Starting phenix.real_space_refine on Tue Jun 10 05:21:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mhh_48278/06_2025/9mhh_48278.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mhh_48278/06_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_48278/06_2025/9mhh_48278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mhh_48278/06_2025/9mhh_48278.map" model { file = "/net/cci-nas-00/data/ceres_data/9mhh_48278/06_2025/9mhh_48278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mhh_48278/06_2025/9mhh_48278.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 59, 'ASP:plan': 66, 'TYR:plan': 35, 'ASN:plan1': 45, 'TRP:plan': 18, 'HIS:plan': 36, 'PHE:plan': 49, 'GLU:plan': 67, 'ARG:plan': 67} 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: {'GLN:plan1': 42, 'ARG:plan': 41, 'TYR:plan': 37, 'ASN:plan1': 31, 'TRP:plan': 11, 'ASP:plan': 54, 'PHE:plan': 32, 'GLU:plan': 54, 'HIS:plan': 18} 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, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 16, 'TRP:plan': 4, 'ASP:plan': 11, 'PHE:plan': 9, 'GLU:plan': 28, 'ARG:plan': 19} 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: {'GLN:plan1': 24, 'HIS:plan': 5, 'TYR:plan': 11, 'ASN:plan1': 19, 'TRP:plan': 7, 'ASP:plan': 16, 'PHE:plan': 15, 'GLU:plan': 39, 'ARG:plan': 14} 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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 9, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 7} 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: 9.00, per 1000 atoms: 0.80 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: 3.55 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.85 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: 6.90 Time building geometry restraints manager: 4.02 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: 4.150 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 36.370 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.110 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (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 hydrogen bonds : bond 0.19198 ( 1267) hydrogen bonds : angle 7.25336 ( 3642) covalent geometry : bond 0.00307 (11230) covalent geometry : angle 0.79873 (14035) 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 : 1.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0963 time to fit residues: 14.7554 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 : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 217 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.082319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.068854 restraints weight = 73189.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.067558 restraints weight = 82549.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067407 restraints weight = 96797.699| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11231 Z= 0.380 Angle : 0.814 14.756 14035 Z= 0.521 Chirality : 0.147 0.336 8 Planarity : 0.006 0.028 2782 Dihedral : 10.476 172.279 2808 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.63 % Favored : 95.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 2764 helix: 0.79 (0.14), residues: 1335 sheet: -0.80 (0.28), residues: 292 loop : -0.74 (0.18), residues: 1137 Details of bonding type rmsd hydrogen bonds : bond 0.06176 ( 1267) hydrogen bonds : angle 6.21976 ( 3642) covalent geometry : bond 0.00505 (11230) covalent geometry : angle 0.81386 (14035) Misc. bond : bond 0.02249 ( 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 : 1.241 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0921 time to fit residues: 14.2806 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 : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 199 optimal weight: 50.0000 chunk 212 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 = 0.082181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.070202 restraints weight = 74073.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.068515 restraints weight = 118033.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067931 restraints weight = 109990.692| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11231 Z= 0.243 Angle : 0.576 10.377 14035 Z= 0.363 Chirality : 0.116 0.228 8 Planarity : 0.004 0.018 2782 Dihedral : 9.001 157.563 2808 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2764 helix: 1.37 (0.14), residues: 1326 sheet: -1.18 (0.30), residues: 260 loop : -1.08 (0.18), residues: 1178 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 1267) hydrogen bonds : angle 5.34322 ( 3642) covalent geometry : bond 0.00323 (11230) covalent geometry : angle 0.57645 (14035) Misc. bond : bond 0.00779 ( 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 : 1.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0940 time to fit residues: 14.5380 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 : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 240 optimal weight: 9.9990 chunk 40 optimal weight: 0.0970 chunk 66 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 169 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 230 optimal weight: 40.0000 chunk 77 optimal weight: 7.9990 chunk 245 optimal weight: 20.0000 overall best weight: 3.6184 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.082267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.069324 restraints weight = 72626.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068004 restraints weight = 123627.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068257 restraints weight = 120581.579| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11231 Z= 0.228 Angle : 0.564 11.137 14035 Z= 0.353 Chirality : 0.131 0.276 8 Planarity : 0.003 0.021 2782 Dihedral : 8.401 145.253 2808 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2764 helix: 1.59 (0.14), residues: 1337 sheet: -1.71 (0.31), residues: 248 loop : -1.38 (0.18), residues: 1179 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 1267) hydrogen bonds : angle 5.16010 ( 3642) covalent geometry : bond 0.00303 (11230) covalent geometry : angle 0.56353 (14035) Misc. bond : bond 0.00041 ( 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 : 1.785 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1256 time to fit residues: 19.2397 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 : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 127 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 200 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 overall best weight: 3.4388 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.082024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.069578 restraints weight = 71751.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.067983 restraints weight = 110310.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.068203 restraints weight = 110401.734| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.4252 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= 0.207 Angle : 0.519 9.813 14035 Z= 0.326 Chirality : 0.113 0.214 8 Planarity : 0.003 0.017 2782 Dihedral : 8.050 142.307 2808 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.91 % Favored : 93.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2764 helix: 1.80 (0.14), residues: 1328 sheet: -1.91 (0.31), residues: 235 loop : -1.53 (0.18), residues: 1201 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 1267) hydrogen bonds : angle 5.09887 ( 3642) covalent geometry : bond 0.00274 (11230) covalent geometry : angle 0.51882 (14035) Misc. bond : bond 0.00098 ( 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 : 1.841 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1256 time to fit residues: 19.2655 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 : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 262 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 186 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 165 optimal weight: 0.0270 chunk 202 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 199 optimal weight: 30.0000 overall best weight: 3.3844 ------------------------------------------------------------------------------- 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 = 0.081692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.070406 restraints weight = 73260.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.068317 restraints weight = 105835.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.066664 restraints weight = 99541.903| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 moved from start: 0.4656 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= 0.209 Angle : 0.530 10.932 14035 Z= 0.331 Chirality : 0.128 0.273 8 Planarity : 0.003 0.017 2782 Dihedral : 7.908 141.325 2808 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2764 helix: 1.81 (0.14), residues: 1344 sheet: -2.28 (0.31), residues: 235 loop : -1.66 (0.18), residues: 1185 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 1267) hydrogen bonds : angle 5.09789 ( 3642) covalent geometry : bond 0.00277 (11230) covalent geometry : angle 0.52961 (14035) Misc. bond : bond 0.00151 ( 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 : 1.321 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0985 time to fit residues: 15.2052 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 : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 121 optimal weight: 10.0000 chunk 247 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 257 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.080279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.068813 restraints weight = 74149.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067429 restraints weight = 101766.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065832 restraints weight = 90321.555| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.5354 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= 0.387 Angle : 0.797 12.470 14035 Z= 0.513 Chirality : 0.156 0.304 8 Planarity : 0.005 0.029 2782 Dihedral : 9.075 136.586 2808 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.51 % Favored : 88.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.16), residues: 2764 helix: 0.61 (0.14), residues: 1312 sheet: -2.19 (0.34), residues: 182 loop : -2.35 (0.16), residues: 1270 Details of bonding type rmsd hydrogen bonds : bond 0.05876 ( 1267) hydrogen bonds : angle 6.64962 ( 3642) covalent geometry : bond 0.00514 (11230) covalent geometry : angle 0.79706 (14035) Misc. bond : bond 0.00418 ( 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 : 1.318 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1050 time to fit residues: 16.3978 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 : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 16 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 266 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.080001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.067629 restraints weight = 73776.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.065766 restraints weight = 108339.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065773 restraints weight = 110627.358| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 11231 Z= 0.364 Angle : 0.776 11.200 14035 Z= 0.498 Chirality : 0.168 0.250 8 Planarity : 0.005 0.026 2782 Dihedral : 9.245 156.299 2808 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.66 % Favored : 87.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.15), residues: 2764 helix: 0.26 (0.14), residues: 1309 sheet: -2.64 (0.33), residues: 187 loop : -2.62 (0.16), residues: 1268 Details of bonding type rmsd hydrogen bonds : bond 0.05668 ( 1267) hydrogen bonds : angle 6.71096 ( 3642) covalent geometry : bond 0.00484 (11230) covalent geometry : angle 0.77609 (14035) Misc. bond : bond 0.00191 ( 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 72 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.575 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1418 time to fit residues: 23.5848 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 : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 242 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 200 optimal weight: 30.0000 chunk 201 optimal weight: 50.0000 chunk 150 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.089195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.078935 restraints weight = 73689.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.077318 restraints weight = 137492.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.077383 restraints weight = 155237.842| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11231 Z= 0.239 Angle : 0.593 8.759 14035 Z= 0.373 Chirality : 0.125 0.197 8 Planarity : 0.003 0.020 2782 Dihedral : 8.554 167.302 2808 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.16), residues: 2764 helix: 0.97 (0.14), residues: 1321 sheet: -2.67 (0.33), residues: 196 loop : -2.44 (0.17), residues: 1247 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 1267) hydrogen bonds : angle 5.89258 ( 3642) covalent geometry : bond 0.00317 (11230) covalent geometry : angle 0.59346 (14035) Misc. bond : bond 0.00291 ( 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 : 1.281 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0962 time to fit residues: 15.0917 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 : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 2 optimal weight: 40.0000 chunk 142 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 202 optimal weight: 0.0050 chunk 187 optimal weight: 20.0000 chunk 267 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 overall best weight: 2.7200 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.089920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.081104 restraints weight = 73677.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.079141 restraints weight = 127455.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.078852 restraints weight = 144018.758| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5756 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 11231 Z= 0.176 Angle : 0.489 8.159 14035 Z= 0.303 Chirality : 0.117 0.187 8 Planarity : 0.003 0.019 2782 Dihedral : 7.579 128.077 2808 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2764 helix: 1.64 (0.14), residues: 1331 sheet: -2.77 (0.32), residues: 216 loop : -2.25 (0.17), residues: 1217 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 1267) hydrogen bonds : angle 5.22643 ( 3642) covalent geometry : bond 0.00232 (11230) covalent geometry : angle 0.48939 (14035) Misc. bond : bond 0.00308 ( 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 71 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.351 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0947 time to fit residues: 14.8215 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 : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 178 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 2 optimal weight: 40.0000 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.080515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.067828 restraints weight = 72889.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.066798 restraints weight = 100107.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.066655 restraints weight = 90450.271| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 11231 Z= 0.279 Angle : 0.634 9.059 14035 Z= 0.403 Chirality : 0.149 0.223 8 Planarity : 0.004 0.020 2782 Dihedral : 8.118 129.161 2808 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.16), residues: 2764 helix: 1.15 (0.14), residues: 1338 sheet: -2.45 (0.35), residues: 179 loop : -2.55 (0.17), residues: 1247 Details of bonding type rmsd hydrogen bonds : bond 0.04838 ( 1267) hydrogen bonds : angle 5.99397 ( 3642) covalent geometry : bond 0.00370 (11230) covalent geometry : angle 0.63354 (14035) Misc. bond : bond 0.00385 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4665.55 seconds wall clock time: 84 minutes 21.62 seconds (5061.62 seconds total)