Starting phenix.real_space_refine on Sat Sep 12 14:21:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jps_22421/09_2026/7jps_22421_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jps_22421/09_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_22421/09_2026/7jps_22421_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jps_22421/09_2026/7jps_22421_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jps_22421/09_2026/7jps_22421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jps_22421/09_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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16352 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2787 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 12, 'TRANS': 338} Chain breaks: 3 Chain: "B" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1640 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain: "C" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4844 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 24, 'TRANS': 566} Chain breaks: 9 Chain: "D" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3297 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 13, 'TRANS': 391} Chain breaks: 2 Chain: "E" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3160 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 368} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "G" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 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: 3.56, per 1000 atoms: 0.22 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: 1.24 Conformation dependent library (CDL) restraints added in 770.2 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: 2.11 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: 2.73 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3109 1.33 - 1.45: 4144 1.45 - 1.58: 9296 1.58 - 1.70: 63 1.70 - 1.83: 125 Bond restraints: 16737 Sorted by residual: bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.56e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.51e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.28e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.65e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.52e+01 ... (remaining 16732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 22362 3.78 - 7.57: 346 7.57 - 11.35: 44 11.35 - 15.13: 3 15.13 - 18.92: 5 Bond angle restraints: 22760 Sorted by residual: angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 120.95 18.92 1.00e+00 1.00e+00 3.58e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.55 18.32 1.00e+00 1.00e+00 3.36e+02 angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 123.67 16.20 1.00e+00 1.00e+00 2.62e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 120.65 16.18 1.00e+00 1.00e+00 2.62e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 121.34 15.49 1.00e+00 1.00e+00 2.40e+02 ... (remaining 22755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 8838 17.60 - 35.19: 962 35.19 - 52.78: 239 52.78 - 70.38: 62 70.38 - 87.97: 38 Dihedral angle restraints: 10139 sinusoidal: 4403 harmonic: 5736 Sorted by residual: dihedral pdb=" CA GLN D 31 " pdb=" C GLN D 31 " pdb=" N SER D 32 " pdb=" CA SER D 32 " ideal model delta harmonic sigma weight residual 180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA HIS E 195 " pdb=" C HIS E 195 " pdb=" N PRO E 196 " pdb=" CA PRO E 196 " ideal model delta harmonic sigma weight residual 180.00 157.49 22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA VAL E 214 " pdb=" C VAL E 214 " pdb=" N PHE E 215 " pdb=" CA PHE E 215 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 10136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2301 0.097 - 0.194: 272 0.194 - 0.291: 21 0.291 - 0.387: 2 0.387 - 0.484: 2 Chirality restraints: 2598 Sorted by residual: chirality pdb=" CB THR E 410 " pdb=" CA THR E 410 " pdb=" OG1 THR E 410 " pdb=" CG2 THR E 410 " both_signs ideal model delta sigma weight residual False 2.55 2.07 0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.10 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CG LEU B 303 " pdb=" CB LEU B 303 " pdb=" CD1 LEU B 303 " pdb=" CD2 LEU B 303 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 2595 not shown) Planarity restraints: 2772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 369 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO C 370 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 370 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 370 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 152 " 0.067 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO D 153 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO D 153 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 153 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 412 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C TYR C 412 " 0.063 2.00e-02 2.50e+03 pdb=" O TYR C 412 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE C 413 " -0.021 2.00e-02 2.50e+03 ... (remaining 2769 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.71: 425 2.71 - 3.32: 18241 3.32 - 3.92: 30926 3.92 - 4.53: 41096 4.53 - 5.14: 61991 Nonbonded interactions: 152679 Sorted by model distance: nonbonded pdb=" O1B ATP A 901 " pdb="MG MG A 902 " model vdw 2.102 2.170 nonbonded pdb=" O1B ATP E 501 " pdb="MG MG E 502 " model vdw 2.110 2.170 nonbonded pdb=" O3G ATP A 901 " pdb="MG MG A 902 " model vdw 2.111 2.170 nonbonded pdb=" O3G ATP E 501 " pdb="MG MG E 502 " model vdw 2.174 2.170 nonbonded pdb=" O LEU B 316 " pdb=" OH TYR B 454 " model vdw 2.236 3.040 ... (remaining 152674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 1 through 11 or resid 13)) selection = (chain 'G' and (resid 1 through 2 or resid 4 through 13)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.410 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4631 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 16737 Z= 0.383 Angle : 1.203 18.915 22760 Z= 0.728 Chirality : 0.063 0.484 2598 Planarity : 0.007 0.112 2772 Dihedral : 16.818 87.973 6381 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.16), residues: 1888 helix: -1.62 (0.13), residues: 1051 sheet: -0.75 (0.39), residues: 156 loop : -1.54 (0.21), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG E 417 TYR 0.032 0.003 TYR C 375 PHE 0.045 0.004 PHE A 637 TRP 0.041 0.004 TRP E 162 HIS 0.015 0.002 HIS C 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.38 (16737) covalent geometry : angle 1.20330 / 0.73 (22760) hydrogen bonds : bond 0.27717 / 18.81 ( 732) hydrogen bonds : angle 7.66721 / 5.39 ( 2132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.645 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: 0.1406 time to fit residues: 78.1020 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 : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 HIS A 654 ASN ** A 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN B 291 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 154 GLN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN C 399 GLN C 409 HIS C 486 HIS ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 HIS ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.076961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.063860 restraints weight = 146177.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.064964 restraints weight = 110732.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.065836 restraints weight = 89931.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.066431 restraints weight = 76250.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.066922 restraints weight = 67331.867| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 16737 Z= 0.176 Angle : 0.722 9.073 22760 Z= 0.381 Chirality : 0.044 0.252 2598 Planarity : 0.005 0.094 2772 Dihedral : 13.490 87.790 2470 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.17 % Allowed : 3.33 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.18), residues: 1888 helix: -0.35 (0.14), residues: 1099 sheet: -0.52 (0.41), residues: 140 loop : -1.33 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 728 TYR 0.045 0.002 TYR C 408 PHE 0.025 0.002 PHE B 380 TRP 0.025 0.002 TRP C 648 HIS 0.005 0.001 HIS E 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (16737) covalent geometry : angle 0.72235 / 0.38 (22760) hydrogen bonds : bond 0.06182 / 4.22 ( 732) hydrogen bonds : angle 4.92312 / 3.53 ( 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 267 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 264 time to evaluate : 0.659 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: 0.5483 (mmt-90) cc_final: 0.4450 (mtt180) REVERT: A 516 ASN cc_start: 0.8536 (m-40) cc_final: 0.8043 (m110) REVERT: A 530 MET cc_start: 0.3237 (tpt) cc_final: 0.2446 (tpt) REVERT: A 647 LEU cc_start: 0.8700 (tp) cc_final: 0.8445 (tp) REVERT: A 700 PHE cc_start: 0.7631 (m-80) cc_final: 0.6971 (m-80) REVERT: A 718 ASP cc_start: 0.8238 (m-30) cc_final: 0.6618 (p0) REVERT: A 820 MET cc_start: 0.9598 (tpt) cc_final: 0.9350 (tpp) REVERT: B 311 ILE cc_start: 0.8998 (mm) cc_final: 0.8751 (mm) REVERT: B 326 PHE cc_start: 0.9314 (t80) cc_final: 0.8990 (t80) REVERT: C 360 ASN cc_start: 0.8526 (t0) cc_final: 0.8292 (t0) REVERT: C 482 TYR cc_start: 0.8494 (t80) cc_final: 0.8157 (t80) REVERT: D 50 LEU cc_start: 0.9536 (mt) cc_final: 0.9249 (tt) REVERT: D 132 PHE cc_start: 0.4875 (t80) cc_final: 0.4077 (t80) REVERT: D 355 LYS cc_start: 0.9666 (mppt) cc_final: 0.9353 (ptmt) REVERT: E 130 LEU cc_start: 0.8738 (mt) cc_final: 0.8478 (mt) REVERT: E 133 MET cc_start: 0.7086 (mtm) cc_final: 0.5938 (ttm) REVERT: E 258 GLU cc_start: 0.5397 (mt-10) cc_final: 0.4959 (tm-30) REVERT: E 265 MET cc_start: 0.8475 (ppp) cc_final: 0.7952 (tpp) outliers start: 3 outliers final: 0 residues processed: 264 average time/residue: 0.1339 time to fit residues: 52.5263 Evaluate side-chains 190 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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: 4.9990 chunk 77 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 188 optimal weight: 0.0020 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 HIS A 696 HIS B 291 ASN B 306 HIS B 393 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 154 GLN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS C 486 HIS ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 HIS D 96 GLN D 354 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.076316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.063595 restraints weight = 148676.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.064728 restraints weight = 111991.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.065540 restraints weight = 90342.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.066104 restraints weight = 76616.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.066574 restraints weight = 67525.202| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16737 Z= 0.132 Angle : 0.623 10.304 22760 Z= 0.327 Chirality : 0.042 0.189 2598 Planarity : 0.004 0.060 2772 Dihedral : 13.539 87.671 2470 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.11 % Allowed : 2.71 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 1888 helix: 0.17 (0.15), residues: 1106 sheet: -0.10 (0.40), residues: 147 loop : -1.27 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 368 TYR 0.027 0.001 TYR C 408 PHE 0.023 0.001 PHE B 380 TRP 0.039 0.002 TRP C 648 HIS 0.016 0.001 HIS A 496 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (16737) covalent geometry : angle 0.62345 / 0.33 (22760) hydrogen bonds : bond 0.04709 / 3.23 ( 732) hydrogen bonds : angle 4.48504 / 3.22 ( 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 252 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 250 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.5392 (mmt-90) cc_final: 0.4206 (mtt180) REVERT: A 496 HIS cc_start: 0.8315 (m90) cc_final: 0.7884 (m-70) REVERT: A 516 ASN cc_start: 0.8513 (m-40) cc_final: 0.7965 (m-40) REVERT: A 530 MET cc_start: 0.2807 (tpt) cc_final: 0.2141 (tpt) REVERT: A 647 LEU cc_start: 0.8670 (tp) cc_final: 0.8447 (tp) REVERT: A 700 PHE cc_start: 0.7460 (m-80) cc_final: 0.6892 (m-80) REVERT: A 718 ASP cc_start: 0.8486 (m-30) cc_final: 0.6539 (p0) REVERT: A 820 MET cc_start: 0.9605 (tpt) cc_final: 0.9360 (tpp) REVERT: B 326 PHE cc_start: 0.9296 (t80) cc_final: 0.8880 (t80) REVERT: C 54 MET cc_start: 0.7546 (mpp) cc_final: 0.7330 (mpp) REVERT: C 360 ASN cc_start: 0.8455 (t0) cc_final: 0.8194 (m-40) REVERT: C 475 CYS cc_start: 0.9246 (t) cc_final: 0.8582 (p) REVERT: C 482 TYR cc_start: 0.8398 (t80) cc_final: 0.8074 (t80) REVERT: C 633 TYR cc_start: 0.8091 (t80) cc_final: 0.7751 (t80) REVERT: D 46 HIS cc_start: 0.9120 (m-70) cc_final: 0.8846 (m90) REVERT: D 50 LEU cc_start: 0.9564 (mt) cc_final: 0.9147 (tt) REVERT: D 132 PHE cc_start: 0.4545 (t80) cc_final: 0.3662 (t80) REVERT: D 174 TYR cc_start: 0.7661 (m-80) cc_final: 0.7179 (m-80) REVERT: D 177 PHE cc_start: 0.8681 (m-10) cc_final: 0.8381 (m-80) REVERT: D 240 PHE cc_start: 0.8280 (t80) cc_final: 0.8006 (t80) REVERT: D 281 MET cc_start: 0.8647 (tpp) cc_final: 0.8431 (tpp) REVERT: D 355 LYS cc_start: 0.9672 (mppt) cc_final: 0.9372 (ptmt) REVERT: E 107 LYS cc_start: 0.8476 (tmmt) cc_final: 0.8170 (tptt) REVERT: E 133 MET cc_start: 0.7234 (mtm) cc_final: 0.6913 (mtm) REVERT: E 258 GLU cc_start: 0.5357 (mt-10) cc_final: 0.5056 (tm-30) REVERT: E 265 MET cc_start: 0.8535 (ppp) cc_final: 0.8006 (tpp) outliers start: 2 outliers final: 0 residues processed: 251 average time/residue: 0.1242 time to fit residues: 47.4677 Evaluate side-chains 182 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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: 7.9990 chunk 13 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 173 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 512 GLN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.074774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.062372 restraints weight = 152585.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.063451 restraints weight = 115108.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.064196 restraints weight = 93219.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.064816 restraints weight = 79710.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.065230 restraints weight = 70192.880| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.3675 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= 0.140 Angle : 0.612 9.230 22760 Z= 0.321 Chirality : 0.041 0.171 2598 Planarity : 0.004 0.037 2772 Dihedral : 13.443 89.463 2470 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -0.31 (0.19), residues: 1888 helix: 0.42 (0.15), residues: 1110 sheet: -0.14 (0.41), residues: 141 loop : -1.21 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 493 TYR 0.038 0.001 TYR C 609 PHE 0.023 0.001 PHE E 175 TRP 0.043 0.002 TRP C 648 HIS 0.016 0.001 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (16737) covalent geometry : angle 0.61152 / 0.32 (22760) hydrogen bonds : bond 0.04379 / 2.95 ( 732) hydrogen bonds : angle 4.36250 / 3.15 ( 2132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.493 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: 0.5834 (mmt-90) cc_final: 0.4590 (mtt180) REVERT: A 496 HIS cc_start: 0.8457 (m90) cc_final: 0.8076 (m-70) REVERT: A 516 ASN cc_start: 0.8477 (m-40) cc_final: 0.7938 (m-40) REVERT: A 530 MET cc_start: 0.3411 (tpt) cc_final: 0.2875 (tpt) REVERT: A 700 PHE cc_start: 0.7570 (m-80) cc_final: 0.6991 (m-80) REVERT: A 820 MET cc_start: 0.9586 (tpt) cc_final: 0.9370 (tpp) REVERT: B 326 PHE cc_start: 0.9253 (t80) cc_final: 0.8802 (t80) REVERT: B 395 LEU cc_start: 0.9536 (mp) cc_final: 0.9032 (tt) REVERT: C 360 ASN cc_start: 0.8458 (t0) cc_final: 0.8150 (m-40) REVERT: C 475 CYS cc_start: 0.9294 (t) cc_final: 0.8619 (p) REVERT: C 482 TYR cc_start: 0.8478 (t80) cc_final: 0.8137 (t80) REVERT: C 633 TYR cc_start: 0.8163 (t80) cc_final: 0.7900 (t80) REVERT: D 85 MET cc_start: 0.9471 (mmp) cc_final: 0.9247 (mmm) REVERT: D 132 PHE cc_start: 0.4751 (t80) cc_final: 0.3771 (t80) REVERT: D 174 TYR cc_start: 0.7512 (m-80) cc_final: 0.7308 (m-80) REVERT: D 240 PHE cc_start: 0.8226 (t80) cc_final: 0.7992 (t80) REVERT: E 133 MET cc_start: 0.7293 (mtm) cc_final: 0.7000 (mtt) REVERT: E 258 GLU cc_start: 0.5519 (mt-10) cc_final: 0.5262 (tm-30) REVERT: E 265 MET cc_start: 0.8631 (ppp) cc_final: 0.8029 (tpp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1206 time to fit residues: 42.5459 Evaluate side-chains 178 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 56 optimal weight: 0.0570 chunk 112 optimal weight: 0.0670 chunk 185 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 35 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 overall best weight: 1.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.074403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.061963 restraints weight = 152191.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.063048 restraints weight = 115810.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.063790 restraints weight = 93506.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.064405 restraints weight = 79625.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.064843 restraints weight = 70105.321| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16737 Z= 0.124 Angle : 0.602 9.851 22760 Z= 0.311 Chirality : 0.041 0.242 2598 Planarity : 0.003 0.046 2772 Dihedral : 13.391 87.536 2470 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.06 % Allowed : 1.98 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 1888 helix: 0.52 (0.15), residues: 1110 sheet: -0.00 (0.42), residues: 141 loop : -1.21 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 205 TYR 0.029 0.001 TYR C 609 PHE 0.030 0.001 PHE B 380 TRP 0.027 0.002 TRP C 648 HIS 0.011 0.001 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (16737) covalent geometry : angle 0.60214 / 0.31 (22760) hydrogen bonds : bond 0.03993 / 2.71 ( 732) hydrogen bonds : angle 4.25373 / 3.07 ( 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 229 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.5784 (mmt-90) cc_final: 0.4717 (mtt180) REVERT: A 496 HIS cc_start: 0.8458 (m90) cc_final: 0.8027 (m90) REVERT: A 516 ASN cc_start: 0.8554 (m-40) cc_final: 0.8022 (m110) REVERT: A 530 MET cc_start: 0.3687 (tpt) cc_final: 0.2689 (tpt) REVERT: A 647 LEU cc_start: 0.8717 (tp) cc_final: 0.8508 (tp) REVERT: A 700 PHE cc_start: 0.7589 (m-80) cc_final: 0.6683 (m-80) REVERT: B 326 PHE cc_start: 0.9245 (t80) cc_final: 0.8771 (t80) REVERT: B 363 MET cc_start: 0.4298 (pmm) cc_final: 0.3831 (ppp) REVERT: B 395 LEU cc_start: 0.9560 (mp) cc_final: 0.9002 (tt) REVERT: C 360 ASN cc_start: 0.8453 (t0) cc_final: 0.8133 (m-40) REVERT: C 633 TYR cc_start: 0.8122 (t80) cc_final: 0.7853 (t80) REVERT: D 46 HIS cc_start: 0.9149 (m-70) cc_final: 0.8863 (m-70) REVERT: D 50 LEU cc_start: 0.9362 (mp) cc_final: 0.8812 (tt) REVERT: D 85 MET cc_start: 0.9401 (mmp) cc_final: 0.9179 (mmm) REVERT: D 132 PHE cc_start: 0.4673 (t80) cc_final: 0.4109 (t80) REVERT: D 218 MET cc_start: 0.3851 (ttt) cc_final: 0.3490 (tmm) REVERT: D 355 LYS cc_start: 0.9673 (mppt) cc_final: 0.9343 (ptmt) REVERT: E 133 MET cc_start: 0.7235 (mtm) cc_final: 0.6963 (mtt) REVERT: E 150 ARG cc_start: 0.7384 (mmp-170) cc_final: 0.7052 (mmp-170) REVERT: E 258 GLU cc_start: 0.5701 (mt-10) cc_final: 0.5399 (tm-30) REVERT: E 265 MET cc_start: 0.8673 (ppp) cc_final: 0.8005 (tpp) REVERT: E 270 LEU cc_start: 0.9061 (mm) cc_final: 0.8692 (mm) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1287 time to fit residues: 45.6251 Evaluate side-chains 177 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 0.0050 chunk 104 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 146 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 239 GLN C 240 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** E 195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.074556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.062202 restraints weight = 153310.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.063273 restraints weight = 115330.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.064074 restraints weight = 93250.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.064624 restraints weight = 79208.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.065093 restraints weight = 69962.556| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16737 Z= 0.118 Angle : 0.599 11.752 22760 Z= 0.307 Chirality : 0.041 0.194 2598 Planarity : 0.003 0.037 2772 Dihedral : 13.309 87.337 2470 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: -0.08 (0.19), residues: 1888 helix: 0.58 (0.15), residues: 1115 sheet: 0.17 (0.43), residues: 141 loop : -1.12 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 728 TYR 0.030 0.001 TYR D 255 PHE 0.032 0.001 PHE B 380 TRP 0.021 0.001 TRP C 648 HIS 0.009 0.001 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (16737) covalent geometry : angle 0.59881 / 0.31 (22760) hydrogen bonds : bond 0.03690 / 2.50 ( 732) hydrogen bonds : angle 4.16056 / 3.00 ( 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 223 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.600 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: 0.5705 (mmt-90) cc_final: 0.4650 (mtt180) REVERT: A 496 HIS cc_start: 0.8460 (m90) cc_final: 0.8033 (m90) REVERT: A 516 ASN cc_start: 0.8465 (m-40) cc_final: 0.7935 (m110) REVERT: A 530 MET cc_start: 0.3495 (tpt) cc_final: 0.2823 (tpt) REVERT: A 700 PHE cc_start: 0.7435 (m-80) cc_final: 0.6969 (m-80) REVERT: A 820 MET cc_start: 0.9572 (tpt) cc_final: 0.9320 (tpp) REVERT: B 326 PHE cc_start: 0.9224 (t80) cc_final: 0.8805 (t80) REVERT: B 363 MET cc_start: 0.4204 (pmm) cc_final: 0.3790 (ppp) REVERT: B 395 LEU cc_start: 0.9535 (mp) cc_final: 0.9004 (tt) REVERT: C 113 ASP cc_start: 0.9335 (p0) cc_final: 0.9072 (p0) REVERT: C 261 ARG cc_start: 0.8239 (tmt170) cc_final: 0.7690 (tpt170) REVERT: C 360 ASN cc_start: 0.8460 (t0) cc_final: 0.8136 (m-40) REVERT: C 633 TYR cc_start: 0.8200 (t80) cc_final: 0.7938 (t80) REVERT: D 50 LEU cc_start: 0.9420 (mp) cc_final: 0.8888 (tt) REVERT: D 85 MET cc_start: 0.9471 (mmp) cc_final: 0.9147 (mmm) REVERT: D 355 LYS cc_start: 0.9678 (mppt) cc_final: 0.9381 (ptmt) REVERT: D 376 PHE cc_start: 0.8991 (t80) cc_final: 0.8740 (t80) REVERT: E 150 ARG cc_start: 0.7361 (mmp-170) cc_final: 0.7063 (mmp-170) REVERT: E 258 GLU cc_start: 0.5929 (mt-10) cc_final: 0.5594 (tm-30) REVERT: E 265 MET cc_start: 0.8671 (ppp) cc_final: 0.8243 (tpt) REVERT: E 407 TYR cc_start: 0.8857 (m-80) cc_final: 0.8349 (m-80) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1240 time to fit residues: 42.8278 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 : 0.611 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 GLN C 137 GLN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 216 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.073107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.060847 restraints weight = 154366.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.061890 restraints weight = 116256.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.062664 restraints weight = 94143.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.063200 restraints weight = 80222.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.063673 restraints weight = 70981.985| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16737 Z= 0.130 Angle : 0.608 16.384 22760 Z= 0.309 Chirality : 0.040 0.166 2598 Planarity : 0.003 0.038 2772 Dihedral : 13.317 85.923 2470 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.06 % Allowed : 1.19 % 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: 0.05 (0.19), residues: 1888 helix: 0.67 (0.15), residues: 1114 sheet: 0.27 (0.44), residues: 142 loop : -1.07 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 289 TYR 0.027 0.001 TYR D 255 PHE 0.034 0.002 PHE B 380 TRP 0.021 0.002 TRP C 51 HIS 0.010 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (16737) covalent geometry : angle 0.60800 / 0.31 (22760) hydrogen bonds : bond 0.03716 / 2.49 ( 732) hydrogen bonds : angle 4.09762 / 2.94 ( 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 218 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 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: A 494 ARG cc_start: 0.5902 (mmt-90) cc_final: 0.4567 (mtt180) REVERT: A 516 ASN cc_start: 0.8409 (m-40) cc_final: 0.7878 (m110) REVERT: A 530 MET cc_start: 0.3606 (tpt) cc_final: 0.3019 (tpt) REVERT: A 647 LEU cc_start: 0.8736 (tp) cc_final: 0.8520 (tp) REVERT: A 700 PHE cc_start: 0.7623 (m-80) cc_final: 0.7078 (m-80) REVERT: A 820 MET cc_start: 0.9574 (tpt) cc_final: 0.9331 (tpp) REVERT: B 326 PHE cc_start: 0.9233 (t80) cc_final: 0.8828 (t80) REVERT: B 363 MET cc_start: 0.4500 (pmm) cc_final: 0.4151 (ppp) REVERT: B 395 LEU cc_start: 0.9567 (mp) cc_final: 0.9027 (tt) REVERT: B 432 MET cc_start: 0.7582 (pmm) cc_final: 0.7360 (pmm) REVERT: C 113 ASP cc_start: 0.9343 (p0) cc_final: 0.9086 (p0) REVERT: C 261 ARG cc_start: 0.8374 (tmt170) cc_final: 0.7885 (tpt170) REVERT: C 325 ILE cc_start: 0.8157 (mm) cc_final: 0.7838 (mm) REVERT: C 360 ASN cc_start: 0.8598 (t0) cc_final: 0.8285 (m-40) REVERT: C 475 CYS cc_start: 0.9307 (t) cc_final: 0.8647 (p) REVERT: C 633 TYR cc_start: 0.8207 (t80) cc_final: 0.7955 (t80) REVERT: D 46 HIS cc_start: 0.9250 (m90) cc_final: 0.8967 (m-70) REVERT: D 50 LEU cc_start: 0.9428 (mp) cc_final: 0.8909 (tt) REVERT: D 85 MET cc_start: 0.9431 (mmp) cc_final: 0.9023 (mmm) REVERT: D 106 ASN cc_start: 0.9470 (t0) cc_final: 0.9220 (t0) REVERT: D 218 MET cc_start: 0.4034 (ttt) cc_final: 0.3248 (tmm) REVERT: E 258 GLU cc_start: 0.5962 (mt-10) cc_final: 0.5720 (tm-30) REVERT: E 265 MET cc_start: 0.8754 (ppp) cc_final: 0.8260 (tpt) REVERT: E 270 LEU cc_start: 0.9249 (mm) cc_final: 0.9034 (mm) REVERT: E 407 TYR cc_start: 0.8917 (m-80) cc_final: 0.8325 (m-80) outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.1228 time to fit residues: 41.3637 Evaluate side-chains 166 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 30.0000 chunk 105 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 696 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS B 435 HIS ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS C 284 HIS ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 HIS C 576 HIS ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN E 193 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.068162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.056725 restraints weight = 168424.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.057679 restraints weight = 126489.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.058385 restraints weight = 102984.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.058906 restraints weight = 88006.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.059298 restraints weight = 77959.027| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 16737 Z= 0.234 Angle : 0.756 13.118 22760 Z= 0.391 Chirality : 0.044 0.165 2598 Planarity : 0.005 0.046 2772 Dihedral : 13.725 79.239 2470 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: -0.55 (0.19), residues: 1888 helix: 0.06 (0.15), residues: 1123 sheet: -0.15 (0.43), residues: 135 loop : -0.96 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 368 TYR 0.029 0.002 TYR C 188 PHE 0.070 0.003 PHE C 244 TRP 0.018 0.003 TRP C 51 HIS 0.011 0.002 HIS D 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.23 (16737) covalent geometry : angle 0.75620 / 0.39 (22760) hydrogen bonds : bond 0.05387 / 3.47 ( 732) hydrogen bonds : angle 4.52206 / 3.23 ( 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 206 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.562 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: 0.6454 (mmt-90) cc_final: 0.4873 (mtt180) REVERT: A 516 ASN cc_start: 0.8137 (m-40) cc_final: 0.7504 (m-40) REVERT: A 530 MET cc_start: 0.4147 (tpt) cc_final: 0.3174 (tpt) REVERT: A 632 ILE cc_start: 0.7542 (mp) cc_final: 0.7240 (mp) REVERT: A 700 PHE cc_start: 0.7890 (m-80) cc_final: 0.7360 (m-80) REVERT: A 820 MET cc_start: 0.9559 (tpt) cc_final: 0.9353 (tpp) REVERT: B 326 PHE cc_start: 0.9246 (t80) cc_final: 0.8763 (t80) REVERT: B 363 MET cc_start: 0.4424 (pmm) cc_final: 0.4031 (ppp) REVERT: B 432 MET cc_start: 0.7952 (pmm) cc_final: 0.7434 (pmm) REVERT: C 113 ASP cc_start: 0.9376 (p0) cc_final: 0.9121 (p0) REVERT: C 261 ARG cc_start: 0.8724 (tmt170) cc_final: 0.8141 (tpt170) REVERT: C 325 ILE cc_start: 0.8230 (mm) cc_final: 0.7753 (mm) REVERT: C 409 HIS cc_start: 0.8459 (m90) cc_final: 0.8254 (m-70) REVERT: C 633 TYR cc_start: 0.8253 (t80) cc_final: 0.8009 (t80) REVERT: D 85 MET cc_start: 0.9417 (mmp) cc_final: 0.9114 (mmm) REVERT: D 106 ASN cc_start: 0.9547 (t0) cc_final: 0.9271 (t0) REVERT: D 218 MET cc_start: 0.4909 (ttt) cc_final: 0.4171 (tmm) REVERT: D 397 ARG cc_start: 0.7752 (mmt180) cc_final: 0.7355 (mmt180) REVERT: E 150 ARG cc_start: 0.7487 (mmp-170) cc_final: 0.7234 (mmp-170) REVERT: E 265 MET cc_start: 0.8788 (ppp) cc_final: 0.8348 (ppp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1363 time to fit residues: 42.5634 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 : 0.608 ------------------------------------------------------------------------------- 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: 7.9990 chunk 74 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 HIS B 406 GLN ** 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 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN ** D 280 HIS ** 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 = 0.3808 r_free = 0.3808 target = 0.068516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.056972 restraints weight = 165818.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.057953 restraints weight = 125188.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.058670 restraints weight = 100943.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.059209 restraints weight = 86019.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.059571 restraints weight = 75987.571| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16737 Z= 0.168 Angle : 0.667 12.567 22760 Z= 0.343 Chirality : 0.043 0.192 2598 Planarity : 0.004 0.047 2772 Dihedral : 13.681 83.153 2470 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -0.44 (0.19), residues: 1888 helix: 0.16 (0.15), residues: 1111 sheet: 0.03 (0.43), residues: 135 loop : -0.98 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 596 TYR 0.025 0.002 TYR D 255 PHE 0.038 0.002 PHE B 380 TRP 0.067 0.003 TRP C 51 HIS 0.009 0.001 HIS C 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (16737) covalent geometry : angle 0.66709 / 0.34 (22760) hydrogen bonds : bond 0.04241 / 2.80 ( 732) hydrogen bonds : angle 4.36324 / 3.10 ( 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 199 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.6264 (mmt-90) cc_final: 0.4832 (mtt180) REVERT: A 530 MET cc_start: 0.4157 (tpt) cc_final: 0.3251 (tpt) REVERT: A 700 PHE cc_start: 0.7807 (m-80) cc_final: 0.7263 (m-80) REVERT: A 820 MET cc_start: 0.9517 (tpt) cc_final: 0.9305 (tpp) REVERT: B 326 PHE cc_start: 0.9252 (t80) cc_final: 0.8798 (t80) REVERT: B 363 MET cc_start: 0.4356 (pmm) cc_final: 0.3992 (ppp) REVERT: B 395 LEU cc_start: 0.9611 (mp) cc_final: 0.9025 (tt) REVERT: B 432 MET cc_start: 0.7834 (pmm) cc_final: 0.7466 (pmm) REVERT: C 113 ASP cc_start: 0.9376 (p0) cc_final: 0.9105 (p0) REVERT: C 261 ARG cc_start: 0.8692 (tmt170) cc_final: 0.8045 (tpt170) REVERT: C 325 ILE cc_start: 0.8091 (mm) cc_final: 0.7869 (mm) REVERT: C 633 TYR cc_start: 0.8222 (t80) cc_final: 0.8003 (t80) REVERT: D 85 MET cc_start: 0.9420 (mmp) cc_final: 0.9103 (mmm) REVERT: D 106 ASN cc_start: 0.9506 (t0) cc_final: 0.9220 (t0) REVERT: D 174 TYR cc_start: 0.8017 (m-10) cc_final: 0.7741 (m-10) REVERT: D 218 MET cc_start: 0.4746 (ttt) cc_final: 0.4182 (tmm) REVERT: D 397 ARG cc_start: 0.7956 (mmt180) cc_final: 0.7525 (mmt180) REVERT: E 150 ARG cc_start: 0.7483 (mmp-170) cc_final: 0.6696 (mmp80) REVERT: E 265 MET cc_start: 0.8734 (ppp) cc_final: 0.8309 (ppp) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1316 time to fit residues: 39.9069 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 : 0.679 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 512 GLN A 516 ASN A 582 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 ASN C 557 ASN ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.067522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.056154 restraints weight = 167127.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.057126 restraints weight = 124834.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.057843 restraints weight = 101000.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.058338 restraints weight = 86007.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.058763 restraints weight = 76499.178| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16737 Z= 0.165 Angle : 0.673 12.911 22760 Z= 0.344 Chirality : 0.043 0.352 2598 Planarity : 0.004 0.050 2772 Dihedral : 13.630 82.519 2470 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.19), residues: 1888 helix: 0.22 (0.15), residues: 1114 sheet: 0.40 (0.42), residues: 141 loop : -1.03 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 728 TYR 0.024 0.002 TYR D 255 PHE 0.036 0.002 PHE B 380 TRP 0.055 0.003 TRP C 51 HIS 0.008 0.001 HIS C 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (16737) covalent geometry : angle 0.67321 / 0.34 (22760) hydrogen bonds : bond 0.04258 / 2.81 ( 732) hydrogen bonds : angle 4.32039 / 3.07 ( 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 201 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 ARG cc_start: 0.6331 (mmt-90) cc_final: 0.4858 (mtt180) REVERT: A 530 MET cc_start: 0.3809 (tpt) cc_final: 0.2974 (tpt) REVERT: A 571 MET cc_start: 0.8804 (mmm) cc_final: 0.8303 (mmm) REVERT: A 636 LEU cc_start: 0.9517 (mt) cc_final: 0.9213 (pp) REVERT: A 700 PHE cc_start: 0.7728 (m-80) cc_final: 0.7188 (m-80) REVERT: B 326 PHE cc_start: 0.9230 (t80) cc_final: 0.8748 (t80) REVERT: B 363 MET cc_start: 0.4427 (pmm) cc_final: 0.4071 (ppp) REVERT: B 432 MET cc_start: 0.7899 (pmm) cc_final: 0.7305 (pmm) REVERT: C 113 ASP cc_start: 0.9389 (p0) cc_final: 0.9105 (p0) REVERT: C 633 TYR cc_start: 0.8257 (t80) cc_final: 0.7951 (t80) REVERT: D 85 MET cc_start: 0.9399 (mmp) cc_final: 0.9111 (mmm) REVERT: D 106 ASN cc_start: 0.9478 (t0) cc_final: 0.9191 (t0) REVERT: D 132 PHE cc_start: 0.5960 (t80) cc_final: 0.5350 (t80) REVERT: D 174 TYR cc_start: 0.7909 (m-10) cc_final: 0.7625 (m-10) REVERT: D 218 MET cc_start: 0.4800 (ttt) cc_final: 0.4472 (tmm) REVERT: D 240 PHE cc_start: 0.7916 (t80) cc_final: 0.7710 (t80) REVERT: D 397 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7817 (mmt180) REVERT: E 150 ARG cc_start: 0.7530 (mmp-170) cc_final: 0.6740 (mmp80) REVERT: E 265 MET cc_start: 0.8735 (ppp) cc_final: 0.8286 (ppp) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1306 time to fit residues: 40.3661 Evaluate side-chains 160 residues out of total 1774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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: 0.0040 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 393 HIS ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 ASN C 409 HIS ** C 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN ** D 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN E 260 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.068144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.056557 restraints weight = 165092.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.057550 restraints weight = 123159.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.058275 restraints weight = 99501.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.058781 restraints weight = 84913.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.059216 restraints weight = 75401.887| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16737 Z= 0.129 Angle : 0.630 9.804 22760 Z= 0.322 Chirality : 0.043 0.438 2598 Planarity : 0.003 0.040 2772 Dihedral : 13.511 83.496 2470 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -0.20 (0.19), residues: 1888 helix: 0.34 (0.15), residues: 1118 sheet: 0.50 (0.41), residues: 147 loop : -0.99 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 728 TYR 0.024 0.002 TYR D 255 PHE 0.036 0.002 PHE B 380 TRP 0.051 0.002 TRP C 51 HIS 0.010 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (16737) covalent geometry : angle 0.62972 / 0.32 (22760) hydrogen bonds : bond 0.03735 / 2.50 ( 732) hydrogen bonds : angle 4.18165 / 2.96 ( 2132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2842.87 seconds wall clock time: 50 minutes 8.34 seconds (3008.34 seconds total)