Starting phenix.real_space_refine on Thu Jun 19 02:46:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpk_60347/06_2025/8zpk_60347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpk_60347/06_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_60347/06_2025/8zpk_60347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpk_60347/06_2025/8zpk_60347.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpk_60347/06_2025/8zpk_60347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpk_60347/06_2025/8zpk_60347.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.08, per 1000 atoms: 0.55 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: 5.25 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 6.58 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: 7.72 Time building geometry restraints manager: 6.32 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 52.470 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.460 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (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 TRP 0.013 0.001 TRP C 58 HIS 0.004 0.001 HIS C 69 PHE 0.026 0.001 PHE F 329 TYR 0.015 0.001 TYR B 473 ARG 0.004 0.000 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.16889 ( 977) hydrogen bonds : angle 5.32964 ( 2759) covalent geometry : bond 0.00295 (22628) covalent geometry : angle 0.54015 (30930) *********************** 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 : 4.238 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: 0.4217 time to fit residues: 71.4414 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 : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 148 optimal weight: 0.0870 chunk 230 optimal weight: 6.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- 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 F 417 GLN A 882 GLN C 138 ASN C 246 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.042033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.028420 restraints weight = 131627.491| |-----------------------------------------------------------------------------| r_work (start): 0.2483 rms_B_bonded: 4.25 r_work: 0.2337 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22628 Z= 0.202 Angle : 0.547 10.528 30930 Z= 0.297 Chirality : 0.040 0.148 3514 Planarity : 0.003 0.046 3621 Dihedral : 17.194 120.358 3645 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.61 % Allowed : 5.52 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2460 helix: 1.69 (0.15), residues: 1333 sheet: -0.09 (0.38), residues: 201 loop : -1.40 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 526 HIS 0.005 0.001 HIS C 69 PHE 0.018 0.001 PHE F 345 TYR 0.016 0.001 TYR F 300 ARG 0.004 0.000 ARG F 336 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 977) hydrogen bonds : angle 4.09622 ( 2759) covalent geometry : bond 0.00451 (22628) covalent geometry : angle 0.54694 (30930) *********************** 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 97 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 2.840 Fit side-chains REVERT: F 307 ASN cc_start: 0.9490 (m110) cc_final: 0.9241 (m110) REVERT: F 327 CYS cc_start: 0.9062 (m) cc_final: 0.8785 (m) REVERT: F 354 MET cc_start: 0.8889 (tpp) cc_final: 0.8200 (tpp) REVERT: C 141 MET cc_start: 0.8685 (mmm) cc_final: 0.8422 (mmm) REVERT: C 488 GLU cc_start: 0.9542 (mm-30) cc_final: 0.9284 (mt-10) REVERT: C 533 MET cc_start: 0.9157 (tmm) cc_final: 0.8586 (tmm) REVERT: D 465 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8764 (tm-30) outliers start: 14 outliers final: 4 residues processed: 88 average time/residue: 0.4462 time to fit residues: 67.9991 Evaluate side-chains 82 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 203 MET 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 189 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 199 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 224 optimal weight: 0.1980 chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 153 optimal weight: 0.0770 chunk 173 optimal weight: 6.9990 overall best weight: 2.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN ** E 397 GLN ** 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 = 0.3044 r_free = 0.3044 target = 0.042166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.028550 restraints weight = 130742.307| |-----------------------------------------------------------------------------| r_work (start): 0.2496 rms_B_bonded: 4.28 r_work: 0.2350 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1225 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= 0.142 Angle : 0.483 9.358 30930 Z= 0.265 Chirality : 0.039 0.152 3514 Planarity : 0.003 0.044 3621 Dihedral : 17.083 116.328 3645 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.61 % Allowed : 7.79 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2460 helix: 1.84 (0.15), residues: 1343 sheet: 0.17 (0.38), residues: 195 loop : -1.40 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 58 HIS 0.007 0.001 HIS C 371 PHE 0.018 0.001 PHE F 345 TYR 0.016 0.001 TYR F 418 ARG 0.003 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 977) hydrogen bonds : angle 3.78211 ( 2759) covalent geometry : bond 0.00315 (22628) covalent geometry : angle 0.48286 (30930) *********************** 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: 14 poor density : 80 time to evaluate : 4.168 Fit side-chains REVERT: E 291 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8224 (pp) REVERT: F 307 ASN cc_start: 0.9438 (m110) cc_final: 0.9194 (m110) REVERT: F 318 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8370 (pm20) REVERT: F 327 CYS cc_start: 0.9075 (m) cc_final: 0.8803 (m) REVERT: A 887 ASP cc_start: 0.9555 (t0) cc_final: 0.9331 (t0) REVERT: C 141 MET cc_start: 0.8714 (mmm) cc_final: 0.8329 (mmm) REVERT: C 371 HIS cc_start: 0.8447 (m-70) cc_final: 0.8242 (m-70) REVERT: C 385 ASN cc_start: 0.9735 (p0) cc_final: 0.9441 (m-40) REVERT: C 488 GLU cc_start: 0.9547 (mm-30) cc_final: 0.9279 (mt-10) REVERT: C 533 MET cc_start: 0.9139 (tmm) cc_final: 0.8545 (tmm) REVERT: D 465 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8770 (tm-30) REVERT: D 522 MET cc_start: 0.9446 (ppp) cc_final: 0.9231 (ppp) outliers start: 14 outliers final: 5 residues processed: 89 average time/residue: 0.4994 time to fit residues: 78.4990 Evaluate side-chains 87 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 3.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain F residue 318 GLN Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 499 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 161 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 90 optimal weight: 40.0000 chunk 107 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN E 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.041881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.028201 restraints weight = 133652.226| |-----------------------------------------------------------------------------| r_work (start): 0.2486 rms_B_bonded: 4.35 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1390 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= 0.155 Angle : 0.476 6.721 30930 Z= 0.260 Chirality : 0.039 0.169 3514 Planarity : 0.003 0.042 3621 Dihedral : 17.059 117.436 3645 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.48 % Allowed : 9.02 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.18), residues: 2460 helix: 1.97 (0.15), residues: 1342 sheet: 0.23 (0.38), residues: 195 loop : -1.35 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 58 HIS 0.004 0.001 HIS C 69 PHE 0.017 0.001 PHE F 345 TYR 0.010 0.001 TYR C 61 ARG 0.010 0.000 ARG D 425 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 977) hydrogen bonds : angle 3.71314 ( 2759) covalent geometry : bond 0.00345 (22628) covalent geometry : angle 0.47568 (30930) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 2.598 Fit side-chains REVERT: E 291 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8276 (pp) REVERT: F 307 ASN cc_start: 0.9423 (m110) cc_final: 0.9157 (m110) REVERT: F 327 CYS cc_start: 0.9113 (m) cc_final: 0.8827 (m) REVERT: F 354 MET cc_start: 0.8857 (tpp) cc_final: 0.8149 (tpt) REVERT: A 887 ASP cc_start: 0.9394 (t0) cc_final: 0.9092 (t0) REVERT: C 141 MET cc_start: 0.8507 (mmm) cc_final: 0.8130 (mmm) REVERT: C 371 HIS cc_start: 0.8345 (m-70) cc_final: 0.8124 (m-70) REVERT: C 488 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9115 (mt-10) REVERT: C 533 MET cc_start: 0.9041 (tmm) cc_final: 0.8373 (tmm) REVERT: D 465 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8707 (tm-30) outliers start: 11 outliers final: 7 residues processed: 88 average time/residue: 0.2917 time to fit residues: 45.1799 Evaluate side-chains 88 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 2.556 ------------------------------------------------------------------------------- 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 365 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 446 CYS 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 222 optimal weight: 9.9990 chunk 107 optimal weight: 0.0040 chunk 35 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 overall best weight: 3.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 397 GLN ** E 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.041426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.027763 restraints weight = 132871.388| |-----------------------------------------------------------------------------| r_work (start): 0.2472 rms_B_bonded: 4.32 r_work: 0.2325 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22628 Z= 0.178 Angle : 0.494 7.923 30930 Z= 0.267 Chirality : 0.039 0.183 3514 Planarity : 0.003 0.042 3621 Dihedral : 17.046 118.873 3645 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.92 % Allowed : 9.89 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.18), residues: 2460 helix: 2.08 (0.15), residues: 1343 sheet: 0.27 (0.38), residues: 195 loop : -1.30 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 465 HIS 0.005 0.001 HIS C 69 PHE 0.017 0.001 PHE F 345 TYR 0.010 0.001 TYR A 580 ARG 0.004 0.000 ARG D 425 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 977) hydrogen bonds : angle 3.69690 ( 2759) covalent geometry : bond 0.00398 (22628) covalent geometry : angle 0.49393 (30930) *********************** 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 101 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 2.417 Fit side-chains REVERT: B 262 THR cc_start: 0.9584 (OUTLIER) cc_final: 0.8939 (t) REVERT: B 265 MET cc_start: 0.9436 (ptp) cc_final: 0.8769 (pmm) REVERT: E 291 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8227 (pp) REVERT: F 307 ASN cc_start: 0.9450 (m110) cc_final: 0.9199 (m110) REVERT: F 327 CYS cc_start: 0.9069 (m) cc_final: 0.8793 (m) REVERT: A 623 MET cc_start: 0.8997 (tpp) cc_final: 0.8784 (tpp) REVERT: A 887 ASP cc_start: 0.9613 (t0) cc_final: 0.9372 (t0) REVERT: C 141 MET cc_start: 0.8888 (mmm) cc_final: 0.8466 (mmm) REVERT: C 371 HIS cc_start: 0.8153 (m-70) cc_final: 0.7922 (m-70) REVERT: C 385 ASN cc_start: 0.9759 (p0) cc_final: 0.9467 (m-40) REVERT: C 488 GLU cc_start: 0.9548 (mm-30) cc_final: 0.9281 (mt-10) REVERT: C 533 MET cc_start: 0.9254 (tmm) cc_final: 0.8554 (tmm) outliers start: 21 outliers final: 13 residues processed: 96 average time/residue: 0.2759 time to fit residues: 46.8282 Evaluate side-chains 94 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 247 ILE 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 217 optimal weight: 5.9990 chunk 226 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.041749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.028183 restraints weight = 131367.116| |-----------------------------------------------------------------------------| r_work (start): 0.2492 rms_B_bonded: 4.30 r_work: 0.2344 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22628 Z= 0.129 Angle : 0.461 8.056 30930 Z= 0.250 Chirality : 0.038 0.185 3514 Planarity : 0.003 0.041 3621 Dihedral : 16.894 118.734 3645 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.01 % Allowed : 10.38 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2460 helix: 2.13 (0.15), residues: 1346 sheet: 0.51 (0.37), residues: 201 loop : -1.28 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 526 HIS 0.004 0.001 HIS C 69 PHE 0.017 0.001 PHE F 345 TYR 0.015 0.001 TYR D 523 ARG 0.002 0.000 ARG C 145 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 977) hydrogen bonds : angle 3.55500 ( 2759) covalent geometry : bond 0.00286 (22628) covalent geometry : angle 0.46141 (30930) *********************** 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 104 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 2.645 Fit side-chains REVERT: E 291 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8192 (pp) REVERT: E 426 GLU cc_start: 0.9609 (tp30) cc_final: 0.9401 (tp30) REVERT: F 307 ASN cc_start: 0.9462 (m110) cc_final: 0.9207 (m110) REVERT: F 327 CYS cc_start: 0.9117 (m) cc_final: 0.8834 (m) REVERT: F 354 MET cc_start: 0.8782 (tpp) cc_final: 0.8391 (tpt) REVERT: A 623 MET cc_start: 0.8950 (tpp) cc_final: 0.8716 (tpp) REVERT: A 887 ASP cc_start: 0.9620 (t0) cc_final: 0.9385 (t0) REVERT: C 141 MET cc_start: 0.8807 (mmm) cc_final: 0.8387 (mmm) REVERT: C 371 HIS cc_start: 0.8271 (m-70) cc_final: 0.8031 (m-70) REVERT: C 385 ASN cc_start: 0.9745 (p0) cc_final: 0.9457 (m-40) REVERT: C 488 GLU cc_start: 0.9533 (mm-30) cc_final: 0.9269 (mt-10) REVERT: C 533 MET cc_start: 0.9230 (tmm) cc_final: 0.8525 (tmm) REVERT: D 418 MET cc_start: 0.9371 (ttt) cc_final: 0.9087 (tpp) REVERT: D 465 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8880 (tm-30) outliers start: 23 outliers final: 14 residues processed: 99 average time/residue: 0.3024 time to fit residues: 52.1084 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 : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain F residue 365 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 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 158 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3036 r_free = 0.3036 target = 0.041610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.028020 restraints weight = 132302.134| |-----------------------------------------------------------------------------| r_work (start): 0.2486 rms_B_bonded: 4.29 r_work: 0.2339 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22628 Z= 0.146 Angle : 0.471 8.946 30930 Z= 0.254 Chirality : 0.038 0.199 3514 Planarity : 0.003 0.041 3621 Dihedral : 16.849 119.540 3645 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.01 % Allowed : 10.77 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2460 helix: 2.18 (0.15), residues: 1350 sheet: 0.49 (0.37), residues: 195 loop : -1.24 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 58 HIS 0.004 0.001 HIS C 69 PHE 0.017 0.001 PHE F 345 TYR 0.011 0.001 TYR D 523 ARG 0.002 0.000 ARG D 478 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 977) hydrogen bonds : angle 3.54774 ( 2759) covalent geometry : bond 0.00326 (22628) covalent geometry : angle 0.47082 (30930) *********************** 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: 23 poor density : 80 time to evaluate : 2.740 Fit side-chains REVERT: B 265 MET cc_start: 0.9432 (ptp) cc_final: 0.8802 (pmm) REVERT: E 291 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8172 (pp) REVERT: E 426 GLU cc_start: 0.9612 (tp30) cc_final: 0.9399 (tp30) REVERT: F 307 ASN cc_start: 0.9460 (m110) cc_final: 0.9213 (m110) REVERT: F 327 CYS cc_start: 0.9105 (m) cc_final: 0.8822 (m) REVERT: F 354 MET cc_start: 0.8790 (tpp) cc_final: 0.8304 (tpp) REVERT: A 623 MET cc_start: 0.8974 (tpp) cc_final: 0.8763 (tpp) REVERT: A 887 ASP cc_start: 0.9635 (t0) cc_final: 0.9411 (t0) REVERT: C 141 MET cc_start: 0.8840 (mmm) cc_final: 0.8405 (mmm) REVERT: C 371 HIS cc_start: 0.8211 (m-70) cc_final: 0.7981 (m-70) REVERT: C 385 ASN cc_start: 0.9763 (p0) cc_final: 0.9481 (m-40) REVERT: C 488 GLU cc_start: 0.9537 (mm-30) cc_final: 0.9261 (mt-10) REVERT: C 533 MET cc_start: 0.9233 (tmm) cc_final: 0.8526 (tmm) REVERT: D 418 MET cc_start: 0.9491 (ttt) cc_final: 0.9025 (tpp) outliers start: 23 outliers final: 12 residues processed: 99 average time/residue: 0.2944 time to fit residues: 51.1817 Evaluate side-chains 92 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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 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 A residue 874 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 499 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 31 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 58 optimal weight: 0.0870 chunk 101 optimal weight: 10.0000 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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 = 0.3038 r_free = 0.3038 target = 0.041646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.028131 restraints weight = 132206.103| |-----------------------------------------------------------------------------| r_work (start): 0.2488 rms_B_bonded: 4.29 r_work: 0.2343 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22628 Z= 0.138 Angle : 0.465 8.067 30930 Z= 0.250 Chirality : 0.038 0.144 3514 Planarity : 0.003 0.042 3621 Dihedral : 16.791 119.984 3645 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.88 % Allowed : 11.16 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 2460 helix: 2.19 (0.15), residues: 1352 sheet: 0.51 (0.37), residues: 196 loop : -1.21 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 58 HIS 0.004 0.001 HIS C 69 PHE 0.017 0.001 PHE F 345 TYR 0.013 0.001 TYR D 523 ARG 0.002 0.000 ARG D 478 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 977) hydrogen bonds : angle 3.50380 ( 2759) covalent geometry : bond 0.00310 (22628) covalent geometry : angle 0.46460 (30930) *********************** 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 100 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 2.798 Fit side-chains revert: symmetry clash REVERT: E 291 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8122 (pp) REVERT: E 426 GLU cc_start: 0.9610 (tp30) cc_final: 0.9396 (tp30) REVERT: F 307 ASN cc_start: 0.9484 (m110) cc_final: 0.9229 (m110) REVERT: F 327 CYS cc_start: 0.9117 (m) cc_final: 0.8844 (m) REVERT: F 354 MET cc_start: 0.8845 (tpp) cc_final: 0.8352 (tpp) REVERT: A 887 ASP cc_start: 0.9646 (t0) cc_final: 0.9333 (t0) REVERT: C 141 MET cc_start: 0.8813 (mmm) cc_final: 0.8367 (mmm) REVERT: C 371 HIS cc_start: 0.8222 (m-70) cc_final: 0.7982 (m-70) REVERT: C 385 ASN cc_start: 0.9761 (p0) cc_final: 0.9482 (m-40) REVERT: C 488 GLU cc_start: 0.9538 (mm-30) cc_final: 0.9262 (mt-10) REVERT: C 533 MET cc_start: 0.9248 (tmm) cc_final: 0.8556 (tmm) outliers start: 20 outliers final: 13 residues processed: 97 average time/residue: 0.3075 time to fit residues: 52.2452 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 : 2.592 ------------------------------------------------------------------------------- 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 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 390 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 3 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 193 optimal weight: 8.9990 chunk 223 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 251 optimal weight: 0.0670 overall best weight: 3.2126 ------------------------------------------------------------------------------- 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 = 0.3026 r_free = 0.3026 target = 0.041309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.027818 restraints weight = 132518.836| |-----------------------------------------------------------------------------| r_work (start): 0.2480 rms_B_bonded: 4.25 r_work: 0.2334 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1997 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= 0.163 Angle : 0.488 9.930 30930 Z= 0.260 Chirality : 0.038 0.227 3514 Planarity : 0.003 0.043 3621 Dihedral : 16.795 120.215 3645 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.70 % Allowed : 11.69 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 2460 helix: 2.23 (0.15), residues: 1351 sheet: 0.48 (0.37), residues: 196 loop : -1.21 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 465 HIS 0.004 0.001 HIS C 69 PHE 0.016 0.001 PHE F 345 TYR 0.013 0.001 TYR D 523 ARG 0.003 0.000 ARG D 478 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 977) hydrogen bonds : angle 3.54796 ( 2759) covalent geometry : bond 0.00367 (22628) covalent geometry : angle 0.48830 (30930) *********************** 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 96 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 2.376 Fit side-chains revert: symmetry clash REVERT: B 265 MET cc_start: 0.9434 (ptp) cc_final: 0.8828 (pmm) REVERT: E 291 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8204 (pp) REVERT: E 426 GLU cc_start: 0.9610 (tp30) cc_final: 0.9396 (tp30) REVERT: F 307 ASN cc_start: 0.9492 (m110) cc_final: 0.9245 (m110) REVERT: F 327 CYS cc_start: 0.9152 (m) cc_final: 0.8887 (m) REVERT: F 354 MET cc_start: 0.8818 (tpp) cc_final: 0.8313 (tpp) REVERT: A 623 MET cc_start: 0.8953 (tpp) cc_final: 0.8705 (tpp) REVERT: A 887 ASP cc_start: 0.9649 (t0) cc_final: 0.9428 (t0) REVERT: C 141 MET cc_start: 0.8861 (mmm) cc_final: 0.8626 (mmp) REVERT: C 371 HIS cc_start: 0.8195 (m-70) cc_final: 0.7958 (m-70) REVERT: C 385 ASN cc_start: 0.9757 (p0) cc_final: 0.9477 (m-40) REVERT: C 488 GLU cc_start: 0.9543 (mm-30) cc_final: 0.9281 (mt-10) REVERT: C 533 MET cc_start: 0.9273 (tmm) cc_final: 0.8539 (tmm) REVERT: D 418 MET cc_start: 0.9475 (ttt) cc_final: 0.9137 (tpp) outliers start: 16 outliers final: 14 residues processed: 93 average time/residue: 0.2814 time to fit residues: 45.7132 Evaluate side-chains 94 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 2.547 ------------------------------------------------------------------------------- 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 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 390 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 499 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 5 optimal weight: 0.9990 chunk 178 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 204 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 154 optimal weight: 0.0030 chunk 215 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- 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 = 0.3033 r_free = 0.3033 target = 0.041484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.027983 restraints weight = 132423.837| |-----------------------------------------------------------------------------| r_work (start): 0.2485 rms_B_bonded: 4.29 r_work: 0.2340 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22628 Z= 0.146 Angle : 0.474 9.379 30930 Z= 0.253 Chirality : 0.038 0.214 3514 Planarity : 0.003 0.043 3621 Dihedral : 16.750 119.938 3645 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.79 % Allowed : 11.73 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 2460 helix: 2.26 (0.15), residues: 1350 sheet: 0.49 (0.37), residues: 196 loop : -1.20 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 526 HIS 0.004 0.001 HIS C 69 PHE 0.016 0.001 PHE F 345 TYR 0.011 0.001 TYR D 523 ARG 0.002 0.000 ARG D 478 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 977) hydrogen bonds : angle 3.51309 ( 2759) covalent geometry : bond 0.00327 (22628) covalent geometry : angle 0.47363 (30930) ********************** 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 98 residues out of total 2293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 2.667 Fit side-chains revert: symmetry clash REVERT: E 291 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8196 (pp) REVERT: E 414 MET cc_start: 0.8679 (tpt) cc_final: 0.8458 (tpt) REVERT: E 426 GLU cc_start: 0.9603 (tp30) cc_final: 0.9392 (tp30) REVERT: F 307 ASN cc_start: 0.9493 (m110) cc_final: 0.9236 (m110) REVERT: F 327 CYS cc_start: 0.9165 (m) cc_final: 0.8895 (m) REVERT: F 354 MET cc_start: 0.8840 (tpp) cc_final: 0.8329 (tpp) REVERT: A 623 MET cc_start: 0.8893 (tpp) cc_final: 0.8676 (tpp) REVERT: C 141 MET cc_start: 0.8836 (mmm) cc_final: 0.8597 (mmp) REVERT: C 371 HIS cc_start: 0.8233 (m-70) cc_final: 0.7977 (m-70) REVERT: C 385 ASN cc_start: 0.9738 (p0) cc_final: 0.9447 (m-40) REVERT: C 488 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9271 (mt-10) REVERT: C 533 MET cc_start: 0.9290 (tmm) cc_final: 0.8559 (tmm) outliers start: 18 outliers final: 15 residues processed: 95 average time/residue: 0.2918 time to fit residues: 48.4357 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 : 2.554 ------------------------------------------------------------------------------- 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 390 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 499 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 59 optimal weight: 30.0000 chunk 175 optimal weight: 0.0050 chunk 133 optimal weight: 20.0000 chunk 234 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- 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 = 0.3043 r_free = 0.3043 target = 0.041762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.028331 restraints weight = 131899.665| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 4.24 r_work: 0.2357 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22628 Z= 0.118 Angle : 0.461 9.109 30930 Z= 0.248 Chirality : 0.038 0.211 3514 Planarity : 0.003 0.042 3621 Dihedral : 16.695 119.697 3645 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.70 % Allowed : 11.87 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.18), residues: 2460 helix: 2.27 (0.15), residues: 1350 sheet: 0.55 (0.37), residues: 196 loop : -1.18 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 58 HIS 0.004 0.001 HIS C 69 PHE 0.017 0.001 PHE F 345 TYR 0.012 0.001 TYR D 523 ARG 0.002 0.000 ARG A 888 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 977) hydrogen bonds : angle 3.42953 ( 2759) covalent geometry : bond 0.00261 (22628) covalent geometry : angle 0.46061 (30930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10290.35 seconds wall clock time: 181 minutes 4.49 seconds (10864.49 seconds total)