Starting phenix.real_space_refine on Wed Mar 4 20:55:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jps_22421/03_2026/7jps_22421_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jps_22421/03_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_22421/03_2026/7jps_22421_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jps_22421/03_2026/7jps_22421_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jps_22421/03_2026/7jps_22421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jps_22421/03_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-5986/lib/python3.9/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, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 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: 3.40, per 1000 atoms: 0.21 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: 1.35 Conformation dependent library (CDL) restraints added in 625.0 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: 1.96 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: 2.70 Time building geometry restraints manager: 1.83 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: 2309 0.097 - 0.194: 264 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.740 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 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: 20.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4824 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= 0.359 Angle : 1.195 18.915 22760 Z= 0.705 Chirality : 0.062 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 covalent geometry : bond 0.00628 (16737) covalent geometry : angle 1.19471 (22760) hydrogen bonds : bond 0.27717 ( 732) hydrogen bonds : angle 7.66721 ( 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 : 0.628 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: 0.1306 time to fit residues: 71.7973 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 : 0.520 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 512 GLN A 654 ASN A 696 HIS A 769 ASN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS C 78 GLN C 87 ASN C 242 HIS ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN C 399 GLN ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 HIS D 96 GLN D 351 ASN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN E 195 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.075663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.063029 restraints weight = 147992.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.064130 restraints weight = 111546.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.064930 restraints weight = 90384.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.065493 restraints weight = 76785.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.065967 restraints weight = 67804.509| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16737 Z= 0.146 Angle : 0.641 8.761 22760 Z= 0.340 Chirality : 0.042 0.195 2598 Planarity : 0.005 0.064 2772 Dihedral : 13.352 84.332 2470 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.17 % Allowed : 2.71 % Favored : 97.12 % 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: -0.98 (0.18), residues: 1888 helix: -0.17 (0.14), residues: 1106 sheet: -0.48 (0.41), residues: 135 loop : -1.34 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 728 TYR 0.033 0.002 TYR C 609 PHE 0.027 0.002 PHE B 380 TRP 0.027 0.002 TRP C 648 HIS 0.006 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00313 (16737) covalent geometry : angle 0.64096 (22760) hydrogen bonds : bond 0.04588 ( 732) hydrogen bonds : angle 4.48195 ( 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 277 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 274 time to evaluate : 0.578 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: A 494 ARG cc_start: 0.5572 (mmt-90) cc_final: 0.4540 (mtt180) REVERT: A 516 ASN cc_start: 0.8487 (m-40) cc_final: 0.7943 (m-40) REVERT: A 530 MET cc_start: 0.2865 (tpt) cc_final: 0.1753 (tpt) REVERT: A 647 LEU cc_start: 0.8643 (tp) cc_final: 0.8439 (tp) REVERT: A 700 PHE cc_start: 0.7312 (m-80) cc_final: 0.6669 (m-10) REVERT: A 820 MET cc_start: 0.9599 (tpt) cc_final: 0.9359 (tpp) REVERT: B 311 ILE cc_start: 0.9142 (mm) cc_final: 0.8888 (mm) REVERT: B 326 PHE cc_start: 0.9298 (t80) cc_final: 0.8904 (t80) REVERT: C 57 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8891 (tm-30) REVERT: C 113 ASP cc_start: 0.9420 (m-30) cc_final: 0.9014 (m-30) REVERT: C 232 ASP cc_start: 0.8999 (m-30) cc_final: 0.8749 (t0) REVERT: C 261 ARG cc_start: 0.8471 (tmt170) cc_final: 0.8229 (tmt170) REVERT: C 360 ASN cc_start: 0.8533 (t0) cc_final: 0.8232 (m-40) REVERT: C 475 CYS cc_start: 0.9261 (t) cc_final: 0.8565 (p) REVERT: C 482 TYR cc_start: 0.8498 (t80) cc_final: 0.8022 (t80) REVERT: C 706 LEU cc_start: 0.8208 (tp) cc_final: 0.7981 (tt) REVERT: D 50 LEU cc_start: 0.9598 (mt) cc_final: 0.9224 (tt) REVERT: D 132 PHE cc_start: 0.4715 (t80) cc_final: 0.3805 (t80) REVERT: D 177 PHE cc_start: 0.8604 (m-80) cc_final: 0.8404 (m-80) REVERT: D 205 ARG cc_start: 0.8897 (mtm-85) cc_final: 0.8224 (mpp80) REVERT: D 240 PHE cc_start: 0.8107 (t80) cc_final: 0.7812 (t80) REVERT: E 107 LYS cc_start: 0.8422 (tmmt) cc_final: 0.8066 (tptt) REVERT: E 133 MET cc_start: 0.6989 (mtm) cc_final: 0.5949 (ttm) REVERT: E 150 ARG cc_start: 0.6507 (mmp80) cc_final: 0.4869 (mmp80) REVERT: E 258 GLU cc_start: 0.5633 (mt-10) cc_final: 0.5311 (tm-30) REVERT: E 265 MET cc_start: 0.8591 (ppp) cc_final: 0.8275 (tpt) outliers start: 3 outliers final: 0 residues processed: 274 average time/residue: 0.1328 time to fit residues: 53.7012 Evaluate side-chains 189 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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: 10.0000 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 42 optimal weight: 9.9990 chunk 173 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 HIS ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 HIS ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS B 416 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 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 46 HIS D 216 HIS ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.069513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.057707 restraints weight = 161603.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.058675 restraints weight = 122076.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.059375 restraints weight = 99130.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.059905 restraints weight = 84728.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.060297 restraints weight = 75101.994| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.4427 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= 0.192 Angle : 0.658 7.639 22760 Z= 0.347 Chirality : 0.042 0.176 2598 Planarity : 0.004 0.043 2772 Dihedral : 13.489 80.181 2470 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 3.22 % 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: -0.63 (0.18), residues: 1888 helix: 0.06 (0.15), residues: 1120 sheet: 0.18 (0.43), residues: 139 loop : -1.24 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 728 TYR 0.026 0.002 TYR C 609 PHE 0.022 0.002 PHE B 380 TRP 0.042 0.003 TRP C 648 HIS 0.010 0.002 HIS A 496 Details of bonding type rmsd covalent geometry : bond 0.00420 (16737) covalent geometry : angle 0.65839 (22760) hydrogen bonds : bond 0.04749 ( 732) hydrogen bonds : angle 4.38065 ( 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 237 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.5509 (mmt-90) cc_final: 0.4251 (mtt180) REVERT: A 496 HIS cc_start: 0.8504 (m90) cc_final: 0.8129 (m-70) REVERT: A 516 ASN cc_start: 0.8251 (m-40) cc_final: 0.7629 (m-40) REVERT: A 530 MET cc_start: 0.4275 (tpt) cc_final: 0.3385 (tpt) REVERT: A 632 ILE cc_start: 0.7719 (mt) cc_final: 0.7418 (mp) REVERT: A 700 PHE cc_start: 0.7744 (m-80) cc_final: 0.7147 (m-80) REVERT: A 752 MET cc_start: 0.3318 (tpt) cc_final: 0.3104 (mtp) REVERT: B 326 PHE cc_start: 0.9221 (t80) cc_final: 0.8738 (t80) REVERT: C 325 ILE cc_start: 0.7963 (mm) cc_final: 0.7645 (mm) REVERT: C 360 ASN cc_start: 0.8692 (t0) cc_final: 0.8340 (m-40) REVERT: D 132 PHE cc_start: 0.5403 (t80) cc_final: 0.4555 (t80) REVERT: D 174 TYR cc_start: 0.7932 (m-10) cc_final: 0.7728 (m-10) REVERT: D 203 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8536 (pt0) REVERT: D 240 PHE cc_start: 0.8259 (t80) cc_final: 0.8040 (t80) REVERT: D 281 MET cc_start: 0.8861 (tmm) cc_final: 0.8570 (tmm) REVERT: E 265 MET cc_start: 0.8790 (ppp) cc_final: 0.7984 (tpt) REVERT: E 269 TYR cc_start: 0.7830 (t80) cc_final: 0.7618 (t80) REVERT: E 270 LEU cc_start: 0.9076 (mm) cc_final: 0.7939 (mm) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1280 time to fit residues: 45.9583 Evaluate side-chains 175 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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: 0.9990 chunk 189 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 105 optimal weight: 0.0670 chunk 173 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 134 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS B 406 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS C 557 ASN ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 214 GLN D 252 ASN E 188 GLN E 195 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.070171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.057814 restraints weight = 158093.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.058850 restraints weight = 119092.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.059611 restraints weight = 96669.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.060176 restraints weight = 82507.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.060594 restraints weight = 72874.473| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16737 Z= 0.127 Angle : 0.577 8.242 22760 Z= 0.300 Chirality : 0.040 0.183 2598 Planarity : 0.003 0.040 2772 Dihedral : 13.193 83.829 2470 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.52 % 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: -0.21 (0.19), residues: 1888 helix: 0.42 (0.15), residues: 1108 sheet: 0.36 (0.43), residues: 141 loop : -1.13 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 728 TYR 0.018 0.001 TYR C 609 PHE 0.028 0.002 PHE B 380 TRP 0.046 0.002 TRP C 648 HIS 0.007 0.001 HIS C 114 Details of bonding type rmsd covalent geometry : bond 0.00275 (16737) covalent geometry : angle 0.57694 (22760) hydrogen bonds : bond 0.03514 ( 732) hydrogen bonds : angle 4.07991 ( 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 228 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.570 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: 0.5229 (mmt-90) cc_final: 0.3786 (mtt180) REVERT: A 516 ASN cc_start: 0.8460 (m-40) cc_final: 0.7857 (m-40) REVERT: A 530 MET cc_start: 0.4022 (tpt) cc_final: 0.3133 (tpt) REVERT: A 571 MET cc_start: 0.9118 (mmm) cc_final: 0.8833 (mmt) REVERT: A 700 PHE cc_start: 0.7550 (m-80) cc_final: 0.6759 (m-80) REVERT: A 820 MET cc_start: 0.9586 (tpt) cc_final: 0.9353 (tpp) REVERT: B 326 PHE cc_start: 0.9291 (t80) cc_final: 0.8852 (t80) REVERT: C 54 MET cc_start: 0.7999 (mpp) cc_final: 0.7751 (mpp) REVERT: C 360 ASN cc_start: 0.8755 (t0) cc_final: 0.8441 (m-40) REVERT: C 633 TYR cc_start: 0.8255 (t80) cc_final: 0.8053 (t80) REVERT: C 648 TRP cc_start: 0.5454 (t60) cc_final: 0.5103 (t60) REVERT: C 684 VAL cc_start: 0.6451 (t) cc_final: 0.6100 (t) REVERT: D 132 PHE cc_start: 0.5406 (t80) cc_final: 0.4477 (t80) REVERT: D 174 TYR cc_start: 0.7959 (m-10) cc_final: 0.6998 (m-10) REVERT: D 177 PHE cc_start: 0.8644 (m-80) cc_final: 0.8414 (m-80) REVERT: D 203 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8537 (pt0) REVERT: E 133 MET cc_start: 0.7248 (mtt) cc_final: 0.7023 (mtm) REVERT: E 150 ARG cc_start: 0.7326 (mmp-170) cc_final: 0.6980 (mmp-170) REVERT: E 265 MET cc_start: 0.8729 (ppp) cc_final: 0.7949 (tpt) REVERT: E 269 TYR cc_start: 0.8034 (t80) cc_final: 0.7716 (t80) REVERT: E 270 LEU cc_start: 0.9280 (mm) cc_final: 0.8274 (mm) REVERT: E 407 TYR cc_start: 0.8827 (m-80) cc_final: 0.8165 (m-80) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.1276 time to fit residues: 43.7405 Evaluate side-chains 169 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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: 1.9990 chunk 112 optimal weight: 10.0000 chunk 185 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 117 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 628 HIS A 769 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS B 393 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 HIS ** 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 19 GLN D 46 HIS ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.067947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.056138 restraints weight = 167082.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.057110 restraints weight = 126106.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.057826 restraints weight = 102790.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.058360 restraints weight = 87930.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.058704 restraints weight = 78121.454| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16737 Z= 0.155 Angle : 0.614 9.973 22760 Z= 0.318 Chirality : 0.042 0.274 2598 Planarity : 0.004 0.087 2772 Dihedral : 13.241 84.302 2470 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % 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: -0.16 (0.19), residues: 1888 helix: 0.43 (0.15), residues: 1114 sheet: 0.38 (0.43), residues: 141 loop : -1.05 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C 354 TYR 0.015 0.002 TYR C 408 PHE 0.028 0.002 PHE B 380 TRP 0.024 0.002 TRP C 648 HIS 0.009 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00343 (16737) covalent geometry : angle 0.61360 (22760) hydrogen bonds : bond 0.03985 ( 732) hydrogen bonds : angle 4.08620 ( 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 220 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.635 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: 0.5734 (mmt-90) cc_final: 0.4433 (mtt180) REVERT: A 496 HIS cc_start: 0.8422 (m90) cc_final: 0.8020 (m90) REVERT: A 530 MET cc_start: 0.3731 (tpt) cc_final: 0.2925 (tpt) REVERT: A 571 MET cc_start: 0.9065 (mmm) cc_final: 0.8747 (mmt) REVERT: A 700 PHE cc_start: 0.7575 (m-80) cc_final: 0.7034 (m-80) REVERT: B 326 PHE cc_start: 0.9145 (t80) cc_final: 0.8537 (t80) REVERT: C 54 MET cc_start: 0.8168 (mpp) cc_final: 0.7798 (mpp) REVERT: C 113 ASP cc_start: 0.9397 (p0) cc_final: 0.9129 (p0) REVERT: C 222 MET cc_start: 0.7734 (ppp) cc_final: 0.7489 (ppp) REVERT: C 261 ARG cc_start: 0.8784 (tmt170) cc_final: 0.8275 (tpt170) REVERT: C 325 ILE cc_start: 0.8189 (mm) cc_final: 0.7941 (mm) REVERT: C 633 TYR cc_start: 0.8327 (t80) cc_final: 0.7956 (t80) REVERT: D 106 ASN cc_start: 0.9496 (t0) cc_final: 0.9222 (t0) REVERT: D 132 PHE cc_start: 0.5610 (t80) cc_final: 0.4802 (t80) REVERT: D 218 MET cc_start: 0.4194 (ttt) cc_final: 0.2671 (tmm) REVERT: E 18 LEU cc_start: 0.9739 (mm) cc_final: 0.9530 (mm) REVERT: E 150 ARG cc_start: 0.7476 (mmp-170) cc_final: 0.7040 (mmp-170) REVERT: E 265 MET cc_start: 0.8777 (ppp) cc_final: 0.7922 (tpt) REVERT: E 269 TYR cc_start: 0.8106 (t80) cc_final: 0.7700 (t80) REVERT: E 270 LEU cc_start: 0.9324 (mm) cc_final: 0.8360 (mm) outliers start: 1 outliers final: 1 residues processed: 219 average time/residue: 0.1289 time to fit residues: 42.2852 Evaluate side-chains 169 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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: 0.6980 chunk 42 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN B 274 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 702 HIS D 46 HIS D 175 ASN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 HIS E 277 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.066491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.054948 restraints weight = 167854.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.055890 restraints weight = 126396.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.056572 restraints weight = 102827.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.057049 restraints weight = 88114.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.057456 restraints weight = 78637.052| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16737 Z= 0.160 Angle : 0.638 12.249 22760 Z= 0.328 Chirality : 0.042 0.231 2598 Planarity : 0.004 0.045 2772 Dihedral : 13.460 89.221 2470 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: -0.16 (0.19), residues: 1888 helix: 0.36 (0.15), residues: 1122 sheet: 0.51 (0.42), residues: 145 loop : -0.95 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 354 TYR 0.020 0.002 TYR D 399 PHE 0.026 0.002 PHE B 380 TRP 0.022 0.002 TRP C 648 HIS 0.012 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00355 (16737) covalent geometry : angle 0.63766 (22760) hydrogen bonds : bond 0.03880 ( 732) hydrogen bonds : angle 4.16897 ( 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 206 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.628 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 496 HIS cc_start: 0.8497 (m90) cc_final: 0.8021 (m90) REVERT: A 530 MET cc_start: 0.3840 (tpt) cc_final: 0.2967 (tpt) REVERT: A 571 MET cc_start: 0.9058 (mmm) cc_final: 0.8814 (mmm) REVERT: A 700 PHE cc_start: 0.7642 (m-80) cc_final: 0.7145 (m-80) REVERT: B 326 PHE cc_start: 0.9197 (t80) cc_final: 0.8604 (t80) REVERT: C 54 MET cc_start: 0.8112 (mpp) cc_final: 0.7850 (mpp) REVERT: C 113 ASP cc_start: 0.9384 (p0) cc_final: 0.9103 (p0) REVERT: C 222 MET cc_start: 0.7713 (ppp) cc_final: 0.7426 (ppp) REVERT: C 261 ARG cc_start: 0.8839 (tmt170) cc_final: 0.8400 (tpt170) REVERT: C 325 ILE cc_start: 0.8192 (mm) cc_final: 0.7982 (mm) REVERT: D 106 ASN cc_start: 0.9475 (t0) cc_final: 0.9226 (t0) REVERT: D 132 PHE cc_start: 0.5704 (t80) cc_final: 0.5279 (t80) REVERT: D 218 MET cc_start: 0.4479 (ttt) cc_final: 0.2691 (tmm) REVERT: E 265 MET cc_start: 0.8785 (ppp) cc_final: 0.8316 (ppp) REVERT: E 269 TYR cc_start: 0.8162 (t80) cc_final: 0.7885 (t80) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1313 time to fit residues: 40.9162 Evaluate side-chains 154 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN C 409 HIS ** 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 175 ASN D 252 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.068042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.056079 restraints weight = 164416.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.057067 restraints weight = 124660.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.057807 restraints weight = 101544.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.058350 restraints weight = 86808.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.058709 restraints weight = 77002.326| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16737 Z= 0.115 Angle : 0.575 9.788 22760 Z= 0.294 Chirality : 0.040 0.228 2598 Planarity : 0.003 0.055 2772 Dihedral : 13.206 86.787 2470 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.19), residues: 1888 helix: 0.67 (0.15), residues: 1125 sheet: 0.71 (0.42), residues: 147 loop : -0.90 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 354 TYR 0.024 0.001 TYR C 429 PHE 0.016 0.001 PHE E 328 TRP 0.021 0.001 TRP C 648 HIS 0.007 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00246 (16737) covalent geometry : angle 0.57486 (22760) hydrogen bonds : bond 0.03240 ( 732) hydrogen bonds : angle 3.90458 ( 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: 0 poor density : 210 time to evaluate : 0.452 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: 0.5692 (mmt-90) cc_final: 0.4395 (mtt180) REVERT: A 496 HIS cc_start: 0.8484 (m90) cc_final: 0.8042 (m-70) REVERT: A 530 MET cc_start: 0.3085 (tpt) cc_final: 0.2467 (tpt) REVERT: A 636 LEU cc_start: 0.9472 (mt) cc_final: 0.9189 (pp) REVERT: A 700 PHE cc_start: 0.7537 (m-80) cc_final: 0.7039 (m-80) REVERT: B 326 PHE cc_start: 0.9177 (t80) cc_final: 0.8501 (t80) REVERT: C 222 MET cc_start: 0.7711 (ppp) cc_final: 0.7431 (ppp) REVERT: C 261 ARG cc_start: 0.8779 (tmt170) cc_final: 0.8395 (tpt170) REVERT: C 325 ILE cc_start: 0.8111 (mm) cc_final: 0.7888 (mm) REVERT: C 360 ASN cc_start: 0.8767 (t0) cc_final: 0.8408 (m-40) REVERT: D 106 ASN cc_start: 0.9430 (t0) cc_final: 0.9182 (t0) REVERT: D 218 MET cc_start: 0.4349 (ttt) cc_final: 0.2956 (tmm) REVERT: D 284 MET cc_start: 0.7802 (mmm) cc_final: 0.7523 (mmm) REVERT: E 150 ARG cc_start: 0.7470 (mmp-170) cc_final: 0.7022 (mmp-170) REVERT: E 265 MET cc_start: 0.8776 (ppp) cc_final: 0.8275 (ppp) REVERT: E 269 TYR cc_start: 0.8134 (t80) cc_final: 0.7921 (t80) REVERT: E 407 TYR cc_start: 0.9135 (m-10) cc_final: 0.8793 (m-80) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1227 time to fit residues: 38.6247 Evaluate side-chains 161 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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: 9.9990 chunk 0 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 105 optimal weight: 0.3980 chunk 69 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 161 optimal weight: 0.0470 overall best weight: 2.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.065180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.053760 restraints weight = 171023.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.054700 restraints weight = 129161.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.055385 restraints weight = 105195.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.055856 restraints weight = 89955.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.056236 restraints weight = 80258.842| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16737 Z= 0.170 Angle : 0.649 12.903 22760 Z= 0.335 Chirality : 0.041 0.171 2598 Planarity : 0.004 0.043 2772 Dihedral : 13.463 89.960 2470 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -0.03 (0.19), residues: 1888 helix: 0.44 (0.15), residues: 1133 sheet: 0.53 (0.41), residues: 157 loop : -0.87 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 205 TYR 0.021 0.002 TYR C 429 PHE 0.029 0.002 PHE B 380 TRP 0.015 0.002 TRP C 648 HIS 0.012 0.002 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00373 (16737) covalent geometry : angle 0.64856 (22760) hydrogen bonds : bond 0.04168 ( 732) hydrogen bonds : angle 4.19198 ( 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 204 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 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: A 496 HIS cc_start: 0.8519 (m90) cc_final: 0.8051 (m-70) REVERT: A 530 MET cc_start: 0.3278 (tpt) cc_final: 0.2545 (tpt) REVERT: A 571 MET cc_start: 0.8908 (mmm) cc_final: 0.8553 (mmt) REVERT: A 599 GLU cc_start: 0.8597 (mp0) cc_final: 0.8290 (pm20) REVERT: A 700 PHE cc_start: 0.7683 (m-80) cc_final: 0.7148 (m-80) REVERT: B 326 PHE cc_start: 0.9112 (t80) cc_final: 0.8453 (t80) REVERT: B 380 PHE cc_start: 0.7637 (m-80) cc_final: 0.7409 (m-80) REVERT: C 54 MET cc_start: 0.7718 (mpp) cc_final: 0.7507 (mpp) REVERT: C 113 ASP cc_start: 0.9430 (p0) cc_final: 0.9152 (p0) REVERT: C 222 MET cc_start: 0.7812 (ppp) cc_final: 0.7489 (ppp) REVERT: C 325 ILE cc_start: 0.8164 (mm) cc_final: 0.7943 (mm) REVERT: D 106 ASN cc_start: 0.9413 (t0) cc_final: 0.9105 (t0) REVERT: D 109 ILE cc_start: 0.9263 (pt) cc_final: 0.8999 (pt) REVERT: D 218 MET cc_start: 0.4614 (ttt) cc_final: 0.2876 (tmm) REVERT: E 265 MET cc_start: 0.8788 (ppp) cc_final: 0.8189 (tmm) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1221 time to fit residues: 38.2087 Evaluate side-chains 153 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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: 0.9980 chunk 74 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 105 optimal weight: 0.0370 chunk 127 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS B 411 GLN B 426 HIS ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.066873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.055048 restraints weight = 163894.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.056024 restraints weight = 124271.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.056742 restraints weight = 101217.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.057281 restraints weight = 86549.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.057629 restraints weight = 76769.923| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16737 Z= 0.117 Angle : 0.611 10.196 22760 Z= 0.311 Chirality : 0.041 0.237 2598 Planarity : 0.003 0.041 2772 Dihedral : 13.275 89.883 2470 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 0.21 (0.20), residues: 1888 helix: 0.65 (0.15), residues: 1131 sheet: 0.64 (0.44), residues: 142 loop : -0.79 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 273 TYR 0.021 0.001 TYR C 429 PHE 0.027 0.001 PHE B 380 TRP 0.019 0.001 TRP C 648 HIS 0.009 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00255 (16737) covalent geometry : angle 0.61057 (22760) hydrogen bonds : bond 0.03313 ( 732) hydrogen bonds : angle 4.05645 ( 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 202 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.613 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: A 496 HIS cc_start: 0.8483 (m90) cc_final: 0.8024 (m-70) REVERT: A 530 MET cc_start: 0.2990 (tpt) cc_final: 0.2465 (tpt) REVERT: A 571 MET cc_start: 0.8860 (mmm) cc_final: 0.8220 (mmt) REVERT: A 636 LEU cc_start: 0.9482 (mt) cc_final: 0.9200 (pp) REVERT: A 700 PHE cc_start: 0.7542 (m-80) cc_final: 0.6992 (m-80) REVERT: B 326 PHE cc_start: 0.9152 (t80) cc_final: 0.8483 (t80) REVERT: C 54 MET cc_start: 0.7961 (mpp) cc_final: 0.7724 (mpp) REVERT: C 222 MET cc_start: 0.7738 (ppp) cc_final: 0.7446 (ppp) REVERT: C 325 ILE cc_start: 0.8174 (mm) cc_final: 0.7945 (mm) REVERT: C 360 ASN cc_start: 0.9046 (t0) cc_final: 0.8783 (m-40) REVERT: D 106 ASN cc_start: 0.9392 (t0) cc_final: 0.9059 (t0) REVERT: D 132 PHE cc_start: 0.6174 (t80) cc_final: 0.5501 (t80) REVERT: D 218 MET cc_start: 0.4353 (ttt) cc_final: 0.2635 (tmm) REVERT: D 284 MET cc_start: 0.7987 (mmm) cc_final: 0.7760 (mmm) REVERT: E 265 MET cc_start: 0.8740 (ppp) cc_final: 0.8266 (ppp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1211 time to fit residues: 37.0796 Evaluate side-chains 154 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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: 2.9990 chunk 2 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 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 = 0.3774 r_free = 0.3774 target = 0.066145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.054523 restraints weight = 168324.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.055480 restraints weight = 128166.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.056159 restraints weight = 104882.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.056652 restraints weight = 90344.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.057029 restraints weight = 80535.813| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.6989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16737 Z= 0.129 Angle : 0.623 10.896 22760 Z= 0.317 Chirality : 0.042 0.202 2598 Planarity : 0.003 0.042 2772 Dihedral : 13.236 89.882 2470 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.25 (0.20), residues: 1888 helix: 0.70 (0.15), residues: 1132 sheet: 0.67 (0.44), residues: 142 loop : -0.82 (0.27), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.021 0.001 TYR C 429 PHE 0.029 0.001 PHE B 380 TRP 0.017 0.001 TRP C 648 HIS 0.014 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00285 (16737) covalent geometry : angle 0.62303 (22760) hydrogen bonds : bond 0.03480 ( 732) hydrogen bonds : angle 4.12344 ( 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 199 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.646 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 496 HIS cc_start: 0.8496 (m90) cc_final: 0.8046 (m-70) REVERT: A 530 MET cc_start: 0.3478 (tpt) cc_final: 0.2872 (tpt) REVERT: A 571 MET cc_start: 0.8805 (mmm) cc_final: 0.8330 (mmt) REVERT: A 636 LEU cc_start: 0.9483 (mt) cc_final: 0.9194 (pp) REVERT: A 700 PHE cc_start: 0.7618 (m-80) cc_final: 0.7169 (m-80) REVERT: B 326 PHE cc_start: 0.9096 (t80) cc_final: 0.8348 (t80) REVERT: C 113 ASP cc_start: 0.9389 (p0) cc_final: 0.9080 (p0) REVERT: C 222 MET cc_start: 0.7741 (ppp) cc_final: 0.7444 (ppp) REVERT: C 246 LEU cc_start: 0.7255 (mt) cc_final: 0.7020 (mp) REVERT: C 261 ARG cc_start: 0.8905 (tmt170) cc_final: 0.8531 (tpt170) REVERT: C 325 ILE cc_start: 0.8166 (mm) cc_final: 0.7957 (mm) REVERT: C 360 ASN cc_start: 0.9046 (t0) cc_final: 0.8765 (m-40) REVERT: D 106 ASN cc_start: 0.9379 (t0) cc_final: 0.9044 (t0) REVERT: D 132 PHE cc_start: 0.6030 (t80) cc_final: 0.5434 (t80) REVERT: D 218 MET cc_start: 0.4432 (ttt) cc_final: 0.2723 (tmm) REVERT: E 107 LYS cc_start: 0.8377 (tmtt) cc_final: 0.7951 (tptp) REVERT: E 150 ARG cc_start: 0.7447 (mmp-170) cc_final: 0.6629 (mmp-170) REVERT: E 265 MET cc_start: 0.8765 (ppp) cc_final: 0.8252 (ppp) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1212 time to fit residues: 36.7902 Evaluate side-chains 156 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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: 0.0770 chunk 43 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS B 426 HIS ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.066326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.054604 restraints weight = 165340.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.055589 restraints weight = 125075.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.056281 restraints weight = 101669.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.056761 restraints weight = 87138.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.057167 restraints weight = 77692.145| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.7181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16737 Z= 0.122 Angle : 0.618 10.266 22760 Z= 0.313 Chirality : 0.041 0.213 2598 Planarity : 0.003 0.042 2772 Dihedral : 13.228 89.358 2470 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1888 helix: 0.75 (0.15), residues: 1137 sheet: 0.75 (0.44), residues: 142 loop : -0.79 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 273 TYR 0.020 0.001 TYR C 429 PHE 0.030 0.001 PHE B 380 TRP 0.018 0.001 TRP C 648 HIS 0.008 0.001 HIS C 409 Details of bonding type rmsd covalent geometry : bond 0.00268 (16737) covalent geometry : angle 0.61800 (22760) hydrogen bonds : bond 0.03286 ( 732) hydrogen bonds : angle 4.07697 ( 2132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.21 seconds wall clock time: 48 minutes 11.40 seconds (2891.40 seconds total)