Starting phenix.real_space_refine on Wed Sep 25 20:56:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/09_2024/6xzq_10665.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/09_2024/6xzq_10665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/09_2024/6xzq_10665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/09_2024/6xzq_10665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/09_2024/6xzq_10665.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzq_10665/09_2024/6xzq_10665.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.021 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 18 5.49 5 S 212 5.16 5 C 17983 2.51 5 N 4850 2.21 5 O 5345 1.98 5 H 28480 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 199 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 56888 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 617 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 14} Chain breaks: 1 Chain: "A" Number of atoms: 11269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 11269 Classifications: {'peptide': 696} Link IDs: {'PTRANS': 32, 'TRANS': 663} Chain breaks: 1 Chain: "B" Number of atoms: 11188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 11188 Classifications: {'peptide': 698} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 672} Chain breaks: 4 Chain: "C" Number of atoms: 12385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 12385 Classifications: {'peptide': 772} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 743} Chain: "D" Number of atoms: 8550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 8550 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 27, 'TRANS': 497} Chain: "E" Number of atoms: 7239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 7239 Classifications: {'peptide': 448} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 433} Chain breaks: 3 Chain: "F" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3101 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "G" Number of atoms: 2539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 2539 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 6, 'TRANS': 151} Time building chain proxies: 19.03, per 1000 atoms: 0.33 Number of scatterers: 56888 At special positions: 0 Unit cell: (121.52, 154.07, 176.855, 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 212 16.00 P 18 15.00 O 5345 8.00 N 4850 7.00 C 17983 6.00 H 28480 1.00 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: 10.97 Conformation dependent library (CDL) restraints added in 3.3 seconds 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6600 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 37 sheets defined 48.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.675A pdb=" N ILE A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A 12 " --> pdb=" O ILE A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 68 through 83 removed outlier: 3.738A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 146 through 166 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.857A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 233 Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.782A pdb=" N LYS A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 309 through 327 removed outlier: 4.050A pdb=" N TYR A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 381 through 390 Processing helix chain 'A' and resid 409 through 427 Processing helix chain 'A' and resid 430 through 452 removed outlier: 3.630A pdb=" N LEU A 451 " --> pdb=" O THR A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 569 through 588 removed outlier: 3.667A pdb=" N ARG A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 Processing helix chain 'A' and resid 617 through 634 removed outlier: 5.091A pdb=" N ARG A 622 " --> pdb=" O ARG A 618 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 666 through 677 removed outlier: 3.707A pdb=" N LEU A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 700 removed outlier: 3.808A pdb=" N LYS A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 removed outlier: 3.771A pdb=" N MET B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 removed outlier: 4.530A pdb=" N SER B 19 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 86 through 102 Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.955A pdb=" N HIS B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 157 Processing helix chain 'B' and resid 164 through 178 removed outlier: 3.707A pdb=" N ASP B 177 " --> pdb=" O ILE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.753A pdb=" N LEU B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 268 removed outlier: 4.132A pdb=" N LYS B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 295 removed outlier: 3.719A pdb=" N LYS B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.631A pdb=" N TYR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 347 removed outlier: 3.771A pdb=" N LYS B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.951A pdb=" N THR B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 425 " --> pdb=" O GLY B 421 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.533A pdb=" N LYS B 433 " --> pdb=" O ASP B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 473 removed outlier: 3.531A pdb=" N TRP B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 Processing helix chain 'B' and resid 519 through 538 removed outlier: 4.102A pdb=" N PHE B 524 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 571 through 582 removed outlier: 3.653A pdb=" N ILE B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS B 582 " --> pdb=" O ASN B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.878A pdb=" N LEU B 605 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 668 through 672 Processing helix chain 'B' and resid 675 through 696 removed outlier: 4.007A pdb=" N MET B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 681 " --> pdb=" O ALA B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 728 removed outlier: 3.546A pdb=" N ILE B 728 " --> pdb=" O MET B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 754 removed outlier: 3.557A pdb=" N ARG B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 17 Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.774A pdb=" N THR C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 37 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TRP C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 removed outlier: 3.786A pdb=" N SER C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 99 through 109 removed outlier: 3.910A pdb=" N ASN C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.923A pdb=" N ASP C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 Processing helix chain 'C' and resid 189 through 200 removed outlier: 3.850A pdb=" N VAL C 193 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 259 through 277 removed outlier: 3.858A pdb=" N LYS C 263 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 294 Processing helix chain 'C' and resid 306 through 313 Processing helix chain 'C' and resid 317 through 328 removed outlier: 3.593A pdb=" N LEU C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 417 Processing helix chain 'C' and resid 420 through 425 removed outlier: 3.979A pdb=" N LYS C 424 " --> pdb=" O GLY C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 removed outlier: 3.947A pdb=" N SER C 436 " --> pdb=" O MET C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 456 removed outlier: 3.580A pdb=" N SER C 456 " --> pdb=" O TRP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 467 removed outlier: 3.580A pdb=" N LEU C 460 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.881A pdb=" N ASP C 535 " --> pdb=" O THR C 532 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU C 536 " --> pdb=" O ILE C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 532 through 536' Processing helix chain 'C' and resid 558 through 574 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 590 through 595 removed outlier: 4.153A pdb=" N LEU C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR C 595 " --> pdb=" O TYR C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 595' Processing helix chain 'C' and resid 597 through 604 Processing helix chain 'C' and resid 605 through 607 No H-bonds generated for 'chain 'C' and resid 605 through 607' Processing helix chain 'C' and resid 611 through 630 removed outlier: 3.801A pdb=" N SER C 624 " --> pdb=" O ARG C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 641 Processing helix chain 'C' and resid 642 through 644 No H-bonds generated for 'chain 'C' and resid 642 through 644' Processing helix chain 'C' and resid 705 through 709 removed outlier: 3.936A pdb=" N LEU C 708 " --> pdb=" O SER C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 732 removed outlier: 3.507A pdb=" N ILE C 730 " --> pdb=" O GLN C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 771 removed outlier: 4.031A pdb=" N ASP C 762 " --> pdb=" O ALA C 758 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C 771 " --> pdb=" O VAL C 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 198 Processing helix chain 'D' and resid 205 through 215 Processing helix chain 'D' and resid 219 through 233 Processing helix chain 'D' and resid 276 through 280 removed outlier: 3.957A pdb=" N SER D 280 " --> pdb=" O PRO D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 292 removed outlier: 3.700A pdb=" N LYS D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 309 through 326 removed outlier: 3.727A pdb=" N TYR D 313 " --> pdb=" O TYR D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 356 through 364 removed outlier: 3.638A pdb=" N ILE D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 390 Processing helix chain 'D' and resid 409 through 427 Processing helix chain 'D' and resid 429 through 452 removed outlier: 3.671A pdb=" N ARG D 433 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 434 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 565 Processing helix chain 'D' and resid 568 through 589 removed outlier: 3.692A pdb=" N ILE D 572 " --> pdb=" O ARG D 568 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 585 " --> pdb=" O ILE D 581 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER D 586 " --> pdb=" O CYS D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 601 Processing helix chain 'D' and resid 617 through 635 removed outlier: 4.595A pdb=" N ARG D 622 " --> pdb=" O ARG D 618 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL D 623 " --> pdb=" O GLU D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 658 removed outlier: 3.875A pdb=" N LYS D 647 " --> pdb=" O CYS D 643 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS D 648 " --> pdb=" O ASN D 644 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE D 649 " --> pdb=" O GLU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 677 removed outlier: 3.603A pdb=" N LEU D 670 " --> pdb=" O ASN D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 700 removed outlier: 4.030A pdb=" N LYS D 700 " --> pdb=" O ILE D 696 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 13 through 18 removed outlier: 3.942A pdb=" N LEU E 17 " --> pdb=" O ASP E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 22 Processing helix chain 'E' and resid 36 through 50 removed outlier: 3.694A pdb=" N SER E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 102 removed outlier: 3.590A pdb=" N LEU E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.791A pdb=" N LYS E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 141 through 158 removed outlier: 3.591A pdb=" N ALA E 145 " --> pdb=" O PRO E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 178 removed outlier: 3.536A pdb=" N ASP E 177 " --> pdb=" O ILE E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 224 Processing helix chain 'E' and resid 250 through 268 removed outlier: 4.388A pdb=" N LYS E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 268 " --> pdb=" O ILE E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 295 Processing helix chain 'E' and resid 316 through 329 removed outlier: 3.669A pdb=" N TYR E 320 " --> pdb=" O GLN E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 341 through 348 Processing helix chain 'E' and resid 374 through 378 Processing helix chain 'E' and resid 383 through 389 Processing helix chain 'E' and resid 390 through 395 removed outlier: 4.438A pdb=" N LYS E 395 " --> pdb=" O GLU E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 426 Processing helix chain 'E' and resid 429 through 436 removed outlier: 3.720A pdb=" N LYS E 433 " --> pdb=" O ASP E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 473 Processing helix chain 'F' and resid 560 through 575 removed outlier: 4.033A pdb=" N LEU F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 589 Processing helix chain 'F' and resid 591 through 596 Processing helix chain 'F' and resid 597 through 604 removed outlier: 3.564A pdb=" N LYS F 601 " --> pdb=" O LEU F 597 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 607 No H-bonds generated for 'chain 'F' and resid 605 through 607' Processing helix chain 'F' and resid 611 through 630 Processing helix chain 'F' and resid 633 through 641 Processing helix chain 'F' and resid 642 through 644 No H-bonds generated for 'chain 'F' and resid 642 through 644' Processing helix chain 'F' and resid 726 through 732 removed outlier: 3.841A pdb=" N ILE F 730 " --> pdb=" O GLN F 727 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 11 Processing helix chain 'G' and resid 29 through 33 Processing helix chain 'G' and resid 82 through 87 Processing helix chain 'G' and resid 106 through 112 Processing helix chain 'G' and resid 123 through 128 Processing helix chain 'G' and resid 130 through 139 removed outlier: 3.762A pdb=" N ASN G 134 " --> pdb=" O ASP G 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 removed outlier: 3.513A pdb=" N VAL A 62 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.753A pdb=" N ALA B 454 " --> pdb=" O PHE B 300 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 274 removed outlier: 3.569A pdb=" N PHE A 271 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS A 551 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 331 removed outlier: 3.545A pdb=" N ILE A 331 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 456 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 457 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA A 463 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU A 484 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER A 465 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASP A 482 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 350 removed outlier: 3.733A pdb=" N GLU B 367 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 369 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 529 through 530 Processing sheet with id=AA7, first strand: chain 'A' and resid 611 through 616 removed outlier: 6.275A pdb=" N GLU A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS A 607 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A 613 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 605 " --> pdb=" O ILE A 613 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN A 615 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 133 removed outlier: 3.690A pdb=" N ARG B 138 " --> pdb=" O ASP B 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 180 through 182 removed outlier: 3.556A pdb=" N ILE B 214 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 227 through 229 Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AB4, first strand: chain 'B' and resid 491 through 492 removed outlier: 3.773A pdb=" N PHE B 491 " --> pdb=" O PHE B 498 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 61 through 63 Processing sheet with id=AB6, first strand: chain 'C' and resid 136 through 142 removed outlier: 6.429A pdb=" N TRP C 137 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN C 252 " --> pdb=" O TRP C 137 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU C 139 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 153 Processing sheet with id=AB8, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AB9, first strand: chain 'C' and resid 335 through 336 removed outlier: 3.555A pdb=" N LEU C 342 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU C 374 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 397 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP C 395 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR C 497 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 396 " --> pdb=" O THR C 497 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 352 through 357 Processing sheet with id=AC2, first strand: chain 'C' and resid 469 through 471 Processing sheet with id=AC3, first strand: chain 'C' and resid 657 through 658 Processing sheet with id=AC4, first strand: chain 'C' and resid 683 through 685 Processing sheet with id=AC5, first strand: chain 'C' and resid 713 through 714 removed outlier: 3.609A pdb=" N SER C 746 " --> pdb=" O VAL C 742 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.309A pdb=" N ILE D 461 " --> pdb=" O PHE D 485 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE D 487 " --> pdb=" O VAL D 459 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL D 459 " --> pdb=" O ILE D 487 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL D 489 " --> pdb=" O LYS D 457 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS D 457 " --> pdb=" O VAL D 489 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 271 through 274 removed outlier: 7.572A pdb=" N PHE D 485 " --> pdb=" O PHE D 509 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 366 through 367 Processing sheet with id=AC9, first strand: chain 'D' and resid 395 through 396 Processing sheet with id=AD1, first strand: chain 'D' and resid 529 through 536 Processing sheet with id=AD2, first strand: chain 'D' and resid 612 through 616 removed outlier: 6.617A pdb=" N ILE D 613 " --> pdb=" O ILE D 605 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU E 2 " --> pdb=" O LYS D 607 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 54 through 58 removed outlier: 4.404A pdb=" N VAL E 54 " --> pdb=" O LYS E 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AD5, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AD6, first strand: chain 'E' and resid 225 through 226 removed outlier: 7.068A pdb=" N ILE E 226 " --> pdb=" O LYS E 352 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 438 through 443 removed outlier: 3.592A pdb=" N ALA E 454 " --> pdb=" O PHE E 300 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 684 through 686 Processing sheet with id=AD9, first strand: chain 'F' and resid 712 through 714 Processing sheet with id=AE1, first strand: chain 'G' and resid 92 through 94 1273 hydrogen bonds defined for protein. 3531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.26 Time building geometry restraints manager: 13.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 28406 1.00 - 1.20: 74 1.20 - 1.41: 11506 1.41 - 1.61: 17127 1.61 - 1.81: 351 Bond restraints: 57464 Sorted by residual: bond pdb=" ND2 ASN C 103 " pdb="HD22 ASN C 103 " ideal model delta sigma weight residual 0.860 0.798 0.062 2.00e-02 2.50e+03 9.53e+00 bond pdb=" NE2 GLN A 627 " pdb="HE22 GLN A 627 " ideal model delta sigma weight residual 0.860 0.803 0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" NE2 GLN B 554 " pdb="HE22 GLN B 554 " ideal model delta sigma weight residual 0.860 0.804 0.056 2.00e-02 2.50e+03 7.85e+00 bond pdb=" ND2 ASN A 318 " pdb="HD22 ASN A 318 " ideal model delta sigma weight residual 0.860 0.805 0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" NE2 GLN D 367 " pdb="HE22 GLN D 367 " ideal model delta sigma weight residual 0.860 0.808 0.052 2.00e-02 2.50e+03 6.74e+00 ... (remaining 57459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.82: 104108 5.82 - 11.64: 27 11.64 - 17.46: 3 17.46 - 23.28: 1 23.28 - 29.10: 5 Bond angle restraints: 104144 Sorted by residual: angle pdb=" CD GLN B 130 " pdb=" NE2 GLN B 130 " pdb="HE22 GLN B 130 " ideal model delta sigma weight residual 120.00 149.10 -29.10 3.00e+00 1.11e-01 9.41e+01 angle pdb="HE21 GLN B 130 " pdb=" NE2 GLN B 130 " pdb="HE22 GLN B 130 " ideal model delta sigma weight residual 120.00 92.50 27.50 3.00e+00 1.11e-01 8.40e+01 angle pdb=" CG ASN A 318 " pdb=" ND2 ASN A 318 " pdb="HD22 ASN A 318 " ideal model delta sigma weight residual 120.00 145.67 -25.67 3.00e+00 1.11e-01 7.32e+01 angle pdb="HD21 ASN A 318 " pdb=" ND2 ASN A 318 " pdb="HD22 ASN A 318 " ideal model delta sigma weight residual 120.00 95.68 24.32 3.00e+00 1.11e-01 6.57e+01 angle pdb=" CD GLN B 130 " pdb=" NE2 GLN B 130 " pdb="HE21 GLN B 130 " ideal model delta sigma weight residual 120.00 96.50 23.50 3.00e+00 1.11e-01 6.14e+01 ... (remaining 104139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.17: 24921 28.17 - 56.33: 1699 56.33 - 84.50: 222 84.50 - 112.66: 18 112.66 - 140.83: 2 Dihedral angle restraints: 26862 sinusoidal: 15037 harmonic: 11825 Sorted by residual: dihedral pdb=" C4' U I 38 " pdb=" C3' U I 38 " pdb=" C2' U I 38 " pdb=" C1' U I 38 " ideal model delta sinusoidal sigma weight residual -35.00 30.50 -65.50 1 8.00e+00 1.56e-02 8.78e+01 dihedral pdb=" C5' U I 38 " pdb=" C4' U I 38 " pdb=" C3' U I 38 " pdb=" O3' U I 38 " ideal model delta sinusoidal sigma weight residual 147.00 87.57 59.43 1 8.00e+00 1.56e-02 7.37e+01 dihedral pdb=" O4' U I 38 " pdb=" C4' U I 38 " pdb=" C3' U I 38 " pdb=" C2' U I 38 " ideal model delta sinusoidal sigma weight residual 24.00 -33.52 57.52 1 8.00e+00 1.56e-02 6.95e+01 ... (remaining 26859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2803 0.034 - 0.068: 1090 0.068 - 0.102: 318 0.102 - 0.136: 95 0.136 - 0.170: 13 Chirality restraints: 4319 Sorted by residual: chirality pdb=" CA PRO B 488 " pdb=" N PRO B 488 " pdb=" C PRO B 488 " pdb=" CB PRO B 488 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" C1' C I 37 " pdb=" O4' C I 37 " pdb=" C2' C I 37 " pdb=" N1 C I 37 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CB THR A 554 " pdb=" CA THR A 554 " pdb=" OG1 THR A 554 " pdb=" CG2 THR A 554 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 4316 not shown) Planarity restraints: 8275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 103 " -0.070 2.00e-02 2.50e+03 9.65e-02 1.40e+02 pdb=" CG ASN C 103 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN C 103 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 103 " 0.155 2.00e-02 2.50e+03 pdb="HD21 ASN C 103 " 0.022 2.00e-02 2.50e+03 pdb="HD22 ASN C 103 " -0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 554 " 0.070 2.00e-02 2.50e+03 9.46e-02 1.34e+02 pdb=" CD GLN B 554 " -0.051 2.00e-02 2.50e+03 pdb=" OE1 GLN B 554 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN B 554 " -0.152 2.00e-02 2.50e+03 pdb="HE21 GLN B 554 " -0.021 2.00e-02 2.50e+03 pdb="HE22 GLN B 554 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 627 " 0.067 2.00e-02 2.50e+03 9.28e-02 1.29e+02 pdb=" CD GLN A 627 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLN A 627 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN A 627 " -0.151 2.00e-02 2.50e+03 pdb="HE21 GLN A 627 " -0.022 2.00e-02 2.50e+03 pdb="HE22 GLN A 627 " 0.149 2.00e-02 2.50e+03 ... (remaining 8272 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 3282 2.17 - 2.78: 111740 2.78 - 3.39: 154867 3.39 - 3.99: 196707 3.99 - 4.60: 312020 Nonbonded interactions: 778616 Sorted by model distance: nonbonded pdb=" OE1 GLU E 385 " pdb=" H GLU E 385 " model vdw 1.567 2.450 nonbonded pdb=" HE ARG E 383 " pdb=" OE2 GLU E 385 " model vdw 1.611 2.450 nonbonded pdb=" OP2 G I 5 " pdb=" H22 G I 5 " model vdw 1.612 2.450 nonbonded pdb=" O LYS B 255 " pdb=" HG1 THR B 259 " model vdw 1.612 2.450 nonbonded pdb=" OD1 ASP G 149 " pdb=" H ARG G 150 " model vdw 1.622 2.450 ... (remaining 778611 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.750 Extract box with map and model: 1.540 Check model and map are aligned: 0.330 Set scattering table: 0.390 Process input model: 90.550 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.150 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 28984 Z= 0.303 Angle : 0.643 6.263 39074 Z= 0.362 Chirality : 0.041 0.170 4319 Planarity : 0.006 0.062 4922 Dihedral : 15.894 140.830 11267 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.26 % Allowed : 13.07 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.13), residues: 3462 helix: -0.17 (0.13), residues: 1519 sheet: -3.19 (0.23), residues: 378 loop : -2.71 (0.13), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 398 HIS 0.006 0.001 HIS B 606 PHE 0.026 0.002 PHE A 378 TYR 0.024 0.002 TYR B 6 ARG 0.007 0.001 ARG F 620 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 332 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7475 (t) REVERT: E 108 HIS cc_start: 0.8485 (t70) cc_final: 0.8123 (t70) REVERT: E 172 MET cc_start: 0.8993 (mmp) cc_final: 0.8295 (mmm) REVERT: E 410 MET cc_start: 0.8718 (pmm) cc_final: 0.8489 (pmm) REVERT: F 717 ASN cc_start: 0.8221 (m110) cc_final: 0.7323 (m110) REVERT: F 736 GLN cc_start: 0.7726 (tt0) cc_final: 0.6318 (tt0) outliers start: 39 outliers final: 19 residues processed: 366 average time/residue: 1.0119 time to fit residues: 538.6628 Evaluate side-chains 252 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 232 time to evaluate : 3.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 568 ARG Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain F residue 706 LEU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 271 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 314 optimal weight: 10.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 615 GLN ** B 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN B 505 ASN B 623 ASN C 103 ASN C 155 GLN C 202 ASN C 212 HIS C 631 HIS C 766 ASN D 231 GLN D 248 GLN D 319 GLN D 496 ASN D 561 ASN D 646 GLN E 62 ASN E 296 ASN E 414 ASN F 610 ASN G 30 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28984 Z= 0.219 Angle : 0.567 7.574 39074 Z= 0.307 Chirality : 0.039 0.185 4319 Planarity : 0.004 0.058 4922 Dihedral : 8.665 122.476 4081 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.97 % Allowed : 13.87 % Favored : 85.16 % 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: -1.30 (0.14), residues: 3462 helix: 0.83 (0.13), residues: 1546 sheet: -2.46 (0.24), residues: 376 loop : -2.26 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 439 HIS 0.008 0.001 HIS G 8 PHE 0.012 0.001 PHE B 556 TYR 0.020 0.001 TYR F 645 ARG 0.009 0.000 ARG D 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 238 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.7466 (ptt) cc_final: 0.7241 (ptt) REVERT: C 703 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.6996 (p0) REVERT: D 248 GLN cc_start: 0.6443 (OUTLIER) cc_final: 0.6226 (pp30) REVERT: E 108 HIS cc_start: 0.8344 (t70) cc_final: 0.7989 (t70) REVERT: E 295 MET cc_start: 0.4671 (ptt) cc_final: 0.4457 (ptt) REVERT: E 408 MET cc_start: 0.6165 (mmm) cc_final: 0.5497 (mmm) REVERT: E 410 MET cc_start: 0.8804 (pmm) cc_final: 0.8586 (pmm) REVERT: E 478 MET cc_start: 0.6254 (tpt) cc_final: 0.6001 (tpt) outliers start: 30 outliers final: 16 residues processed: 265 average time/residue: 0.8789 time to fit residues: 356.5951 Evaluate side-chains 236 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 218 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain D residue 248 GLN Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 314 optimal weight: 9.9990 chunk 340 optimal weight: 10.0000 chunk 280 optimal weight: 6.9990 chunk 312 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 252 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 496 ASN B 130 GLN B 505 ASN B 578 ASN ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 646 GLN D 689 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 717 ASN F 736 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 28984 Z= 0.375 Angle : 0.601 6.382 39074 Z= 0.327 Chirality : 0.040 0.152 4319 Planarity : 0.004 0.066 4922 Dihedral : 8.267 123.668 4061 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.22 % Allowed : 13.94 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 3462 helix: 0.83 (0.13), residues: 1541 sheet: -1.98 (0.26), residues: 372 loop : -2.17 (0.14), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 439 HIS 0.010 0.001 HIS E 121 PHE 0.012 0.002 PHE F 646 TYR 0.018 0.002 TYR A 502 ARG 0.007 0.001 ARG G 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 222 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 108 HIS cc_start: 0.8284 (t70) cc_final: 0.7896 (t70) REVERT: E 408 MET cc_start: 0.6335 (mmm) cc_final: 0.5612 (mmm) REVERT: E 410 MET cc_start: 0.8854 (pmm) cc_final: 0.8580 (pmm) REVERT: E 478 MET cc_start: 0.6709 (tpt) cc_final: 0.6439 (tpt) outliers start: 38 outliers final: 21 residues processed: 254 average time/residue: 0.8816 time to fit residues: 348.2538 Evaluate side-chains 236 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 215 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 151 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 chunk 150 optimal weight: 0.2980 chunk 211 optimal weight: 0.6980 chunk 315 optimal weight: 3.9990 chunk 334 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 299 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 ASN B 623 ASN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 262 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28984 Z= 0.137 Angle : 0.489 5.802 39074 Z= 0.257 Chirality : 0.037 0.153 4319 Planarity : 0.003 0.055 4922 Dihedral : 7.983 124.888 4053 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.80 % Allowed : 14.23 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3462 helix: 1.34 (0.14), residues: 1543 sheet: -1.68 (0.26), residues: 368 loop : -1.88 (0.14), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 311 HIS 0.009 0.001 HIS G 8 PHE 0.011 0.001 PHE C 126 TYR 0.014 0.001 TYR F 645 ARG 0.005 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 3.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6837 (tt) REVERT: C 703 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: E 108 HIS cc_start: 0.8297 (t70) cc_final: 0.7927 (t70) REVERT: E 408 MET cc_start: 0.6106 (mmm) cc_final: 0.5459 (mmm) REVERT: E 410 MET cc_start: 0.8749 (pmm) cc_final: 0.8532 (pmm) REVERT: E 478 MET cc_start: 0.6807 (tpt) cc_final: 0.6544 (tpt) REVERT: F 744 GLN cc_start: 0.8020 (tp40) cc_final: 0.7722 (tp-100) outliers start: 25 outliers final: 16 residues processed: 244 average time/residue: 0.8695 time to fit residues: 330.3379 Evaluate side-chains 231 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 213 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain B residue 632 PHE Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 546 ASP Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 130 GLN Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 249 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 285 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN B 147 GLN B 505 ASN B 600 ASN B 623 ASN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN E 262 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 28984 Z= 0.348 Angle : 0.563 6.683 39074 Z= 0.306 Chirality : 0.039 0.147 4319 Planarity : 0.004 0.062 4922 Dihedral : 8.024 125.265 4052 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.87 % Allowed : 14.32 % Favored : 84.81 % 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: -0.80 (0.14), residues: 3462 helix: 1.07 (0.13), residues: 1545 sheet: -1.71 (0.26), residues: 375 loop : -1.93 (0.14), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 439 HIS 0.010 0.001 HIS G 8 PHE 0.012 0.001 PHE C 386 TYR 0.016 0.001 TYR G 131 ARG 0.006 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 216 time to evaluate : 3.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 261 GLN cc_start: 0.5886 (tp40) cc_final: 0.5676 (tp40) REVERT: E 69 CYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8488 (m) REVERT: E 108 HIS cc_start: 0.8118 (t70) cc_final: 0.7755 (t70) REVERT: E 262 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8551 (tm-30) REVERT: E 375 MET cc_start: 0.7746 (mtm) cc_final: 0.7494 (mtm) REVERT: E 410 MET cc_start: 0.8856 (pmm) cc_final: 0.8590 (pmm) outliers start: 27 outliers final: 17 residues processed: 238 average time/residue: 0.8471 time to fit residues: 317.3322 Evaluate side-chains 223 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 3.9990 chunk 301 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 334 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 623 ASN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28984 Z= 0.290 Angle : 0.532 6.264 39074 Z= 0.287 Chirality : 0.038 0.161 4319 Planarity : 0.004 0.053 4922 Dihedral : 8.009 126.460 4051 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.93 % Allowed : 14.93 % Favored : 84.13 % 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: -0.77 (0.14), residues: 3462 helix: 1.10 (0.13), residues: 1553 sheet: -1.79 (0.25), residues: 390 loop : -1.90 (0.14), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 311 HIS 0.011 0.001 HIS G 8 PHE 0.012 0.001 PHE B 692 TYR 0.013 0.001 TYR G 131 ARG 0.006 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 207 time to evaluate : 3.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6856 (pm20) cc_final: 0.6636 (pm20) REVERT: E 108 HIS cc_start: 0.8090 (t70) cc_final: 0.7664 (t70) REVERT: E 262 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8230 (tm-30) REVERT: E 473 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8491 (mt) outliers start: 29 outliers final: 21 residues processed: 231 average time/residue: 0.8128 time to fit residues: 296.4634 Evaluate side-chains 222 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 200 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain F residue 706 LEU Chi-restraints excluded: chain G residue 131 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 333 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 623 ASN C 148 GLN C 240 HIS ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28984 Z= 0.316 Angle : 0.554 10.028 39074 Z= 0.299 Chirality : 0.039 0.175 4319 Planarity : 0.004 0.054 4922 Dihedral : 8.040 126.786 4051 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.06 % Allowed : 15.22 % Favored : 83.71 % 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: -0.85 (0.14), residues: 3462 helix: 1.02 (0.13), residues: 1557 sheet: -1.80 (0.26), residues: 371 loop : -1.96 (0.14), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 311 HIS 0.009 0.001 HIS G 8 PHE 0.013 0.001 PHE B 692 TYR 0.013 0.001 TYR G 131 ARG 0.007 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 205 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 612 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7760 (mp) REVERT: E 108 HIS cc_start: 0.8002 (t70) cc_final: 0.7547 (t70) REVERT: E 295 MET cc_start: 0.6494 (ptt) cc_final: 0.6152 (ptt) REVERT: F 734 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7170 (m-80) outliers start: 33 outliers final: 25 residues processed: 232 average time/residue: 0.8324 time to fit residues: 308.9680 Evaluate side-chains 226 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 199 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain F residue 631 HIS Chi-restraints excluded: chain F residue 734 PHE Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 151 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 262 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 ASN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28984 Z= 0.237 Angle : 0.516 6.691 39074 Z= 0.275 Chirality : 0.038 0.167 4319 Planarity : 0.003 0.046 4922 Dihedral : 7.977 127.265 4051 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.00 % Allowed : 15.16 % Favored : 83.84 % 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 (0.14), residues: 3462 helix: 1.23 (0.13), residues: 1554 sheet: -1.79 (0.25), residues: 381 loop : -1.85 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 311 HIS 0.005 0.001 HIS G 8 PHE 0.011 0.001 PHE B 692 TYR 0.012 0.001 TYR F 645 ARG 0.007 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 203 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 734 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7132 (m-80) outliers start: 31 outliers final: 27 residues processed: 228 average time/residue: 0.8098 time to fit residues: 293.5628 Evaluate side-chains 227 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 569 GLU Chi-restraints excluded: chain F residue 631 HIS Chi-restraints excluded: chain F residue 734 PHE Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 151 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 303 optimal weight: 9.9990 chunk 319 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 293 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 28984 Z= 0.508 Angle : 0.673 7.238 39074 Z= 0.369 Chirality : 0.042 0.178 4319 Planarity : 0.005 0.057 4922 Dihedral : 8.296 127.382 4051 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.16 % Allowed : 15.03 % Favored : 83.81 % 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: -1.46 (0.14), residues: 3462 helix: 0.43 (0.13), residues: 1546 sheet: -1.97 (0.26), residues: 366 loop : -2.21 (0.14), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 439 HIS 0.009 0.002 HIS B 563 PHE 0.017 0.002 PHE D 339 TYR 0.021 0.002 TYR D 630 ARG 0.007 0.001 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 197 time to evaluate : 3.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8211 (t0) REVERT: D 612 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7843 (mp) REVERT: F 734 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.7156 (m-80) outliers start: 36 outliers final: 26 residues processed: 225 average time/residue: 0.8058 time to fit residues: 288.2782 Evaluate side-chains 222 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 631 HIS Chi-restraints excluded: chain F residue 734 PHE Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 151 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 204 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 228 optimal weight: 0.9990 chunk 344 optimal weight: 7.9990 chunk 317 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.259 28984 Z= 0.476 Angle : 0.819 59.200 39074 Z= 0.491 Chirality : 0.041 0.232 4319 Planarity : 0.005 0.144 4922 Dihedral : 8.288 127.320 4050 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.16 % Allowed : 15.22 % Favored : 83.62 % Cbeta Deviations : 0.03 % 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: -1.51 (0.13), residues: 3462 helix: 0.39 (0.13), residues: 1547 sheet: -2.01 (0.25), residues: 376 loop : -2.22 (0.14), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 269 HIS 0.009 0.002 HIS B 563 PHE 0.017 0.002 PHE D 339 TYR 0.022 0.002 TYR D 630 ARG 0.006 0.001 ARG C 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 195 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 612 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7854 (mp) REVERT: F 734 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7149 (m-80) outliers start: 36 outliers final: 33 residues processed: 217 average time/residue: 0.7962 time to fit residues: 273.8747 Evaluate side-chains 230 residues out of total 3107 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 195 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 71 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 388 ARG Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 703 ASP Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 494 HIS Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 631 HIS Chi-restraints excluded: chain F residue 710 GLU Chi-restraints excluded: chain F residue 716 GLU Chi-restraints excluded: chain F residue 734 PHE Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 151 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 218 optimal weight: 8.9990 chunk 292 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 274 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 282 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.060042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.045774 restraints weight = 369062.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.047906 restraints weight = 139143.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.049237 restraints weight = 75869.798| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.259 28984 Z= 0.476 Angle : 0.819 59.200 39074 Z= 0.491 Chirality : 0.041 0.232 4319 Planarity : 0.005 0.144 4922 Dihedral : 8.288 127.320 4050 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.13 % Allowed : 15.22 % Favored : 83.65 % Cbeta Deviations : 0.03 % 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: -1.51 (0.13), residues: 3462 helix: 0.39 (0.13), residues: 1547 sheet: -2.01 (0.25), residues: 376 loop : -2.22 (0.14), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 269 HIS 0.009 0.002 HIS B 563 PHE 0.017 0.002 PHE D 339 TYR 0.022 0.002 TYR D 630 ARG 0.006 0.001 ARG C 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8131.58 seconds wall clock time: 140 minutes 57.93 seconds (8457.93 seconds total)