 Dihedral : 16.776 141.614 8710 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 aren 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 covalent geometry : bond 0.00295 (22628) covalent geometry : angle 0.54015 (30930) hydrogen bonds : bond 0.16889 ( 977) hydrogen bonds : angle 5.32964 ( 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 : 0.576 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: 0.1293 time to fit residues: 21.1795 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 : 0.812 ------------------------------------------------------------------------------- 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: 6.9990 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: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 HIS E 36 GLN E 82 GLN ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 GLN A 882 GLN C 138 ASN C 246 ASN C 383 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.042142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.028491 restraints weight = 131916.819| |-----------------------------------------------------------------------------| r_work (start): 0.2483 rms_B_bonded: 4.28 r_work: 0.2338 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22628 Z= 0.193 Angle : 0.539 10.293 30930 Z= 0.293 Chirality : 0.040 0.148 3514 Planarity : 0.003 0.046 3621 Dihedral : 17.185 120.184 3645 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.48 % Allowed : 5.34 % Favored : 94.18 % 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 aren not related in a simple way. whole: 0.63 (0.18), residues: 2460 helix: 1.70 (0.15), residues: 1333 sheet: -0.09 (0.38), residues: 201 loop : -1.40 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 336 TYR 0.016 0.001 TYR F 300 PHE 0.018 0.001 PHE F 345 TRP 0.011 0.001 TRP D 526 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00430 (22628) covalent geometry : angle 0.53858 (30930) hydrogen bonds : bond 0.04730 ( 977) hydrogen bonds : angle 4.07235 ( 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: 11 poor density : 84 time to evaluate : 0.812 Fit side-chains REVERT: F 307 ASN cc_start: 0.9486 (m110) cc_final: 0.9239 (m110) REVERT: F 327 CYS cc_start: 0.9044 (m) cc_final: 0.8774 (m) REVERT: F 354 MET cc_start: 0.8849 (tpp) cc_final: 0.8159 (tpp) REVERT: C 141 MET cc_start: 0.8673 (mmm) cc_final: 0.8460 (mmm) REVERT: C 488 GLU cc_start: 0.9542 (mm-30) cc_final: 0.9290 (mt-10) REVERT: C 533 MET cc_start: 0.9160 (tmm) cc_final: 0.8590 (tmm) REVERT: D 465 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8735 (tm-30) outliers start: 11 outliers final: 3 residues processed: 87 average time/residue: 0.1174 time to fit residues: 17.6616 Evaluate side-chains 82 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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: 10.0000 chunk 231 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 154 optimal weight: 30.0000 chunk 251 optimal weight: 0.0060 chunk 146 optimal weight: 0.6980 chunk 161 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 160 optimal weight: 5.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 ASN E 82 GLN E 153 ASN ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN F 410 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.042704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.029033 restraints weight = 131164.641| |-----------------------------------------------------------------------------| r_work (start): 0.2514 rms_B_bonded: 4.29 r_work: 0.2370 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22628 Z= 0.108 Angle : 0.469 9.732 30930 Z= 0.257 Chirality : 0.038 0.154 3514 Planarity : 0.003 0.044 3621 Dihedral : 17.050 115.745 3645 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.57 % Allowed : 7.36 % Favored : 92.08 % 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 aren not related in a simple way. whole: 0.79 (0.18), residues: 2460 helix: 1.81 (0.15), residues: 1344 sheet: 0.16 (0.38), residues: 199 loop : -1.40 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 409 TYR 0.015 0.001 TYR F 418 PHE 0.018 0.001 PHE F 345 TRP 0.012 0.001 TRP F 421 HIS 0.010 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00231 (22628) covalent geometry : angle 0.46856 (30930) hydrogen bonds : bond 0.03861 ( 977) hydrogen bonds : angle 3.73033 ( 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 94 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.758 Fit side-chains REVERT: E 291 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8178 (pp) REVERT: F 307 ASN cc_start: 0.9435 (m110) cc_final: 0.9179 (m110) REVERT: F 327 CYS cc_start: 0.9072 (m) cc_final: 0.8803 (m) REVERT: C 141 MET cc_start: 0.8636 (mmm) cc_final: 0.8418 (mmm) REVERT: C 385 ASN cc_start: 0.9754 (p0) cc_final: 0.9484 (m-40) REVERT: C 488 GLU cc_start: 0.9530 (mm-30) cc_final: 0.9264 (mt-10) REVERT: C 533 MET cc_start: 0.9091 (tmm) cc_final: 0.8557 (tmm) REVERT: D 465 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8730 (tm-30) REVERT: D 522 MET cc_start: 0.9425 (ppp) cc_final: 0.9175 (ppp) outliers start: 13 outliers final: 2 residues processed: 89 average time/residue: 0.1180 time to fit residues: 18.0639 Evaluate side-chains 84 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain C residue 397 VAL 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: 7.9990 chunk 118 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 146 optimal weight: 0.0770 chunk 144 optimal weight: 4.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3029 r_free = 0.3029 target = 0.041611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.027988 restraints weight = 132856.799| |-----------------------------------------------------------------------------| r_work (start): 0.2478 rms_B_bonded: 4.29 r_work: 0.2330 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1432 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 : 0.510 7.891 30930 Z= 0.275 Chirality : 0.039 0.176 3514 Planarity : 0.003 0.041 3621 Dihedral : 17.102 117.362 3645 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.61 % Allowed : 9.02 % Favored : 90.37 % 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 aren not related in a simple way. whole: 0.96 (0.18), residues: 2460 helix: 1.98 (0.15), residues: 1340 sheet: 0.15 (0.38), residues: 197 loop : -1.34 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 478 TYR 0.013 0.001 TYR F 418 PHE 0.017 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 covalent geometry : bond 0.00427 (22628) covalent geometry : angle 0.51029 (30930) hydrogen bonds : bond 0.04136 ( 977) hydrogen bonds : angle 3.77253 ( 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 94 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.636 Fit side-chains REVERT: E 291 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8191 (pp) REVERT: F 307 ASN cc_start: 0.9432 (m110) cc_final: 0.9178 (m110) REVERT: F 318 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8427 (pm20) REVERT: F 327 CYS cc_start: 0.9117 (m) cc_final: 0.8835 (m) REVERT: F 354 MET cc_start: 0.8826 (tpp) cc_final: 0.8203 (tpp) REVERT: C 141 MET cc_start: 0.8832 (mmm) cc_final: 0.8502 (mmm) REVERT: C 488 GLU cc_start: 0.9557 (mm-30) cc_final: 0.9288 (mt-10) REVERT: C 533 MET cc_start: 0.9188 (tmm) cc_final: 0.8537 (tmm) REVERT: D 465 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8884 (tm-30) outliers start: 14 outliers final: 10 residues processed: 88 average time/residue: 0.1133 time to fit residues: 17.3963 Evaluate side-chains 92 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 318 GLN Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 843 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=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: 0.6980 chunk 154 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 221 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN ** E 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.042096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.028514 restraints weight = 131083.690| |-----------------------------------------------------------------------------| r_work (start): 0.2501 rms_B_bonded: 4.29 r_work: 0.2355 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22628 Z= 0.115 Angle : 0.453 7.207 30930 Z= 0.249 Chirality : 0.038 0.153 3514 Planarity : 0.003 0.042 3621 Dihedral : 16.968 117.243 3645 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.53 % Allowed : 9.89 % 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 aren not related in a simple way. whole: 1.05 (0.18), residues: 2460 helix: 2.03 (0.15), residues: 1350 sheet: 0.31 (0.38), residues: 195 loop : -1.31 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 425 TYR 0.010 0.001 TYR D 523 PHE 0.017 0.001 PHE F 345 TRP 0.008 0.001 TRP C 58 HIS 0.005 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00252 (22628) covalent geometry : angle 0.45312 (30930) hydrogen bonds : bond 0.03561 ( 977) hydrogen bonds : angle 3.57116 ( 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 92 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.827 Fit side-chains REVERT: B 262 THR cc_start: 0.9594 (OUTLIER) cc_final: 0.8991 (t) REVERT: B 265 MET cc_start: 0.9428 (ptp) cc_final: 0.8895 (pmm) REVERT: E 291 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8186 (pp) REVERT: F 307 ASN cc_start: 0.9443 (m110) cc_final: 0.9199 (m110) REVERT: F 318 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8479 (pm20) REVERT: F 327 CYS cc_start: 0.9110 (m) cc_final: 0.8820 (m) REVERT: A 623 MET cc_start: 0.8971 (tpp) cc_final: 0.8754 (tpp) REVERT: C 141 MET cc_start: 0.8754 (mmm) cc_final: 0.8399 (mmm) REVERT: C 385 ASN cc_start: 0.9766 (p0) cc_final: 0.9474 (m-40) REVERT: C 488 GLU cc_start: 0.9525 (mm-30) cc_final: 0.9263 (mt-10) REVERT: C 533 MET cc_start: 0.9177 (tmm) cc_final: 0.8527 (tmm) REVERT: D 465 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8894 (tm-30) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 0.1038 time to fit residues: 16.1704 Evaluate side-chains 90 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 THR 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 318 GLN Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain C residue 397 VAL 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: 6.9990 chunk 193 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 179 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 ASN E 82 GLN ** E 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.041238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.027606 restraints weight = 133164.038| |-----------------------------------------------------------------------------| r_work (start): 0.2469 rms_B_bonded: 4.31 r_work: 0.2321 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22628 Z= 0.212 Angle : 0.510 8.118 30930 Z= 0.273 Chirality : 0.039 0.144 3514 Planarity : 0.003 0.042 3621 Dihedral : 17.001 118.603 3645 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.09 % Allowed : 10.03 % Favored : 88.88 % 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 aren not related in a simple way. whole: 1.12 (0.18), residues: 2460 helix: 2.11 (0.15), residues: 1342 sheet: 0.33 (0.38), residues: 195 loop : -1.29 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 478 TYR 0.009 0.001 TYR E 38 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 covalent geometry : bond 0.00475 (22628) covalent geometry : angle 0.51033 (30930) hydrogen bonds : bond 0.04015 ( 977) hydrogen bonds : angle 3.72599 ( 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 105 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.713 Fit side-chains REVERT: E 291 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8205 (pp) REVERT: F 280 MET cc_start: 0.8297 (mmt) cc_final: 0.8039 (mmm) REVERT: F 307 ASN cc_start: 0.9457 (m110) cc_final: 0.9202 (m110) REVERT: F 327 CYS cc_start: 0.9088 (m) cc_final: 0.8809 (m) REVERT: F 354 MET cc_start: 0.8694 (tpp) cc_final: 0.8078 (tpp) REVERT: A 623 MET cc_start: 0.8992 (tpp) cc_final: 0.8751 (tpp) REVERT: C 141 MET cc_start: 0.8888 (mmm) cc_final: 0.8444 (mmm) REVERT: C 385 ASN cc_start: 0.9755 (p0) cc_final: 0.9468 (m-40) REVERT: C 488 GLU cc_start: 0.9555 (mm-30) cc_final: 0.9278 (mt-10) REVERT: C 533 MET cc_start: 0.9242 (tmm) cc_final: 0.8539 (tmm) REVERT: D 418 MET cc_start: 0.9446 (ttm) cc_final: 0.9068 (tpp) outliers start: 25 outliers final: 15 residues processed: 98 average time/residue: 0.1072 time to fit residues: 18.4118 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 : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain E residue 188 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 574 LYS Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 874 LEU 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 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: 4.9990 chunk 45 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 184 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.041304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.027724 restraints weight = 132325.075| |-----------------------------------------------------------------------------| r_work (start): 0.2472 rms_B_bonded: 4.28 r_work: 0.2325 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1779 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= 0.176 Angle : 0.489 8.179 30930 Z= 0.264 Chirality : 0.039 0.254 3514 Planarity : 0.003 0.045 3621 Dihedral : 16.906 119.336 3645 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.96 % Allowed : 10.60 % Favored : 88.44 % 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 aren not related in a simple way. whole: 1.18 (0.18), residues: 2460 helix: 2.16 (0.15), residues: 1344 sheet: 0.41 (0.38), residues: 195 loop : -1.29 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 478 TYR 0.010 0.001 TYR D 523 PHE 0.017 0.001 PHE F 345 TRP 0.007 0.001 TRP B 465 HIS 0.006 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00393 (22628) covalent geometry : angle 0.48861 (30930) hydrogen bonds : bond 0.03846 ( 977) hydrogen bonds : angle 3.65741 ( 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 103 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.650 Fit side-chains REVERT: E 291 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8200 (pp) REVERT: E 426 GLU cc_start: 0.9608 (tp30) cc_final: 0.9400 (tp30) REVERT: F 280 MET cc_start: 0.8243 (mmt) cc_final: 0.8006 (mmm) REVERT: F 307 ASN cc_start: 0.9463 (m110) cc_final: 0.9208 (m110) REVERT: F 327 CYS cc_start: 0.9122 (m) cc_final: 0.8838 (m) REVERT: F 354 MET cc_start: 0.8791 (tpp) cc_final: 0.8350 (tpp) REVERT: C 141 MET cc_start: 0.8880 (mmm) cc_final: 0.8450 (mmm) REVERT: C 385 ASN cc_start: 0.9760 (p0) cc_final: 0.9467 (m-40) REVERT: C 488 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9277 (mt-10) REVERT: C 533 MET cc_start: 0.9253 (tmm) cc_final: 0.8533 (tmm) REVERT: D 465 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8898 (tm-30) outliers start: 22 outliers final: 14 residues processed: 96 average time/residue: 0.1083 time to fit residues: 17.8827 Evaluate side-chains 95 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain E residue 188 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 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 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: 6.9990 chunk 21 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 223 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 218 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.041942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.028438 restraints weight = 130792.678| |-----------------------------------------------------------------------------| r_work (start): 0.2503 rms_B_bonded: 4.28 r_work: 0.2358 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22628 Z= 0.110 Angle : 0.455 7.523 30930 Z= 0.247 Chirality : 0.038 0.186 3514 Planarity : 0.003 0.042 3621 Dihedral : 16.761 119.766 3645 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.92 % Allowed : 10.99 % Favored : 88.09 % 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 aren not related in a simple way. whole: 1.27 (0.18), residues: 2460 helix: 2.18 (0.15), residues: 1355 sheet: 0.63 (0.37), residues: 201 loop : -1.25 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 145 TYR 0.012 0.001 TYR D 523 PHE 0.017 0.001 PHE F 345 TRP 0.009 0.001 TRP C 58 HIS 0.004 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00240 (22628) covalent geometry : angle 0.45524 (30930) hydrogen bonds : bond 0.03267 ( 977) hydrogen bonds : angle 3.46805 ( 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 101 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: B 265 MET cc_start: 0.9413 (ptp) cc_final: 0.8747 (pmm) REVERT: E 291 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8213 (pp) REVERT: E 426 GLU cc_start: 0.9599 (tp30) cc_final: 0.9394 (tp30) REVERT: F 280 MET cc_start: 0.8222 (mmt) cc_final: 0.7917 (mmm) REVERT: F 307 ASN cc_start: 0.9461 (m110) cc_final: 0.9212 (m110) REVERT: F 327 CYS cc_start: 0.9146 (m) cc_final: 0.8857 (m) REVERT: F 354 MET cc_start: 0.8818 (tpp) cc_final: 0.8344 (tpp) REVERT: A 623 MET cc_start: 0.8941 (tpp) cc_final: 0.8709 (tpp) REVERT: C 141 MET cc_start: 0.8749 (mmm) cc_final: 0.8296 (mmm) REVERT: C 385 ASN cc_start: 0.9743 (p0) cc_final: 0.9451 (m-40) REVERT: C 488 GLU cc_start: 0.9531 (mm-30) cc_final: 0.9267 (mt-10) REVERT: C 533 MET cc_start: 0.9243 (tmm) cc_final: 0.8540 (tmm) outliers start: 21 outliers final: 13 residues processed: 98 average time/residue: 0.1108 time to fit residues: 18.8750 Evaluate side-chains 94 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 188 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 574 LYS Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 397 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 251 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 224 optimal weight: 9.9990 chunk 204 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.041839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.028441 restraints weight = 131247.446| |-----------------------------------------------------------------------------| r_work (start): 0.2504 rms_B_bonded: 4.24 r_work: 0.2360 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22628 Z= 0.118 Angle : 0.453 8.722 30930 Z= 0.245 Chirality : 0.038 0.160 3514 Planarity : 0.003 0.041 3621 Dihedral : 16.747 120.047 3645 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.79 % Allowed : 11.21 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.18), residues: 2460 helix: 2.23 (0.15), residues: 1355 sheet: 0.52 (0.36), residues: 212 loop : -1.21 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 888 TYR 0.012 0.001 TYR D 523 PHE 0.017 0.001 PHE F 345 TRP 0.008 0.001 TRP C 58 HIS 0.004 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00261 (22628) covalent geometry : angle 0.45334 (30930) hydrogen bonds : bond 0.03307 ( 977) hydrogen bonds : angle 3.43818 ( 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 : 0.688 Fit side-chains REVERT: B 265 MET cc_start: 0.9394 (ptp) cc_final: 0.8715 (pmm) REVERT: E 291 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8237 (pp) REVERT: E 426 GLU cc_start: 0.9598 (tp30) cc_final: 0.9389 (tp30) REVERT: F 280 MET cc_start: 0.8232 (mmt) cc_final: 0.7984 (mmm) REVERT: F 307 ASN cc_start: 0.9480 (m110) cc_final: 0.9230 (m110) REVERT: F 327 CYS cc_start: 0.9145 (m) cc_final: 0.8873 (m) REVERT: F 354 MET cc_start: 0.8740 (tpp) cc_final: 0.8268 (tpp) REVERT: A 623 MET cc_start: 0.8869 (tpp) cc_final: 0.8639 (tpp) REVERT: C 141 MET cc_start: 0.8758 (mmm) cc_final: 0.8296 (mmm) REVERT: C 385 ASN cc_start: 0.9762 (p0) cc_final: 0.9475 (m-40) REVERT: C 488 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9265 (mt-10) REVERT: C 533 MET cc_start: 0.9235 (tmm) cc_final: 0.8530 (tmm) outliers start: 18 outliers final: 13 residues processed: 94 average time/residue: 0.1104 time to fit residues: 18.0197 Evaluate side-chains 94 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 181 THR Chi-restraints excluded: chain E residue 188 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 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 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: 0.9990 chunk 86 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.041315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.027849 restraints weight = 132677.246| |-----------------------------------------------------------------------------| r_work (start): 0.2480 rms_B_bonded: 4.27 r_work: 0.2332 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2035 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= 0.177 Angle : 0.493 9.166 30930 Z= 0.264 Chirality : 0.039 0.144 3514 Planarity : 0.003 0.042 3621 Dihedral : 16.780 120.052 3645 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.70 % Allowed : 11.43 % 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 aren not related in a simple way. whole: 1.34 (0.18), residues: 2460 helix: 2.26 (0.15), residues: 1356 sheet: 0.40 (0.37), residues: 205 loop : -1.21 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 478 TYR 0.011 0.001 TYR D 523 PHE 0.016 0.001 PHE F 345 TRP 0.011 0.001 TRP F 421 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00397 (22628) covalent geometry : angle 0.49343 (30930) hydrogen bonds : bond 0.03741 ( 977) hydrogen bonds : angle 3.56190 ( 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 96 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: E 291 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8169 (pp) REVERT: E 426 GLU cc_start: 0.9604 (tp30) cc_final: 0.9393 (tp30) REVERT: F 280 MET cc_start: 0.8176 (mmt) cc_final: 0.7975 (mmm) REVERT: F 307 ASN cc_start: 0.9487 (m110) cc_final: 0.9232 (m110) REVERT: F 327 CYS cc_start: 0.9182 (m) cc_final: 0.8907 (m) REVERT: F 354 MET cc_start: 0.8808 (tpp) cc_final: 0.8328 (tpp) REVERT: C 141 MET cc_start: 0.8858 (mmm) cc_final: 0.8419 (mmm) REVERT: C 385 ASN cc_start: 0.9757 (p0) cc_final: 0.9470 (m-40) REVERT: C 488 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9267 (mt-10) REVERT: C 517 MET cc_start: 0.9354 (ttp) cc_final: 0.9083 (ttt) REVERT: C 533 MET cc_start: 0.9267 (tmm) cc_final: 0.8533 (tmm) REVERT: D 418 MET cc_start: 0.9348 (ttm) cc_final: 0.9147 (tpp) outliers start: 16 outliers final: 13 residues processed: 92 average time/residue: 0.1165 time to fit residues: 18.4021 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 : 0.530 ------------------------------------------------------------------------------- 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 188 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 574 LYS Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 390 GLU Chi-restraints excluded: chain C residue 397 VAL 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: 9.9990 chunk 210 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.041279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.027846 restraints weight = 132231.714| |-----------------------------------------------------------------------------| r_work (start): 0.2484 rms_B_bonded: 4.25 r_work: 0.2336 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2075 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= 0.160 Angle : 0.483 10.626 30930 Z= 0.259 Chirality : 0.038 0.151 3514 Planarity : 0.003 0.042 3621 Dihedral : 16.743 119.825 3645 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.83 % Allowed : 11.30 % 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 aren not related in a simple way. whole: 1.36 (0.18), residues: 2460 helix: 2.28 (0.15), residues: 1349 sheet: 0.40 (0.37), residues: 205 loop : -1.18 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 478 TYR 0.010 0.001 TYR D 523 PHE 0.017 0.001 PHE F 345 TRP 0.008 0.001 TRP F 421 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00360 (22628) covalent geometry : angle 0.48266 (30930) hydrogen bonds : bond 0.03627 ( 977) hydrogen bonds : angle 3.53603 ( 2759) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4444.82 seconds wall clock time: 76 minutes 48.52 seconds (4608.52 seconds total)