Starting phenix.real_space_refine on Fri Jul 3 21:36:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jps_22421/07_2026/7jps_22421_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jps_22421/07_2026/7jps_22421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jps_22421/07_2026/7jps_22421_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jps_22421/07_2026/7jps_22421_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jps_22421/07_2026/7jps_22421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jps_22421/07_2026/7jps_22421.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 33 5.49 5 Mg 3 5.21 5 S 82 5.16 5 C 10402 2.51 5 N 2772 2.21 5 O 3059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16352 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2787 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 12, 'TRANS': 338} Chain breaks: 3 Chain: "B" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1640 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain: "C" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4844 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 24, 'TRANS': 566} Chain breaks: 9 Chain: "D" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3297 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 13, 'TRANS': 391} Chain breaks: 2 Chain: "E" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3160 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 368} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "G" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.10, per 1000 atoms: 0.19 Number of scatterers: 16352 At special positions: 0 Unit cell: (93.09, 133.75, 163.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 82 16.00 P 33 15.00 Mg 3 11.99 O 3059 8.00 N 2772 7.00 C 10402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 824.6 milliseconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3758 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 9 sheets defined 64.0% alpha, 6.1% beta 11 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.728A pdb=" N ALA A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 523 removed outlier: 3.610A pdb=" N PHE A 511 " --> pdb=" O ARG A 507 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 521 " --> pdb=" O PHE A 517 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 557 Processing helix chain 'A' and resid 577 through 588 removed outlier: 4.441A pdb=" N VAL A 581 " --> pdb=" O HIS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 605 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.748A pdb=" N LEU A 624 " --> pdb=" O GLU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 682 through 694 removed outlier: 3.506A pdb=" N LEU A 686 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 716 Processing helix chain 'A' and resid 718 through 736 removed outlier: 3.933A pdb=" N CYS A 722 " --> pdb=" O ASP A 718 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 759 removed outlier: 3.629A pdb=" N SER A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 756 " --> pdb=" O MET A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 769 Processing helix chain 'A' and resid 771 through 789 Processing helix chain 'A' and resid 794 through 810 removed outlier: 4.028A pdb=" N ALA A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 829 removed outlier: 4.037A pdb=" N ALA A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 829 " --> pdb=" O HIS A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 859 Processing helix chain 'B' and resid 271 through 276 removed outlier: 4.382A pdb=" N LEU B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 removed outlier: 3.515A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 306 removed outlier: 3.682A pdb=" N GLN B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B 297 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HIS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS B 300 " --> pdb=" O LYS B 296 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N HIS B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 347 through 359 removed outlier: 3.800A pdb=" N ILE B 355 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 383 removed outlier: 3.584A pdb=" N ASP B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 414 Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.615A pdb=" N MET B 432 " --> pdb=" O ALA B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 463 removed outlier: 3.548A pdb=" N SER B 459 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 65 removed outlier: 4.195A pdb=" N SER C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 87 removed outlier: 3.950A pdb=" N ASN C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 113 through 129 removed outlier: 3.581A pdb=" N THR C 122 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU C 123 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 141 removed outlier: 3.613A pdb=" N ASP C 140 " --> pdb=" O GLN C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 158 removed outlier: 3.515A pdb=" N LEU C 148 " --> pdb=" O MET C 144 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 193 Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.684A pdb=" N LEU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE C 235 " --> pdb=" O GLN C 231 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 removed outlier: 3.677A pdb=" N ARG C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.504A pdb=" N SER C 269 " --> pdb=" O HIS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 291 removed outlier: 3.579A pdb=" N THR C 286 " --> pdb=" O LYS C 282 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 316 removed outlier: 3.694A pdb=" N PHE C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 339 removed outlier: 3.526A pdb=" N PHE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 345 removed outlier: 3.586A pdb=" N LEU C 344 " --> pdb=" O LEU C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 removed outlier: 3.536A pdb=" N ASN C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 368 removed outlier: 3.584A pdb=" N ARG C 368 " --> pdb=" O GLU C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.579A pdb=" N LYS C 378 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN C 379 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 390 removed outlier: 3.640A pdb=" N GLN C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN C 390 " --> pdb=" O ALA C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 426 removed outlier: 3.508A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C 413 " --> pdb=" O HIS C 409 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 414 " --> pdb=" O MET C 410 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C 415 " --> pdb=" O ASN C 411 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N CYS C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 445 removed outlier: 3.611A pdb=" N CYS C 442 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 462 removed outlier: 3.918A pdb=" N SER C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET C 462 " --> pdb=" O GLN C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 482 removed outlier: 3.614A pdb=" N PHE C 479 " --> pdb=" O CYS C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 501 removed outlier: 3.691A pdb=" N ALA C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE C 501 " --> pdb=" O PHE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 567 removed outlier: 3.692A pdb=" N ASN C 554 " --> pdb=" O VAL C 550 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE C 559 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP C 560 " --> pdb=" O VAL C 556 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS C 561 " --> pdb=" O ASN C 557 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 562 " --> pdb=" O PHE C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 573 Processing helix chain 'C' and resid 575 through 580 removed outlier: 3.613A pdb=" N VAL C 578 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 592 removed outlier: 3.766A pdb=" N HIS C 590 " --> pdb=" O ALA C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 605 removed outlier: 3.672A pdb=" N ALA C 602 " --> pdb=" O ALA C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 609 removed outlier: 3.692A pdb=" N TYR C 609 " --> pdb=" O PRO C 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 606 through 609' Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.672A pdb=" N ALA C 632 " --> pdb=" O ASP C 628 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS C 634 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS C 636 " --> pdb=" O ALA C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 660 removed outlier: 3.708A pdb=" N THR C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 658 " --> pdb=" O THR C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 690 removed outlier: 4.219A pdb=" N LEU C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 40 through 57 Processing helix chain 'D' and resid 72 through 86 removed outlier: 3.677A pdb=" N ILE D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.707A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.631A pdb=" N GLY D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 141 removed outlier: 3.534A pdb=" N LEU D 139 " --> pdb=" O ASN D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 167 removed outlier: 3.978A pdb=" N LEU D 163 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 165 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS D 167 " --> pdb=" O PHE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'D' and resid 197 through 201 removed outlier: 3.593A pdb=" N LEU D 201 " --> pdb=" O ILE D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 209 Processing helix chain 'D' and resid 222 through 234 removed outlier: 3.706A pdb=" N LEU D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 258 removed outlier: 3.585A pdb=" N GLU D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 removed outlier: 3.776A pdb=" N GLN D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.945A pdb=" N LEU D 279 " --> pdb=" O ASN D 275 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET D 284 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 285 " --> pdb=" O MET D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 310 removed outlier: 3.569A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 308 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 320 removed outlier: 3.658A pdb=" N ASN D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D 317 " --> pdb=" O SER D 313 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 339 removed outlier: 3.672A pdb=" N ILE D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 331 " --> pdb=" O CYS D 327 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D 336 " --> pdb=" O MET D 332 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP D 337 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE D 338 " --> pdb=" O HIS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 359 removed outlier: 3.782A pdb=" N LYS D 355 " --> pdb=" O ASN D 351 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 383 removed outlier: 3.685A pdb=" N VAL D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D 374 " --> pdb=" O PRO D 370 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN D 381 " --> pdb=" O GLU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.617A pdb=" N MET D 412 " --> pdb=" O ASN D 408 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN D 413 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 416 " --> pdb=" O MET D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 431 removed outlier: 3.521A pdb=" N ARG D 426 " --> pdb=" O PRO D 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 23 Processing helix chain 'E' and resid 43 through 54 removed outlier: 3.817A pdb=" N THR E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 85 removed outlier: 3.558A pdb=" N LEU E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU E 74 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 111 Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 129 through 134 removed outlier: 3.698A pdb=" N MET E 133 " --> pdb=" O TYR E 129 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 129 through 134' Processing helix chain 'E' and resid 136 through 143 Processing helix chain 'E' and resid 143 through 149 Processing helix chain 'E' and resid 161 through 166 removed outlier: 4.068A pdb=" N PHE E 165 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 192 removed outlier: 3.732A pdb=" N ILE E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 216 removed outlier: 3.622A pdb=" N TYR E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 205 " --> pdb=" O ALA E 201 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR E 207 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 214 " --> pdb=" O ILE E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 237 removed outlier: 3.538A pdb=" N LEU E 231 " --> pdb=" O HIS E 227 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Proline residue: E 234 - end of helix Processing helix chain 'E' and resid 237 through 243 removed outlier: 3.612A pdb=" N VAL E 241 " --> pdb=" O CYS E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 265 Proline residue: E 259 - end of helix removed outlier: 3.828A pdb=" N LYS E 262 " --> pdb=" O GLU E 258 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS E 263 " --> pdb=" O PRO E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 284 removed outlier: 3.801A pdb=" N GLN E 282 " --> pdb=" O TRP E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 318 removed outlier: 3.506A pdb=" N ILE E 311 " --> pdb=" O LYS E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.500A pdb=" N PHE E 327 " --> pdb=" O THR E 323 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 328 " --> pdb=" O ASP E 324 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 329 " --> pdb=" O LYS E 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 323 through 329' Processing helix chain 'E' and resid 358 through 370 removed outlier: 3.552A pdb=" N ALA E 364 " --> pdb=" O ASP E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 390 removed outlier: 3.674A pdb=" N ILE E 384 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR E 385 " --> pdb=" O PHE E 381 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 424 removed outlier: 3.792A pdb=" N ILE E 416 " --> pdb=" O SER E 412 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 418 " --> pdb=" O ASP E 414 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE E 419 " --> pdb=" O PHE E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 432 removed outlier: 4.261A pdb=" N TYR E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 431 " --> pdb=" O ILE E 427 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR E 432 " --> pdb=" O ILE E 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 426 through 432' Processing sheet with id=AA1, first strand: chain 'A' and resid 528 through 529 removed outlier: 7.177A pdb=" N GLY A 528 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N ALA A 651 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 568 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 529 removed outlier: 7.177A pdb=" N GLY A 528 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N ALA A 651 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR A 531 " --> pdb=" O MET A 676 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 832 through 833 Processing sheet with id=AA4, first strand: chain 'B' and resid 335 through 339 removed outlier: 6.478A pdb=" N ILE B 311 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE B 424 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B 313 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 446 " --> pdb=" O VAL B 312 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.681A pdb=" N TYR C 132 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE C 218 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 134 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL C 215 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE C 249 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL C 217 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY C 251 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU C 219 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N PHE C 250 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA C 103 " --> pdb=" O PHE C 250 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE C 252 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU C 105 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 106 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 95 through 100 removed outlier: 6.532A pdb=" N LEU D 95 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE D 157 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL D 97 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASP D 159 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU D 99 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 188 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN D 61 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG D 213 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 64 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 385 through 387 Processing sheet with id=AA8, first strand: chain 'E' and resid 58 through 62 removed outlier: 5.951A pdb=" N VAL E 59 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP E 125 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL E 61 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL E 120 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU E 155 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE E 122 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU E 157 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU E 124 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER E 32 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LEU E 177 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE E 34 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 393 through 394 710 hydrogen bonds defined for protein. 2088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3109 1.33 - 1.45: 4144 1.45 - 1.58: 9296 1.58 - 1.70: 63 1.70 - 1.83: 125 Bond restraints: 16737 Sorted by residual: bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.51e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.28e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.65e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.52e+01 ... (remaining 16732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 22362 3.78 - 7.57: 346 7.57 - 11.35: 44 11.35 - 15.13: 3 15.13 - 18.92: 5 Bond angle restraints: 22760 Sorted by residual: angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 120.95 18.92 1.00e+00 1.00e+00 3.58e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.55 18.32 1.00e+00 1.00e+00 3.36e+02 angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 123.67 16.20 1.00e+00 1.00e+00 2.62e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 120.65 16.18 1.00e+00 1.00e+00 2.62e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 121.34 15.49 1.00e+00 1.00e+00 2.40e+02 ... (remaining 22755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 8838 17.60 - 35.19: 962 35.19 - 52.78: 239 52.78 - 70.38: 62 70.38 - 87.97: 38 Dihedral angle restraints: 10139 sinusoidal: 4403 harmonic: 5736 Sorted by residual: dihedral pdb=" CA GLN D 31 " pdb=" C GLN D 31 " pdb=" N SER D 32 " pdb=" CA SER D 32 " ideal model delta harmonic sigma weight residual 180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA HIS E 195 " pdb=" C HIS E 195 " pdb=" N PRO E 196 " pdb=" CA PRO E 196 " ideal model delta harmonic sigma weight residual 180.00 157.49 22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA VAL E 214 " pdb=" C VAL E 214 " pdb=" N PHE E 215 " pdb=" CA PHE E 215 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 10136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2301 0.097 - 0.194: 272 0.194 - 0.291: 21 0.291 - 0.387: 2 0.387 - 0.484: 2 Chirality restraints: 2598 Sorted by residual: chirality pdb=" CB THR E 410 " pdb=" CA THR E 410 " pdb=" OG1 THR E 410 " pdb=" CG2 THR E 410 " both_signs ideal model delta sigma weight residual False 2.55 2.07 0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.10 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CG LEU B 303 " pdb=" CB LEU B 303 " pdb=" CD1 LEU B 303 " pdb=" CD2 LEU B 303 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 2595 not shown) Planarity restraints: 2772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 369 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO C 370 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 370 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 370 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 152 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO D 153 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO D 153 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 153 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 412 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C TYR C 412 " 0.063 2.00e-02 2.50e+03 pdb=" O TYR C 412 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE C 413 " -0.021 2.00e-02 2.50e+03 ... (remaining 2769 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.71: 425 2.71 - 3.32: 18241 3.32 - 3.92: 30926 3.92 - 4.53: 41096 4.53 - 5.14: 61991 Nonbonded interactions: 152679 Sorted by model distance: nonbonded pdb=" O1B ATP A 901 " pdb="MG MG A 902 " model vdw 2.102 2.170 nonbonded pdb=" O1B ATP E 501 " pdb="MG MG E 502 " model vdw 2.110 2.170 nonbonded pdb=" O3G ATP A 901 " pdb="MG MG A 902 " model vdw 2.111 2.170 nonbonded pdb=" O3G ATP E 501 " pdb="MG MG E 502 " model vdw 2.174 2.170 nonbonded pdb=" O LEU B 316 " pdb=" OH TYR B 454 " model vdw 2.236 3.040 ... (remaining 152674 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 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 1 through 11 or resid 13)) selection = (chain 'G' and (resid 1 through 2 or resid 4 through 13)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.140 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4631 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 : 0.006 0.081 16737 Z= 0.383 Angle : 1.203 18.915 22760 Z= 0.728 Chirality : 0.063 0.484 2598 Planarity : 0.007 0.112 2772 Dihedral : 16.818 87.973 6381 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.16), residues: 1888 helix: -1.62 (0.13), residues: 1051 sheet: -0.75 (0.39), residues: 156 loop : -1.54 (0.21), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG E 417 TYR 0.032 0.003 TYR C 375 PHE 0.045 0.004 PHE A 637 TRP 0.041 0.004 TRP E 162 HIS 0.015 0.002 HIS C 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.38 (16737) covalent geometry : angle 1.20288 / 0.73 (22760) hydrogen bonds : bond 0.27717 / 18.81 ( 732) hydrogen bonds : angle 7.66721 / 5.39 ( 2132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.566 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: A 494 ARG cc_start: 0.6024 (mmt-90) cc_final: 0.5123 (mtt180) REVERT: A 566 ILE cc_start: 0.6766 (mp) cc_final: 0.6560 (mm) REVERT: D 29 CYS cc_start: 0.6659 (m) cc_final: 0.5792 (m) REVERT: D 50 LEU cc_start: 0.7853 (mt) cc_final: 0.7509 (tp) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.1421 time to fit residues: 78.6769 Evaluate side-chains 205 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 HIS A 654 ASN ** A 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 291 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN B 416 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 154 GLN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN C 399 GLN C 409 HIS C 486 HIS D 57 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS E 145 GLN E 195 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.076958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.063872 restraints weight = 146261.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.065029 restraints weight = 110290.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.065873 restraints weight = 89161.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.066457 restraints weight = 75781.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.066944 restraints weight = 66889.965| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16737 Z= 0.181 Angle : 0.732 9.127 22760 Z= 0.389 Chirality : 0.044 0.228 2598 Planarity : 0.005 0.095 2772 Dihedral : 13.498 88.743 2470 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.17 % Allowed : 3.16 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.18), residues: 1888 helix: -0.36 (0.14), residues: 1099 sheet: -0.54 (0.40), residues: 140 loop : -1.34 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 728 TYR 0.046 0.002 TYR C 408 PHE 0.025 0.002 PHE B 380 TRP 0.024 0.002 TRP C 648 HIS 0.006 0.001 HIS E 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (16737) covalent geometry : angle 0.73238 / 0.39 (22760) hydrogen bonds : bond 0.06096 / 4.17 ( 732) hydrogen bonds : angle 4.94361 / 3.54 ( 2132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 263 time to evaluate : 0.608 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: A 494 ARG cc_start: 0.5487 (mmt-90) cc_final: 0.4454 (mtt180) REVERT: A 516 ASN cc_start: 0.8534 (m-40) cc_final: 0.8041 (m110) REVERT: A 530 MET cc_start: 0.3165 (tpt) cc_final: 0.2404 (tpt) REVERT: A 647 LEU cc_start: 0.8701 (tp) cc_final: 0.8446 (tp) REVERT: A 700 PHE cc_start: 0.7616 (m-80) cc_final: 0.6952 (m-80) REVERT: A 718 ASP cc_start: 0.8241 (m-30) cc_final: 0.6624 (p0) REVERT: A 820 MET cc_start: 0.9596 (tpt) cc_final: 0.9346 (tpp) REVERT: B 311 ILE cc_start: 0.9008 (mm) cc_final: 0.8778 (mm) REVERT: B 326 PHE cc_start: 0.9314 (t80) cc_final: 0.8990 (t80) REVERT: C 360 ASN cc_start: 0.8526 (t0) cc_final: 0.8292 (t0) REVERT: C 482 TYR cc_start: 0.8479 (t80) cc_final: 0.8161 (t80) REVERT: C 610 LEU cc_start: 0.7894 (mt) cc_final: 0.7603 (mp) REVERT: D 50 LEU cc_start: 0.9539 (mt) cc_final: 0.9250 (tt) REVERT: D 132 PHE cc_start: 0.4869 (t80) cc_final: 0.4073 (t80) REVERT: D 205 ARG cc_start: 0.8903 (mtm-85) cc_final: 0.8157 (mpp80) REVERT: D 355 LYS cc_start: 0.9668 (mppt) cc_final: 0.9353 (ptmt) REVERT: E 130 LEU cc_start: 0.8733 (mt) cc_final: 0.8473 (mt) REVERT: E 133 MET cc_start: 0.7153 (mtm) cc_final: 0.5970 (ttm) REVERT: E 258 GLU cc_start: 0.5399 (mt-10) cc_final: 0.4963 (tm-30) REVERT: E 265 MET cc_start: 0.8475 (ppp) cc_final: 0.7959 (tpp) outliers start: 3 outliers final: 0 residues processed: 263 average time/residue: 0.1316 time to fit residues: 51.2978 Evaluate side-chains 191 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 80 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 173 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 180 optimal weight: 0.5980 chunk 88 optimal weight: 0.4980 chunk 188 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 HIS ** A 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 154 GLN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS C 486 HIS ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 96 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.076283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.063554 restraints weight = 148900.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.064677 restraints weight = 112107.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.065496 restraints weight = 90498.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.066060 restraints weight = 76771.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.066531 restraints weight = 67686.175| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16737 Z= 0.131 Angle : 0.625 9.918 22760 Z= 0.329 Chirality : 0.042 0.181 2598 Planarity : 0.004 0.056 2772 Dihedral : 13.539 88.179 2470 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.06 % Allowed : 2.48 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.18), residues: 1888 helix: 0.14 (0.15), residues: 1106 sheet: -0.14 (0.40), residues: 147 loop : -1.25 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 728 TYR 0.027 0.001 TYR C 408 PHE 0.022 0.001 PHE B 380 TRP 0.040 0.002 TRP C 648 HIS 0.015 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (16737) covalent geometry : angle 0.62458 / 0.33 (22760) hydrogen bonds : bond 0.04874 / 3.34 ( 732) hydrogen bonds : angle 4.53690 / 3.26 ( 2132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 0.685 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: A 494 ARG cc_start: 0.5388 (mmt-90) cc_final: 0.4169 (mtt180) REVERT: A 496 HIS cc_start: 0.8302 (m90) cc_final: 0.7878 (m-70) REVERT: A 516 ASN cc_start: 0.8502 (m-40) cc_final: 0.7947 (m-40) REVERT: A 530 MET cc_start: 0.2551 (tpt) cc_final: 0.1988 (tpt) REVERT: A 647 LEU cc_start: 0.8735 (tp) cc_final: 0.8502 (tp) REVERT: A 700 PHE cc_start: 0.7512 (m-80) cc_final: 0.7022 (m-80) REVERT: A 718 ASP cc_start: 0.8538 (m-30) cc_final: 0.6576 (p0) REVERT: A 820 MET cc_start: 0.9589 (tpt) cc_final: 0.9335 (tpp) REVERT: B 326 PHE cc_start: 0.9288 (t80) cc_final: 0.8879 (t80) REVERT: C 54 MET cc_start: 0.7576 (mpp) cc_final: 0.7335 (mpp) REVERT: C 222 MET cc_start: 0.7836 (ppp) cc_final: 0.7535 (ppp) REVERT: C 360 ASN cc_start: 0.8450 (t0) cc_final: 0.8186 (m-40) REVERT: C 475 CYS cc_start: 0.9244 (t) cc_final: 0.8577 (p) REVERT: C 482 TYR cc_start: 0.8393 (t80) cc_final: 0.8081 (t80) REVERT: D 46 HIS cc_start: 0.9120 (m-70) cc_final: 0.8869 (m-70) REVERT: D 50 LEU cc_start: 0.9605 (mt) cc_final: 0.9216 (tt) REVERT: D 85 MET cc_start: 0.9425 (tpp) cc_final: 0.9207 (mmm) REVERT: D 132 PHE cc_start: 0.4673 (t80) cc_final: 0.3846 (t80) REVERT: D 177 PHE cc_start: 0.8663 (m-80) cc_final: 0.8403 (m-80) REVERT: D 240 PHE cc_start: 0.8290 (t80) cc_final: 0.8030 (t80) REVERT: D 281 MET cc_start: 0.8631 (tpp) cc_final: 0.8416 (tpp) REVERT: D 355 LYS cc_start: 0.9677 (mppt) cc_final: 0.9374 (ptmt) REVERT: E 107 LYS cc_start: 0.8517 (tmmt) cc_final: 0.8216 (tptt) REVERT: E 133 MET cc_start: 0.7309 (mtm) cc_final: 0.6506 (ttm) REVERT: E 258 GLU cc_start: 0.5449 (mt-10) cc_final: 0.5117 (tm-30) REVERT: E 265 MET cc_start: 0.8527 (ppp) cc_final: 0.7966 (tpp) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.1360 time to fit residues: 49.8722 Evaluate side-chains 184 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 512 GLN ** A 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS C 242 HIS ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN C 411 ASN C 576 HIS ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS D 280 HIS D 351 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.072077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.059908 restraints weight = 156308.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.060919 restraints weight = 118037.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.061660 restraints weight = 96153.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.062154 restraints weight = 82283.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.062574 restraints weight = 73299.859| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 16737 Z= 0.184 Angle : 0.681 9.726 22760 Z= 0.356 Chirality : 0.042 0.163 2598 Planarity : 0.004 0.039 2772 Dihedral : 13.606 87.725 2470 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.17 % Allowed : 3.05 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.19), residues: 1888 helix: 0.27 (0.15), residues: 1108 sheet: -0.21 (0.41), residues: 140 loop : -1.18 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 693 TYR 0.034 0.002 TYR C 609 PHE 0.028 0.002 PHE B 380 TRP 0.047 0.003 TRP C 648 HIS 0.010 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (16737) covalent geometry : angle 0.68128 / 0.36 (22760) hydrogen bonds : bond 0.04912 / 3.21 ( 732) hydrogen bonds : angle 4.45313 / 3.21 ( 2132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 227 time to evaluate : 0.687 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: A 494 ARG cc_start: 0.6115 (mmt-90) cc_final: 0.4851 (mtt180) REVERT: A 496 HIS cc_start: 0.8516 (m90) cc_final: 0.8121 (m-70) REVERT: A 516 ASN cc_start: 0.8429 (m-40) cc_final: 0.7881 (m-40) REVERT: A 530 MET cc_start: 0.4411 (tpt) cc_final: 0.3433 (tpt) REVERT: A 700 PHE cc_start: 0.7867 (m-80) cc_final: 0.7329 (m-80) REVERT: A 820 MET cc_start: 0.9605 (tpt) cc_final: 0.9398 (tpp) REVERT: B 326 PHE cc_start: 0.9259 (t80) cc_final: 0.8806 (t80) REVERT: C 48 GLN cc_start: 0.6073 (OUTLIER) cc_final: 0.5860 (pm20) REVERT: C 360 ASN cc_start: 0.8564 (t0) cc_final: 0.8226 (m-40) REVERT: C 475 CYS cc_start: 0.9358 (t) cc_final: 0.8713 (p) REVERT: C 706 LEU cc_start: 0.8137 (tp) cc_final: 0.7896 (tt) REVERT: D 85 MET cc_start: 0.9471 (tpp) cc_final: 0.9226 (mmm) REVERT: D 132 PHE cc_start: 0.4839 (t80) cc_final: 0.4377 (t80) REVERT: D 177 PHE cc_start: 0.8732 (m-80) cc_final: 0.8388 (m-80) REVERT: D 205 ARG cc_start: 0.9033 (mpp80) cc_final: 0.8773 (mpp80) REVERT: D 240 PHE cc_start: 0.8305 (t80) cc_final: 0.8064 (t80) REVERT: E 107 LYS cc_start: 0.8377 (tmmt) cc_final: 0.8060 (tptt) REVERT: E 130 LEU cc_start: 0.8531 (mt) cc_final: 0.7770 (mt) REVERT: E 133 MET cc_start: 0.7439 (mtm) cc_final: 0.6488 (ttm) REVERT: E 258 GLU cc_start: 0.5523 (mt-10) cc_final: 0.5283 (tm-30) REVERT: E 265 MET cc_start: 0.8739 (ppp) cc_final: 0.8043 (tpt) REVERT: E 270 LEU cc_start: 0.9088 (mm) cc_final: 0.8140 (mm) outliers start: 3 outliers final: 0 residues processed: 230 average time/residue: 0.1249 time to fit residues: 43.4497 Evaluate side-chains 176 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 56 optimal weight: 0.6980 chunk 112 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 214 GLN E 193 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.069553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.057872 restraints weight = 164002.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.058855 restraints weight = 123408.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.059558 restraints weight = 100062.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.060030 restraints weight = 85522.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.060454 restraints weight = 76168.608| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 16737 Z= 0.210 Angle : 0.693 9.532 22760 Z= 0.363 Chirality : 0.043 0.213 2598 Planarity : 0.004 0.052 2772 Dihedral : 13.843 80.334 2470 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1888 helix: 0.00 (0.15), residues: 1124 sheet: -0.17 (0.43), residues: 133 loop : -1.12 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 22 TYR 0.025 0.002 TYR C 609 PHE 0.034 0.002 PHE B 380 TRP 0.049 0.003 TRP C 648 HIS 0.019 0.002 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (16737) covalent geometry : angle 0.69282 / 0.36 (22760) hydrogen bonds : bond 0.04903 / 3.24 ( 732) hydrogen bonds : angle 4.56605 / 3.28 ( 2132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.604 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: A 494 ARG cc_start: 0.6197 (mmt-90) cc_final: 0.5107 (mtt180) REVERT: A 496 HIS cc_start: 0.8564 (m90) cc_final: 0.8138 (m90) REVERT: A 516 ASN cc_start: 0.8251 (m-40) cc_final: 0.7617 (m-40) REVERT: A 530 MET cc_start: 0.4721 (tpt) cc_final: 0.3657 (tpt) REVERT: A 632 ILE cc_start: 0.7356 (mp) cc_final: 0.6892 (mp) REVERT: A 700 PHE cc_start: 0.7899 (m-80) cc_final: 0.7363 (m-80) REVERT: B 326 PHE cc_start: 0.9239 (t80) cc_final: 0.8894 (t80) REVERT: B 363 MET cc_start: 0.3622 (pmm) cc_final: 0.3120 (ppp) REVERT: B 395 LEU cc_start: 0.9679 (mp) cc_final: 0.9098 (tt) REVERT: B 432 MET cc_start: 0.7986 (pmm) cc_final: 0.7609 (pmm) REVERT: C 222 MET cc_start: 0.7916 (ppp) cc_final: 0.7637 (ppp) REVERT: C 261 ARG cc_start: 0.8586 (tmt170) cc_final: 0.8109 (tpt170) REVERT: C 325 ILE cc_start: 0.8309 (mm) cc_final: 0.8088 (mm) REVERT: C 360 ASN cc_start: 0.8661 (t0) cc_final: 0.8318 (m-40) REVERT: C 706 LEU cc_start: 0.8339 (tp) cc_final: 0.8057 (tt) REVERT: D 46 HIS cc_start: 0.9267 (m-70) cc_final: 0.9010 (m-70) REVERT: D 50 LEU cc_start: 0.9409 (mp) cc_final: 0.8832 (tt) REVERT: D 132 PHE cc_start: 0.5275 (t80) cc_final: 0.4541 (t80) REVERT: D 174 TYR cc_start: 0.7874 (m-10) cc_final: 0.7650 (m-10) REVERT: D 218 MET cc_start: 0.4660 (ttt) cc_final: 0.3772 (tmm) REVERT: D 240 PHE cc_start: 0.8289 (t80) cc_final: 0.8076 (t80) REVERT: E 133 MET cc_start: 0.7482 (mtm) cc_final: 0.6389 (ttm) REVERT: E 258 GLU cc_start: 0.5769 (mt-10) cc_final: 0.5516 (tm-30) REVERT: E 265 MET cc_start: 0.8774 (ppp) cc_final: 0.8043 (tpt) REVERT: E 270 LEU cc_start: 0.9076 (mm) cc_final: 0.8270 (mm) REVERT: E 407 TYR cc_start: 0.9177 (m-10) cc_final: 0.8836 (m-80) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1208 time to fit residues: 41.1541 Evaluate side-chains 170 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 426 HIS ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 ASN ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 195 HIS E 260 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.070026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.058116 restraints weight = 160978.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.059086 restraints weight = 122337.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.059795 restraints weight = 100034.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.060332 restraints weight = 85812.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.060729 restraints weight = 76194.027| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 16737 Z= 0.144 Angle : 0.631 10.669 22760 Z= 0.323 Chirality : 0.042 0.312 2598 Planarity : 0.003 0.045 2772 Dihedral : 13.695 81.346 2470 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.06 % Allowed : 1.98 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.19), residues: 1888 helix: 0.26 (0.15), residues: 1118 sheet: 0.11 (0.42), residues: 140 loop : -1.09 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 205 TYR 0.030 0.002 TYR D 399 PHE 0.037 0.002 PHE B 380 TRP 0.027 0.002 TRP C 648 HIS 0.008 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (16737) covalent geometry : angle 0.63075 / 0.32 (22760) hydrogen bonds : bond 0.04111 / 2.73 ( 732) hydrogen bonds : angle 4.32280 / 3.09 ( 2132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.474 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: A 494 ARG cc_start: 0.6343 (mmt-90) cc_final: 0.5092 (mtt180) REVERT: A 496 HIS cc_start: 0.8587 (m90) cc_final: 0.8152 (m90) REVERT: A 530 MET cc_start: 0.4480 (tpt) cc_final: 0.3610 (tpt) REVERT: A 700 PHE cc_start: 0.7729 (m-80) cc_final: 0.7263 (m-80) REVERT: A 820 MET cc_start: 0.9543 (tpt) cc_final: 0.9312 (tpp) REVERT: B 326 PHE cc_start: 0.9245 (t80) cc_final: 0.8841 (t80) REVERT: B 363 MET cc_start: 0.4233 (pmm) cc_final: 0.3784 (ppp) REVERT: B 432 MET cc_start: 0.7742 (pmm) cc_final: 0.7334 (pmm) REVERT: C 261 ARG cc_start: 0.8607 (tmt170) cc_final: 0.8144 (tpt170) REVERT: C 325 ILE cc_start: 0.8170 (mm) cc_final: 0.7892 (mm) REVERT: C 360 ASN cc_start: 0.8674 (t0) cc_final: 0.8343 (m-40) REVERT: D 46 HIS cc_start: 0.9242 (m-70) cc_final: 0.9011 (m90) REVERT: D 50 LEU cc_start: 0.9435 (mp) cc_final: 0.8853 (tt) REVERT: D 132 PHE cc_start: 0.5177 (t80) cc_final: 0.4778 (t80) REVERT: D 174 TYR cc_start: 0.7884 (m-10) cc_final: 0.7645 (m-10) REVERT: E 130 LEU cc_start: 0.8627 (mt) cc_final: 0.7933 (mt) REVERT: E 133 MET cc_start: 0.7500 (mtm) cc_final: 0.6341 (ttm) REVERT: E 265 MET cc_start: 0.8776 (ppp) cc_final: 0.8146 (tpt) REVERT: E 269 TYR cc_start: 0.7924 (t80) cc_final: 0.7517 (t80) REVERT: E 270 LEU cc_start: 0.9292 (mm) cc_final: 0.8575 (mm) outliers start: 1 outliers final: 1 residues processed: 224 average time/residue: 0.1200 time to fit residues: 41.0163 Evaluate side-chains 167 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 112 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 512 GLN A 516 ASN A 582 GLN A 585 GLN A 769 ASN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 HIS ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.069098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.057377 restraints weight = 164512.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.058360 restraints weight = 124858.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.059075 restraints weight = 101210.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.059536 restraints weight = 86718.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.059974 restraints weight = 77582.620| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16737 Z= 0.152 Angle : 0.640 10.722 22760 Z= 0.329 Chirality : 0.042 0.239 2598 Planarity : 0.004 0.042 2772 Dihedral : 13.630 80.585 2470 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.06 % Allowed : 1.64 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.19), residues: 1888 helix: 0.27 (0.15), residues: 1127 sheet: 0.17 (0.42), residues: 140 loop : -1.03 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 205 TYR 0.022 0.001 TYR C 609 PHE 0.037 0.002 PHE B 380 TRP 0.025 0.002 TRP C 51 HIS 0.009 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16737) covalent geometry : angle 0.64000 / 0.33 (22760) hydrogen bonds : bond 0.04124 / 2.75 ( 732) hydrogen bonds : angle 4.32972 / 3.07 ( 2132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.658 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: A 494 ARG cc_start: 0.6249 (mmt-90) cc_final: 0.4810 (mtt180) REVERT: A 530 MET cc_start: 0.4171 (tpt) cc_final: 0.3286 (tpt) REVERT: A 700 PHE cc_start: 0.7764 (m-80) cc_final: 0.7284 (m-80) REVERT: A 820 MET cc_start: 0.9548 (tpt) cc_final: 0.9321 (tpp) REVERT: B 326 PHE cc_start: 0.9209 (t80) cc_final: 0.8776 (t80) REVERT: B 363 MET cc_start: 0.4238 (pmm) cc_final: 0.3836 (ppp) REVERT: B 432 MET cc_start: 0.7892 (pmm) cc_final: 0.7474 (pmm) REVERT: C 261 ARG cc_start: 0.8668 (tmt170) cc_final: 0.8147 (tpt170) REVERT: C 325 ILE cc_start: 0.8179 (mm) cc_final: 0.7768 (mm) REVERT: D 106 ASN cc_start: 0.9524 (t0) cc_final: 0.9269 (t0) REVERT: D 132 PHE cc_start: 0.5249 (t80) cc_final: 0.4844 (t80) REVERT: D 174 TYR cc_start: 0.7931 (m-10) cc_final: 0.7689 (m-10) REVERT: D 218 MET cc_start: 0.5272 (tmm) cc_final: 0.4899 (tmm) REVERT: E 133 MET cc_start: 0.7554 (mtm) cc_final: 0.6483 (ttm) REVERT: E 265 MET cc_start: 0.8761 (ppp) cc_final: 0.8036 (tpp) REVERT: E 269 TYR cc_start: 0.8002 (t80) cc_final: 0.7709 (t80) REVERT: E 270 LEU cc_start: 0.9263 (mm) cc_final: 0.8509 (mm) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.1212 time to fit residues: 38.8597 Evaluate side-chains 160 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 30.0000 chunk 105 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 GLN A 585 GLN B 393 HIS B 406 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.066917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.055549 restraints weight = 171420.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.056505 restraints weight = 128930.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.057196 restraints weight = 104667.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.057718 restraints weight = 89499.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.058092 restraints weight = 79279.983| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 16737 Z= 0.194 Angle : 0.698 9.189 22760 Z= 0.362 Chirality : 0.044 0.203 2598 Planarity : 0.004 0.048 2772 Dihedral : 13.740 82.101 2470 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 1888 helix: 0.13 (0.15), residues: 1121 sheet: 0.11 (0.43), residues: 133 loop : -1.06 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 205 TYR 0.022 0.002 TYR C 609 PHE 0.040 0.002 PHE B 380 TRP 0.056 0.003 TRP C 51 HIS 0.018 0.002 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (16737) covalent geometry : angle 0.69774 / 0.36 (22760) hydrogen bonds : bond 0.04653 / 3.05 ( 732) hydrogen bonds : angle 4.44736 / 3.15 ( 2132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.643 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: A 494 ARG cc_start: 0.6335 (mmt-90) cc_final: 0.4987 (mtt180) REVERT: A 530 MET cc_start: 0.4372 (tpt) cc_final: 0.3442 (tpt) REVERT: A 571 MET cc_start: 0.8973 (mmm) cc_final: 0.8671 (mmm) REVERT: A 632 ILE cc_start: 0.7468 (mp) cc_final: 0.7110 (mp) REVERT: A 700 PHE cc_start: 0.7845 (m-80) cc_final: 0.7348 (m-80) REVERT: B 326 PHE cc_start: 0.9206 (t80) cc_final: 0.8715 (t80) REVERT: B 363 MET cc_start: 0.4087 (pmm) cc_final: 0.3684 (ppp) REVERT: B 432 MET cc_start: 0.7902 (pmm) cc_final: 0.7433 (pmm) REVERT: C 54 MET cc_start: 0.6326 (mpp) cc_final: 0.6090 (mpp) REVERT: C 113 ASP cc_start: 0.9264 (p0) cc_final: 0.9004 (p0) REVERT: C 325 ILE cc_start: 0.8183 (mm) cc_final: 0.7959 (mm) REVERT: D 106 ASN cc_start: 0.9525 (t0) cc_final: 0.9250 (t0) REVERT: D 132 PHE cc_start: 0.5383 (t80) cc_final: 0.5007 (t80) REVERT: D 174 TYR cc_start: 0.7928 (m-10) cc_final: 0.7627 (m-10) REVERT: D 218 MET cc_start: 0.5499 (tmm) cc_final: 0.5040 (tmm) REVERT: D 284 MET cc_start: 0.8089 (mmm) cc_final: 0.7836 (mmm) REVERT: E 265 MET cc_start: 0.8791 (ppp) cc_final: 0.8048 (tpt) REVERT: E 269 TYR cc_start: 0.7993 (t80) cc_final: 0.7617 (t80) REVERT: E 270 LEU cc_start: 0.9192 (mm) cc_final: 0.8560 (mm) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1250 time to fit residues: 39.0706 Evaluate side-chains 160 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 163 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 105 optimal weight: 0.0010 chunk 127 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 overall best weight: 2.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS B 426 HIS ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.067433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.055710 restraints weight = 166411.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.056723 restraints weight = 124721.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.057430 restraints weight = 101047.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.057970 restraints weight = 86440.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.058319 restraints weight = 76626.551| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16737 Z= 0.144 Angle : 0.649 8.936 22760 Z= 0.332 Chirality : 0.043 0.244 2598 Planarity : 0.004 0.044 2772 Dihedral : 13.677 83.974 2470 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.19), residues: 1888 helix: 0.23 (0.15), residues: 1126 sheet: 0.20 (0.43), residues: 133 loop : -1.04 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 289 TYR 0.016 0.002 TYR C 609 PHE 0.039 0.002 PHE B 380 TRP 0.054 0.002 TRP C 51 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (16737) covalent geometry : angle 0.64873 / 0.33 (22760) hydrogen bonds : bond 0.04048 / 2.70 ( 732) hydrogen bonds : angle 4.28949 / 3.04 ( 2132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.382 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: A 494 ARG cc_start: 0.6121 (mmt-90) cc_final: 0.4811 (mtt180) REVERT: A 530 MET cc_start: 0.3986 (tpt) cc_final: 0.3148 (tpt) REVERT: A 571 MET cc_start: 0.8955 (mmm) cc_final: 0.8572 (mmm) REVERT: A 636 LEU cc_start: 0.9486 (mt) cc_final: 0.9225 (pp) REVERT: A 700 PHE cc_start: 0.7734 (m-80) cc_final: 0.7295 (m-80) REVERT: A 820 MET cc_start: 0.9543 (tpt) cc_final: 0.9335 (tpp) REVERT: B 326 PHE cc_start: 0.9231 (t80) cc_final: 0.8726 (t80) REVERT: B 363 MET cc_start: 0.4189 (pmm) cc_final: 0.3808 (ppp) REVERT: B 432 MET cc_start: 0.7859 (pmm) cc_final: 0.7389 (pmm) REVERT: C 261 ARG cc_start: 0.8714 (tmt170) cc_final: 0.8219 (tpt170) REVERT: C 291 LYS cc_start: 0.9590 (mptt) cc_final: 0.9229 (tptp) REVERT: C 325 ILE cc_start: 0.8132 (mm) cc_final: 0.7775 (mm) REVERT: C 603 LEU cc_start: 0.8323 (mt) cc_final: 0.8066 (mt) REVERT: C 633 TYR cc_start: 0.8297 (t80) cc_final: 0.8021 (t80) REVERT: D 106 ASN cc_start: 0.9519 (t0) cc_final: 0.9251 (t0) REVERT: D 132 PHE cc_start: 0.5350 (t80) cc_final: 0.4950 (t80) REVERT: D 174 TYR cc_start: 0.7869 (m-10) cc_final: 0.7550 (m-10) REVERT: D 218 MET cc_start: 0.5660 (tmm) cc_final: 0.5180 (tmm) REVERT: E 130 LEU cc_start: 0.8921 (mt) cc_final: 0.8631 (mt) REVERT: E 133 MET cc_start: 0.7368 (mtp) cc_final: 0.6988 (ttm) REVERT: E 150 ARG cc_start: 0.7694 (mmp-170) cc_final: 0.7296 (mmp-170) REVERT: E 265 MET cc_start: 0.8778 (ppp) cc_final: 0.8000 (tpt) REVERT: E 269 TYR cc_start: 0.8001 (t80) cc_final: 0.7597 (t80) REVERT: E 270 LEU cc_start: 0.9203 (mm) cc_final: 0.8581 (mm) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1137 time to fit residues: 35.5280 Evaluate side-chains 160 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 77 optimal weight: 0.5980 chunk 2 optimal weight: 0.0670 chunk 31 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 578 GLN A 582 GLN B 393 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 240 HIS ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 252 ASN D 307 GLN E 62 ASN E 260 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.068403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.056464 restraints weight = 163497.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.057494 restraints weight = 122624.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.058242 restraints weight = 99164.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.058795 restraints weight = 84528.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.059198 restraints weight = 74706.375| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16737 Z= 0.120 Angle : 0.631 13.114 22760 Z= 0.320 Chirality : 0.042 0.249 2598 Planarity : 0.003 0.041 2772 Dihedral : 13.500 82.589 2470 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.19), residues: 1888 helix: 0.51 (0.15), residues: 1112 sheet: 0.33 (0.42), residues: 142 loop : -0.92 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 289 TYR 0.019 0.001 TYR D 174 PHE 0.038 0.002 PHE B 380 TRP 0.046 0.002 TRP C 51 HIS 0.009 0.001 HIS D 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (16737) covalent geometry : angle 0.63094 / 0.32 (22760) hydrogen bonds : bond 0.03633 / 2.44 ( 732) hydrogen bonds : angle 4.16264 / 2.95 ( 2132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.620 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: A 494 ARG cc_start: 0.6124 (mmt-90) cc_final: 0.4755 (mtt180) REVERT: A 530 MET cc_start: 0.4017 (tpt) cc_final: 0.3144 (tpt) REVERT: A 571 MET cc_start: 0.8773 (mmm) cc_final: 0.8319 (mmm) REVERT: A 632 ILE cc_start: 0.7516 (mp) cc_final: 0.7169 (mm) REVERT: A 636 LEU cc_start: 0.9463 (mt) cc_final: 0.9186 (pp) REVERT: A 700 PHE cc_start: 0.7606 (m-80) cc_final: 0.7204 (m-80) REVERT: A 820 MET cc_start: 0.9536 (tpt) cc_final: 0.9332 (tpp) REVERT: B 326 PHE cc_start: 0.9210 (t80) cc_final: 0.8671 (t80) REVERT: B 363 MET cc_start: 0.4296 (pmm) cc_final: 0.3932 (ppp) REVERT: B 391 LEU cc_start: 0.9626 (mm) cc_final: 0.9402 (mt) REVERT: B 432 MET cc_start: 0.7888 (pmm) cc_final: 0.7380 (pmm) REVERT: C 261 ARG cc_start: 0.8648 (tmt170) cc_final: 0.8218 (tpt170) REVERT: C 291 LYS cc_start: 0.9581 (mptt) cc_final: 0.9226 (tptp) REVERT: C 603 LEU cc_start: 0.8302 (mt) cc_final: 0.8035 (mt) REVERT: C 633 TYR cc_start: 0.8218 (t80) cc_final: 0.7954 (t80) REVERT: D 106 ASN cc_start: 0.9484 (t0) cc_final: 0.9217 (t0) REVERT: D 132 PHE cc_start: 0.5210 (t80) cc_final: 0.4773 (t80) REVERT: D 174 TYR cc_start: 0.7824 (m-10) cc_final: 0.7513 (m-10) REVERT: D 177 PHE cc_start: 0.8593 (m-80) cc_final: 0.8349 (m-80) REVERT: D 218 MET cc_start: 0.5511 (tmm) cc_final: 0.5022 (tmm) REVERT: D 297 MET cc_start: 0.8874 (tpp) cc_final: 0.8581 (tpp) REVERT: E 107 LYS cc_start: 0.8317 (tmtt) cc_final: 0.7891 (tptm) REVERT: E 130 LEU cc_start: 0.8901 (mt) cc_final: 0.8671 (mt) REVERT: E 150 ARG cc_start: 0.7710 (mmp-170) cc_final: 0.6527 (mmp-170) REVERT: E 265 MET cc_start: 0.8761 (ppp) cc_final: 0.7960 (tpt) REVERT: E 269 TYR cc_start: 0.7946 (t80) cc_final: 0.7467 (t80) REVERT: E 270 LEU cc_start: 0.9214 (mm) cc_final: 0.8525 (mm) REVERT: E 407 TYR cc_start: 0.9126 (m-10) cc_final: 0.8714 (m-80) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1235 time to fit residues: 38.7540 Evaluate side-chains 165 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 111 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 393 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.066687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.055315 restraints weight = 169830.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.056274 restraints weight = 127897.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.056989 restraints weight = 103779.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.057508 restraints weight = 88593.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.057880 restraints weight = 78440.701| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16737 Z= 0.163 Angle : 0.668 10.488 22760 Z= 0.346 Chirality : 0.042 0.209 2598 Planarity : 0.004 0.043 2772 Dihedral : 13.539 81.592 2470 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.19), residues: 1888 helix: 0.33 (0.15), residues: 1126 sheet: 0.30 (0.43), residues: 140 loop : -1.05 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 492 TYR 0.025 0.002 TYR C 429 PHE 0.036 0.002 PHE B 380 TRP 0.041 0.002 TRP C 51 HIS 0.010 0.002 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (16737) covalent geometry : angle 0.66767 / 0.35 (22760) hydrogen bonds : bond 0.04199 / 2.80 ( 732) hydrogen bonds : angle 4.32923 / 3.09 ( 2132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2700.70 seconds wall clock time: 47 minutes 43.37 seconds (2863.37 seconds total)