Starting phenix.real_space_refine on Wed Sep 17 21:07:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mhh_48278/09_2025/9mhh_48278.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mhh_48278/09_2025/9mhh_48278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mhh_48278/09_2025/9mhh_48278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mhh_48278/09_2025/9mhh_48278.map" model { file = "/net/cci-nas-00/data/ceres_data/9mhh_48278/09_2025/9mhh_48278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mhh_48278/09_2025/9mhh_48278.cif" } resolution = 4.5 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= 0.005 sd= 0.020 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 C 5608 2.51 5 N 2804 2.21 5 O 2823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11243 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1191, 4764 Classifications: {'peptide': 1191} Incomplete info: {'backbone_only': 1134} Link IDs: {'PCIS': 2, 'PTRANS': 54, 'TRANS': 1134} Chain breaks: 6 Unresolved chain link angles: 56 Unresolved non-hydrogen bonds: 4940 Unresolved non-hydrogen angles: 7146 Unresolved non-hydrogen dihedrals: 3191 Unresolved non-hydrogen chiralities: 1481 Planarities with less than four sites: {'GLU:plan': 67, 'TYR:plan': 35, 'PHE:plan': 49, 'ASP:plan': 66, 'HIS:plan': 36, 'ARG:plan': 67, 'GLN:plan1': 59, 'ASN:plan1': 45, 'TRP:plan': 18} Unresolved non-hydrogen planarities: 2302 Chain: "B" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 3284 Classifications: {'peptide': 821} Incomplete info: {'backbone_only': 782} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 782} Chain breaks: 2 Unresolved chain link angles: 38 Unresolved non-hydrogen bonds: 3525 Unresolved non-hydrogen angles: 5059 Unresolved non-hydrogen dihedrals: 2317 Unresolved non-hydrogen chiralities: 1008 Planarities with less than four sites: {'GLU:plan': 54, 'PHE:plan': 32, 'HIS:plan': 18, 'TYR:plan': 37, 'ASP:plan': 54, 'ASN:plan1': 31, 'GLN:plan1': 42, 'ARG:plan': 41, 'TRP:plan': 11} Unresolved non-hydrogen planarities: 1667 Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 1172 Classifications: {'peptide': 293} Incomplete info: {'backbone_only': 282} Link IDs: {'PTRANS': 8, 'TRANS': 284} Chain breaks: 2 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1275 Unresolved non-hydrogen angles: 1813 Unresolved non-hydrogen dihedrals: 837 Unresolved non-hydrogen chiralities: 357 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 11, 'PHE:plan': 9, 'TYR:plan': 10, 'ARG:plan': 19, 'GLU:plan': 28, 'TRP:plan': 4, 'ASN:plan1': 16, 'HIS:plan': 8} Unresolved non-hydrogen planarities: 606 Chain: "D" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 1253 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 297} Link IDs: {'PTRANS': 5, 'TRANS': 307} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1390 Unresolved non-hydrogen angles: 1989 Unresolved non-hydrogen dihedrals: 918 Unresolved non-hydrogen chiralities: 374 Planarities with less than four sites: {'GLU:plan': 39, 'ASP:plan': 16, 'GLN:plan1': 24, 'ASN:plan1': 19, 'TYR:plan': 11, 'ARG:plan': 14, 'PHE:plan': 15, 'HIS:plan': 5, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 755 Chain: "E" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 704 Classifications: {'peptide': 176} Incomplete info: {'backbone_only': 166} Link IDs: {'PTRANS': 2, 'TRANS': 173} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 724 Unresolved non-hydrogen angles: 1047 Unresolved non-hydrogen dihedrals: 462 Unresolved non-hydrogen chiralities: 222 Planarities with less than four sites: {'ASN:plan1': 8, 'GLU:plan': 11, 'TYR:plan': 9, 'ASP:plan': 13, 'PHE:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 337 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.60, per 1000 atoms: 0.32 Number of scatterers: 11243 At special positions: 0 Unit cell: (82.792, 179.208, 216.936, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) P 6 15.00 Mg 2 11.99 O 2823 8.00 N 2804 7.00 C 5608 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 910.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 21 sheets defined 55.8% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 removed outlier: 3.755A pdb=" N ASP A 22 " --> pdb=" O TYR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.546A pdb=" N TYR A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 121 through 142 Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.682A pdb=" N ASP A 182 " --> pdb=" O ASN A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.832A pdb=" N PHE A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 253 removed outlier: 3.686A pdb=" N ASP A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.684A pdb=" N LEU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 317 through 323 removed outlier: 4.236A pdb=" N TYR A 321 " --> pdb=" O PRO A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.936A pdb=" N GLN A 330 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 338 through 359 removed outlier: 4.788A pdb=" N GLY A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 384 removed outlier: 3.978A pdb=" N LEU A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE A 377 " --> pdb=" O ASN A 373 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.801A pdb=" N LEU A 389 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 410 through 418 Processing helix chain 'A' and resid 418 through 426 removed outlier: 3.517A pdb=" N LEU A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS A 424 " --> pdb=" O PRO A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 447 removed outlier: 3.600A pdb=" N LEU A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.724A pdb=" N ILE A 456 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.507A pdb=" N GLN A 472 " --> pdb=" O HIS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 510 removed outlier: 4.555A pdb=" N ALA A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 545 Processing helix chain 'A' and resid 549 through 569 removed outlier: 3.811A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG A 563 " --> pdb=" O ASN A 559 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 582 removed outlier: 3.643A pdb=" N ASN A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 587 Processing helix chain 'A' and resid 590 through 609 removed outlier: 3.740A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL A 602 " --> pdb=" O PHE A 598 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLY A 603 " --> pdb=" O ASP A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 624 Proline residue: A 618 - end of helix Processing helix chain 'A' and resid 628 through 645 Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.510A pdb=" N TYR A 654 " --> pdb=" O LYS A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 removed outlier: 3.569A pdb=" N CYS A 665 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 686 Processing helix chain 'A' and resid 687 through 694 Processing helix chain 'A' and resid 694 through 700 removed outlier: 3.820A pdb=" N TYR A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 720 Processing helix chain 'A' and resid 725 through 734 Processing helix chain 'A' and resid 737 through 753 Processing helix chain 'A' and resid 764 through 777 Processing helix chain 'A' and resid 780 through 790 Processing helix chain 'A' and resid 790 through 808 removed outlier: 3.547A pdb=" N GLN A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 825 Processing helix chain 'A' and resid 939 through 967 Processing helix chain 'A' and resid 1023 through 1027 removed outlier: 3.522A pdb=" N GLU A1026 " --> pdb=" O GLN A1023 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY A1027 " --> pdb=" O LYS A1024 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1023 through 1027' Processing helix chain 'A' and resid 1138 through 1142 Processing helix chain 'A' and resid 1272 through 1276 Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 34 through 41 Processing helix chain 'B' and resid 42 through 51 removed outlier: 6.004A pdb=" N GLY B 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU B 49 " --> pdb=" O PHE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 170 through 184 Processing helix chain 'B' and resid 190 through 212 removed outlier: 3.564A pdb=" N LEU B 196 " --> pdb=" O TRP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 289 through 301 Processing helix chain 'B' and resid 309 through 319 removed outlier: 3.940A pdb=" N GLN B 313 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 341 through 353 removed outlier: 3.556A pdb=" N GLY B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 365 through 368 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 388 through 402 removed outlier: 3.980A pdb=" N MET B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN B 398 " --> pdb=" O MET B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 407 through 413 removed outlier: 4.166A pdb=" N ILE B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 484 removed outlier: 3.670A pdb=" N ALA B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 503 Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 510 through 530 Processing helix chain 'B' and resid 532 through 562 Processing helix chain 'B' and resid 565 through 579 Processing helix chain 'B' and resid 641 through 661 Processing helix chain 'B' and resid 690 through 698 Processing helix chain 'B' and resid 699 through 708 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 739 Processing helix chain 'B' and resid 745 through 747 No H-bonds generated for 'chain 'B' and resid 745 through 747' Processing helix chain 'B' and resid 780 through 787 Processing helix chain 'B' and resid 792 through 812 Processing helix chain 'B' and resid 812 through 823 Processing helix chain 'B' and resid 828 through 834 removed outlier: 4.079A pdb=" N GLU B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 847 removed outlier: 4.436A pdb=" N VAL B 839 " --> pdb=" O PRO B 835 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYS B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 868 Processing helix chain 'B' and resid 870 through 887 removed outlier: 4.181A pdb=" N VAL B 874 " --> pdb=" O LEU B 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 74 through 205 removed outlier: 4.416A pdb=" N GLY C 102 " --> pdb=" O LYS C 98 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 285 removed outlier: 3.959A pdb=" N TYR C 280 " --> pdb=" O TYR C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 322 Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 340 through 362 Processing helix chain 'C' and resid 373 through 382 Processing helix chain 'C' and resid 398 through 406 Processing helix chain 'D' and resid 139 through 172 Processing helix chain 'D' and resid 176 through 267 Processing helix chain 'D' and resid 268 through 274 Processing helix chain 'D' and resid 299 through 322 Processing helix chain 'D' and resid 333 through 336 Processing helix chain 'D' and resid 355 through 360 removed outlier: 3.734A pdb=" N PHE D 360 " --> pdb=" O GLY D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 387 removed outlier: 3.591A pdb=" N ASP D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 386 " --> pdb=" O GLU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 448 Processing helix chain 'E' and resid 23 through 33 Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.576A pdb=" N PHE E 73 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.863A pdb=" N TYR E 81 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 101 Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 128 through 132 removed outlier: 3.622A pdb=" N LYS E 132 " --> pdb=" O THR E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 147 removed outlier: 3.831A pdb=" N PHE E 142 " --> pdb=" O THR E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 176 removed outlier: 3.913A pdb=" N GLN E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 34 removed outlier: 6.798A pdb=" N ARG A 42 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER A 31 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 40 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA A 98 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LYS A 93 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 3.542A pdb=" N ASP A 108 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 removed outlier: 5.904A pdb=" N LEU A 175 " --> pdb=" O VAL A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 818 through 820 removed outlier: 6.011A pdb=" N ILE A 819 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL B 224 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU B 230 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS B 8 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 984 through 989 removed outlier: 6.293A pdb=" N LEU A 985 " --> pdb=" O LYS A1358 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS A1358 " --> pdb=" O LEU A 985 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A1334 " --> pdb=" O ALA A1348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 996 through 1001 removed outlier: 6.713A pdb=" N CYS A1011 " --> pdb=" O ASN A 997 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 999 " --> pdb=" O ALA A1009 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A1009 " --> pdb=" O ILE A 999 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL A1001 " --> pdb=" O LEU A1007 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU A1007 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1045 through 1051 removed outlier: 4.307A pdb=" N THR A1047 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR A1056 " --> pdb=" O CYS A1051 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1065 " --> pdb=" O SER A1061 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY A1070 " --> pdb=" O PRO A1084 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1098 through 1105 removed outlier: 3.829A pdb=" N ASP A1100 " --> pdb=" O ALA A1115 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A1120 " --> pdb=" O THR A1116 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP A1133 " --> pdb=" O GLY A1123 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ASP A1125 " --> pdb=" O ASN A1131 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASN A1131 " --> pdb=" O ASP A1125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1144 through 1149 removed outlier: 4.305A pdb=" N THR A1164 " --> pdb=" O THR A1160 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A1177 " --> pdb=" O CYS A1167 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP A1169 " --> pdb=" O PRO A1175 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1187 through 1192 removed outlier: 6.702A pdb=" N ALA A1203 " --> pdb=" O ARG A1188 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A1190 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A1201 " --> pdb=" O LEU A1190 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N MET A1192 " --> pdb=" O TRP A1199 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N TRP A1199 " --> pdb=" O MET A1192 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A1222 " --> pdb=" O MET A1212 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP A1214 " --> pdb=" O ARG A1220 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG A1220 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1242 through 1248 removed outlier: 6.712A pdb=" N ILE A1265 " --> pdb=" O VAL A1279 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 85 through 96 removed outlier: 4.274A pdb=" N TRP B 85 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY B 24 " --> pdb=" O TRP B 87 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU B 89 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS B 22 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B 91 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN B 20 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU B 93 " --> pdb=" O ASN B 18 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASN B 18 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N MET B 218 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU B 26 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR B 216 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AB5, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.596A pdb=" N TYR B 58 " --> pdb=" O TRP B 111 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ALA B 104 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N SER B 128 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL B 106 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR B 126 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B 108 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY B 124 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 110 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 591 through 592 removed outlier: 3.928A pdb=" N GLY B 603 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N PHE B 622 " --> pdb=" O ILE B 605 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N GLU B 607 " --> pdb=" O GLN B 620 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N GLN B 620 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 688 through 689 Processing sheet with id=AB8, first strand: chain 'C' and resid 208 through 210 Processing sheet with id=AB9, first strand: chain 'D' and resid 276 through 279 removed outlier: 4.589A pdb=" N GLY D 283 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 328 through 331 Processing sheet with id=AC2, first strand: chain 'D' and resid 395 through 397 Processing sheet with id=AC3, first strand: chain 'E' and resid 48 through 55 removed outlier: 4.051A pdb=" N LYS E 49 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR E 10 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLN E 63 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE E 12 " --> pdb=" O GLN E 63 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TRP E 65 " --> pdb=" O PHE E 12 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU E 14 " --> pdb=" O TRP E 65 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE E 88 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU E 15 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL E 90 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE E 17 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ASP E 92 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL E 89 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN E 124 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TYR E 91 " --> pdb=" O ASN E 124 " (cutoff:3.500A) 1269 hydrogen bonds defined for protein. 3642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 2797 1.30 - 1.38: 2798 1.38 - 1.46: 1758 1.46 - 1.54: 3867 1.54 - 1.62: 10 Bond restraints: 11230 Sorted by residual: bond pdb=" C MET A1192 " pdb=" N HIS A1193 " ideal model delta sigma weight residual 1.329 1.300 0.029 1.60e-02 3.91e+03 3.18e+00 bond pdb=" CA PRO A 975 " pdb=" C PRO A 975 " ideal model delta sigma weight residual 1.514 1.523 -0.008 5.50e-03 3.31e+04 2.30e+00 bond pdb=" C2' GTP E1002 " pdb=" C3' GTP E1002 " ideal model delta sigma weight residual 1.524 1.494 0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" O3B GTP E1002 " pdb=" PG GTP E1002 " ideal model delta sigma weight residual 1.610 1.582 0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1' GTP E1002 " pdb=" C2' GTP E1002 " ideal model delta sigma weight residual 1.524 1.496 0.028 2.00e-02 2.50e+03 1.91e+00 ... (remaining 11225 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 13669 2.14 - 4.29: 327 4.29 - 6.43: 30 6.43 - 8.58: 4 8.58 - 10.72: 5 Bond angle restraints: 14035 Sorted by residual: angle pdb=" C PRO A1237 " pdb=" N SER A1238 " pdb=" CA SER A1238 " ideal model delta sigma weight residual 120.49 126.40 -5.91 1.42e+00 4.96e-01 1.73e+01 angle pdb=" C MET A1192 " pdb=" N HIS A1193 " pdb=" CA HIS A1193 " ideal model delta sigma weight residual 120.49 114.59 5.90 1.42e+00 4.96e-01 1.73e+01 angle pdb=" N GLY A 560 " pdb=" CA GLY A 560 " pdb=" C GLY A 560 " ideal model delta sigma weight residual 113.18 121.98 -8.80 2.37e+00 1.78e-01 1.38e+01 angle pdb=" N VAL A1017 " pdb=" CA VAL A1017 " pdb=" C VAL A1017 " ideal model delta sigma weight residual 108.11 102.94 5.17 1.40e+00 5.10e-01 1.36e+01 angle pdb=" C1' GTP A2001 " pdb=" C2' GTP A2001 " pdb=" C3' GTP A2001 " ideal model delta sigma weight residual 111.00 100.28 10.72 3.00e+00 1.11e-01 1.28e+01 ... (remaining 14030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 2789 35.06 - 70.11: 5 70.11 - 105.17: 6 105.17 - 140.22: 2 140.22 - 175.28: 6 Dihedral angle restraints: 2808 sinusoidal: 29 harmonic: 2779 Sorted by residual: dihedral pdb=" O3A GTP A2001 " pdb=" O3B GTP A2001 " pdb=" PB GTP A2001 " pdb=" PG GTP A2001 " ideal model delta sinusoidal sigma weight residual -56.21 119.07 -175.28 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C8 GTP A2001 " pdb=" C1' GTP A2001 " pdb=" N9 GTP A2001 " pdb=" O4' GTP A2001 " ideal model delta sinusoidal sigma weight residual 104.59 -66.63 171.22 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' GTP A2001 " pdb=" O5' GTP A2001 " pdb=" PA GTP A2001 " pdb=" O3A GTP A2001 " ideal model delta sinusoidal sigma weight residual 69.27 -124.18 -166.56 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 2805 not shown) Histogram of chiral volume deviations from ideal: 0.036 - 0.083: 2 0.083 - 0.130: 1 0.130 - 0.177: 1 0.177 - 0.223: 2 0.223 - 0.270: 2 Chirality restraints: 8 Sorted by residual: chirality pdb=" C2' GTP E1002 " pdb=" C1' GTP E1002 " pdb=" C3' GTP E1002 " pdb=" O2' GTP E1002 " both_signs ideal model delta sigma weight residual False -2.47 -2.74 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2' GTP A2001 " pdb=" C1' GTP A2001 " pdb=" C3' GTP A2001 " pdb=" O2' GTP A2001 " both_signs ideal model delta sigma weight residual False -2.47 -2.72 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C4' GTP E1002 " pdb=" C3' GTP E1002 " pdb=" C5' GTP E1002 " pdb=" O4' GTP E1002 " both_signs ideal model delta sigma weight residual False -2.47 -2.26 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 5 not shown) Planarity restraints: 2782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 330 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C LEU B 330 " -0.027 2.00e-02 2.50e+03 pdb=" O LEU B 330 " 0.010 2.00e-02 2.50e+03 pdb=" N THR B 331 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 160 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C PRO B 160 " 0.026 2.00e-02 2.50e+03 pdb=" O PRO B 160 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY B 161 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 138 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.03e+00 pdb=" C GLN B 138 " 0.025 2.00e-02 2.50e+03 pdb=" O GLN B 138 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY B 139 " -0.008 2.00e-02 2.50e+03 ... (remaining 2779 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 11 2.10 - 2.80: 3999 2.80 - 3.50: 13571 3.50 - 4.20: 18017 4.20 - 4.90: 29605 Nonbonded interactions: 65203 Sorted by model distance: nonbonded pdb="MG MG E1001 " pdb=" O1A GTP E1002 " model vdw 1.401 2.170 nonbonded pdb="MG MG E1001 " pdb=" O2B GTP E1002 " model vdw 1.528 2.170 nonbonded pdb=" PA GTP A2001 " pdb="MG MG A2002 " model vdw 1.662 2.530 nonbonded pdb="MG MG E1001 " pdb=" PA GTP E1002 " model vdw 1.715 2.530 nonbonded pdb=" O2A GTP A2001 " pdb="MG MG A2002 " model vdw 1.763 2.170 ... (remaining 65198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.410 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.610 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 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 : 0.007 0.632 11231 Z= 0.638 Angle : 0.799 10.719 14035 Z= 0.521 Chirality : 0.175 0.270 8 Planarity : 0.004 0.016 2782 Dihedral : 10.147 175.277 2808 Min Nonbonded Distance : 1.401 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.42 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.48 (0.15), residues: 2764 helix: 0.73 (0.13), residues: 1363 sheet: 0.64 (0.27), residues: 338 loop : -0.16 (0.19), residues: 1063 Details of bonding type rmsd covalent geometry : bond 0.00307 (11230) covalent geometry : angle 0.79873 (14035) hydrogen bonds : bond 0.19198 ( 1267) hydrogen bonds : angle 7.25336 ( 3642) Misc. bond : bond 0.63156 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.448 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0469 time to fit residues: 6.9551 Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.082940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.070467 restraints weight = 73609.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.068905 restraints weight = 107170.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069162 restraints weight = 100140.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068685 restraints weight = 85773.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068777 restraints weight = 84901.612| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11231 Z= 0.317 Angle : 0.709 15.027 14035 Z= 0.450 Chirality : 0.156 0.345 8 Planarity : 0.005 0.021 2782 Dihedral : 10.075 174.624 2808 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.57 (0.16), residues: 2764 helix: 1.29 (0.14), residues: 1350 sheet: -0.42 (0.29), residues: 287 loop : -0.44 (0.19), residues: 1127 Details of bonding type rmsd covalent geometry : bond 0.00423 (11230) covalent geometry : angle 0.70880 (14035) hydrogen bonds : bond 0.05318 ( 1267) hydrogen bonds : angle 5.74435 ( 3642) Misc. bond : bond 0.00656 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.418 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0461 time to fit residues: 6.8232 Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 8 optimal weight: 30.0000 chunk 212 optimal weight: 20.0000 chunk 165 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 202 optimal weight: 40.0000 chunk 163 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.081976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.069704 restraints weight = 73290.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.067997 restraints weight = 108367.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067913 restraints weight = 113335.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.067462 restraints weight = 102366.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067585 restraints weight = 98800.203| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11231 Z= 0.319 Angle : 0.703 11.578 14035 Z= 0.451 Chirality : 0.134 0.298 8 Planarity : 0.005 0.027 2782 Dihedral : 9.358 141.233 2808 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.02 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.28 (0.16), residues: 2764 helix: 1.02 (0.14), residues: 1339 sheet: -1.37 (0.31), residues: 241 loop : -1.33 (0.18), residues: 1184 Details of bonding type rmsd covalent geometry : bond 0.00421 (11230) covalent geometry : angle 0.70344 (14035) hydrogen bonds : bond 0.05711 ( 1267) hydrogen bonds : angle 6.01937 ( 3642) Misc. bond : bond 0.00167 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.451 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0442 time to fit residues: 6.4263 Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 54 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 63 optimal weight: 0.0070 chunk 123 optimal weight: 3.9990 chunk 75 optimal weight: 0.0980 chunk 271 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 overall best weight: 2.2204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.083008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.069702 restraints weight = 72838.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.068335 restraints weight = 106170.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068659 restraints weight = 102839.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.068566 restraints weight = 83319.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068614 restraints weight = 78498.750| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 11231 Z= 0.149 Angle : 0.456 9.194 14035 Z= 0.279 Chirality : 0.104 0.190 8 Planarity : 0.002 0.016 2782 Dihedral : 8.191 143.640 2808 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.55 (0.16), residues: 2764 helix: 1.97 (0.14), residues: 1341 sheet: -1.43 (0.31), residues: 252 loop : -1.15 (0.18), residues: 1171 Details of bonding type rmsd covalent geometry : bond 0.00198 (11230) covalent geometry : angle 0.45635 (14035) hydrogen bonds : bond 0.03591 ( 1267) hydrogen bonds : angle 4.71354 ( 3642) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.458 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0434 time to fit residues: 6.4597 Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 193 optimal weight: 9.9990 chunk 204 optimal weight: 30.0000 chunk 247 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.080971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.069009 restraints weight = 72742.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067586 restraints weight = 102682.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067586 restraints weight = 92435.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067586 restraints weight = 92435.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067586 restraints weight = 92435.430| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11231 Z= 0.363 Angle : 0.772 13.262 14035 Z= 0.498 Chirality : 0.153 0.327 8 Planarity : 0.005 0.025 2782 Dihedral : 9.168 138.447 2808 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.62 % Favored : 90.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.84 (0.16), residues: 2764 helix: 0.86 (0.14), residues: 1311 sheet: -2.06 (0.32), residues: 225 loop : -1.87 (0.17), residues: 1228 Details of bonding type rmsd covalent geometry : bond 0.00484 (11230) covalent geometry : angle 0.77167 (14035) hydrogen bonds : bond 0.05896 ( 1267) hydrogen bonds : angle 6.45935 ( 3642) Misc. bond : bond 0.00606 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.554 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0478 time to fit residues: 7.1080 Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 11 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 247 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 217 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 271 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.081731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.068659 restraints weight = 72903.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.066933 restraints weight = 107402.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.066916 restraints weight = 95362.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.066845 restraints weight = 86019.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.066847 restraints weight = 78008.837| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 11231 Z= 0.206 Angle : 0.532 10.628 14035 Z= 0.333 Chirality : 0.121 0.242 8 Planarity : 0.003 0.017 2782 Dihedral : 8.242 139.859 2808 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.33 (0.16), residues: 2764 helix: 1.49 (0.14), residues: 1317 sheet: -2.03 (0.32), residues: 218 loop : -1.86 (0.17), residues: 1229 Details of bonding type rmsd covalent geometry : bond 0.00274 (11230) covalent geometry : angle 0.53159 (14035) hydrogen bonds : bond 0.04108 ( 1267) hydrogen bonds : angle 5.33187 ( 3642) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.457 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0467 time to fit residues: 6.8448 Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 262 optimal weight: 0.5980 chunk 188 optimal weight: 20.0000 chunk 240 optimal weight: 9.9990 chunk 144 optimal weight: 0.0770 chunk 50 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 275 optimal weight: 9.9990 chunk 217 optimal weight: 0.0050 chunk 93 optimal weight: 7.9990 chunk 272 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 overall best weight: 3.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.081559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.069259 restraints weight = 72967.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067991 restraints weight = 110858.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.067834 restraints weight = 107813.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067273 restraints weight = 97865.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067359 restraints weight = 101240.460| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11231 Z= 0.207 Angle : 0.531 11.049 14035 Z= 0.331 Chirality : 0.129 0.264 8 Planarity : 0.003 0.016 2782 Dihedral : 8.028 137.967 2808 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.20 (0.16), residues: 2764 helix: 1.71 (0.14), residues: 1340 sheet: -2.31 (0.31), residues: 226 loop : -1.91 (0.18), residues: 1198 Details of bonding type rmsd covalent geometry : bond 0.00275 (11230) covalent geometry : angle 0.53060 (14035) hydrogen bonds : bond 0.04029 ( 1267) hydrogen bonds : angle 5.18388 ( 3642) Misc. bond : bond 0.00195 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.477 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0477 time to fit residues: 7.0668 Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 79 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 271 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 43 optimal weight: 0.0030 chunk 208 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 overall best weight: 4.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.080998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.068530 restraints weight = 73053.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.066970 restraints weight = 111682.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.066545 restraints weight = 99575.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.066370 restraints weight = 91983.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.066367 restraints weight = 85836.558| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 11231 Z= 0.269 Angle : 0.624 11.466 14035 Z= 0.394 Chirality : 0.146 0.282 8 Planarity : 0.004 0.020 2782 Dihedral : 8.402 136.724 2808 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.59 (0.16), residues: 2764 helix: 1.34 (0.14), residues: 1337 sheet: -2.45 (0.31), residues: 216 loop : -2.06 (0.18), residues: 1211 Details of bonding type rmsd covalent geometry : bond 0.00356 (11230) covalent geometry : angle 0.62441 (14035) hydrogen bonds : bond 0.04693 ( 1267) hydrogen bonds : angle 5.74961 ( 3642) Misc. bond : bond 0.00270 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.465 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0486 time to fit residues: 7.1941 Evaluate side-chains 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 61 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 200 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.079475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067364 restraints weight = 73337.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.065706 restraints weight = 107893.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.064773 restraints weight = 93972.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.064375 restraints weight = 96239.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.064480 restraints weight = 93871.443| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 11231 Z= 0.456 Angle : 0.915 11.869 14035 Z= 0.595 Chirality : 0.172 0.281 8 Planarity : 0.006 0.040 2782 Dihedral : 9.899 160.533 2808 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 14.33 % Favored : 85.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 aren not related in a simple way. whole: -2.22 (0.15), residues: 2764 helix: -0.14 (0.14), residues: 1309 sheet: -2.64 (0.35), residues: 170 loop : -2.80 (0.16), residues: 1285 Details of bonding type rmsd covalent geometry : bond 0.00605 (11230) covalent geometry : angle 0.91454 (14035) hydrogen bonds : bond 0.06926 ( 1267) hydrogen bonds : angle 7.47255 ( 3642) Misc. bond : bond 0.00518 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.376 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0475 time to fit residues: 7.1212 Evaluate side-chains 72 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 130 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 138 optimal weight: 0.3980 chunk 268 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.081536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068044 restraints weight = 72732.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.066576 restraints weight = 104596.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067206 restraints weight = 95718.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.066898 restraints weight = 81955.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.066935 restraints weight = 76632.835| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 11231 Z= 0.130 Angle : 0.473 9.278 14035 Z= 0.287 Chirality : 0.110 0.162 8 Planarity : 0.002 0.017 2782 Dihedral : 8.183 162.747 2808 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 0.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: -0.65 (0.16), residues: 2764 helix: 1.43 (0.14), residues: 1338 sheet: -2.69 (0.32), residues: 211 loop : -2.25 (0.17), residues: 1215 Details of bonding type rmsd covalent geometry : bond 0.00170 (11230) covalent geometry : angle 0.47276 (14035) hydrogen bonds : bond 0.03608 ( 1267) hydrogen bonds : angle 5.23496 ( 3642) Misc. bond : bond 0.00064 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5528 Ramachandran restraints generated. 2764 Oldfield, 0 Emsley, 2764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.423 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0474 time to fit residues: 7.0626 Evaluate side-chains 72 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 9 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 176 optimal weight: 40.0000 chunk 235 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 237 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.079661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.067922 restraints weight = 73959.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.066659 restraints weight = 101745.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065381 restraints weight = 95322.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.065291 restraints weight = 97383.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.065291 restraints weight = 96009.339| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11231 Z= 0.401 Angle : 0.815 10.216 14035 Z= 0.529 Chirality : 0.162 0.234 8 Planarity : 0.005 0.033 2782 Dihedral : 9.181 147.195 2808 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.33 % Allowed : 14.33 % Favored : 85.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.91 (0.15), residues: 2764 helix: 0.29 (0.14), residues: 1310 sheet: -2.68 (0.33), residues: 187 loop : -2.83 (0.16), residues: 1267 Details of bonding type rmsd covalent geometry : bond 0.00532 (11230) covalent geometry : angle 0.81531 (14035) hydrogen bonds : bond 0.06191 ( 1267) hydrogen bonds : angle 6.96387 ( 3642) Misc. bond : bond 0.00602 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.47 seconds wall clock time: 33 minutes 29.26 seconds (2009.26 seconds total)