Starting phenix.real_space_refine on Sun Jul 5 02:15:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rxa_54363/07_2026/9rxa_54363.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rxa_54363/07_2026/9rxa_54363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rxa_54363/07_2026/9rxa_54363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rxa_54363/07_2026/9rxa_54363.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rxa_54363/07_2026/9rxa_54363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rxa_54363/07_2026/9rxa_54363.map" } resolution = 4.0 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 5 5.49 5 Mg 2 5.21 5 S 119 5.16 5 C 15294 2.51 5 N 4148 2.21 5 O 4486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24055 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6562 Classifications: {'peptide': 810} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 38, 'TRANS': 768} Chain breaks: 2 Chain: "B" Number of atoms: 9518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1197, 9518 Classifications: {'peptide': 1197} Link IDs: {'CIS': 6, 'PCIS': 4, 'PTRANS': 52, 'TRANS': 1134} Chain breaks: 5 Chain: "C" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3120 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 370} Chain breaks: 2 Chain: "D" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3456 Classifications: {'peptide': 423} Link IDs: {'CIS': 3, 'PTRANS': 12, 'TRANS': 407} Chain breaks: 1 Chain: "F" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1321 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' MG': 1, 'MYR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16110 SG CYS C 18 42.489 136.041 39.685 1.00188.41 S ATOM 16136 SG CYS C 21 40.759 134.657 42.123 1.00182.67 S ATOM 16607 SG CYS C 137 38.657 138.008 41.312 1.00218.89 S ATOM 16631 SG CYS C 140 40.700 137.931 42.697 1.00228.79 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="MG MG F 300 " occ=0.68 residue: pdb=" C1' GTP F 301 " occ=0.90 ... (30 atoms not shown) pdb=" PG GTP F 301 " occ=0.90 Time building chain proxies: 4.12, per 1000 atoms: 0.17 Number of scatterers: 24055 At special positions: 0 Unit cell: (107.31, 181.77, 244.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 119 16.00 P 5 15.00 Mg 2 11.99 O 4486 8.00 N 4148 7.00 C 15294 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: 1.65 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 140 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 18 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 21 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 137 " Number of angles added : 6 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5666 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 25 sheets defined 48.5% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 4.061A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.592A pdb=" N PHE A 46 " --> pdb=" O MET A 43 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 184 Processing helix chain 'A' and resid 190 through 212 removed outlier: 4.569A pdb=" N LEU A 196 " --> pdb=" O TRP A 192 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N MET A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.528A pdb=" N ARG A 275 " --> pdb=" O HIS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 286 removed outlier: 4.297A pdb=" N HIS A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.668A pdb=" N THR A 324 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 335 removed outlier: 4.018A pdb=" N LYS A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 351 Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.610A pdb=" N LEU A 364 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 365 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.830A pdb=" N ARG A 377 " --> pdb=" O ASN A 373 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 394 removed outlier: 3.638A pdb=" N MET A 394 " --> pdb=" O ASP A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.588A pdb=" N GLN A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 407 through 412 removed outlier: 4.306A pdb=" N ILE A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 486 through 501 removed outlier: 3.540A pdb=" N ALA A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU A 500 " --> pdb=" O TYR A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 510 through 530 removed outlier: 3.617A pdb=" N HIS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 562 removed outlier: 3.961A pdb=" N ARG A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 578 removed outlier: 3.907A pdb=" N GLY A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 661 removed outlier: 3.956A pdb=" N ASP A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.733A pdb=" N PHE A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 740 removed outlier: 3.620A pdb=" N GLY A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS A 733 " --> pdb=" O CYS A 729 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 735 " --> pdb=" O GLY A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 787 removed outlier: 3.805A pdb=" N MET A 787 " --> pdb=" O MET A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 810 removed outlier: 4.077A pdb=" N GLN A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 823 removed outlier: 3.609A pdb=" N ILE A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN A 818 " --> pdb=" O ASN A 814 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 822 " --> pdb=" O ASN A 818 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N MET A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 826 No H-bonds generated for 'chain 'A' and resid 824 through 826' Processing helix chain 'A' and resid 828 through 833 removed outlier: 3.813A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 847 removed outlier: 4.178A pdb=" N LYS A 845 " --> pdb=" O LYS A 841 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 847 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 869 removed outlier: 3.671A pdb=" N SER A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 64 through 78 Processing helix chain 'B' and resid 110 through 114 Processing helix chain 'B' and resid 121 through 141 removed outlier: 3.551A pdb=" N LYS B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 236 through 253 removed outlier: 4.103A pdb=" N ASP B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.506A pdb=" N LYS B 280 " --> pdb=" O VAL B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 303 through 311 removed outlier: 3.501A pdb=" N TYR B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.660A pdb=" N ARG B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 359 removed outlier: 3.964A pdb=" N HIS B 355 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 removed outlier: 4.207A pdb=" N LEU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.582A pdb=" N LYS B 395 " --> pdb=" O TYR B 391 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.642A pdb=" N ASP B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 425 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 430 through 446 removed outlier: 3.514A pdb=" N ARG B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 446 " --> pdb=" O THR B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 473 removed outlier: 3.589A pdb=" N ALA B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 472 " --> pdb=" O HIS B 469 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 473 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.828A pdb=" N ARG B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 506 removed outlier: 3.928A pdb=" N LEU B 489 " --> pdb=" O ASN B 485 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.851A pdb=" N ASP B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 removed outlier: 4.296A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 removed outlier: 4.086A pdb=" N LEU B 564 " --> pdb=" O GLY B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 577 removed outlier: 3.512A pdb=" N ASN B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 removed outlier: 3.683A pdb=" N ASP B 587 " --> pdb=" O PHE B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 600 Processing helix chain 'B' and resid 600 through 609 removed outlier: 4.348A pdb=" N VAL B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 624 removed outlier: 3.613A pdb=" N LYS B 617 " --> pdb=" O SER B 613 " (cutoff:3.500A) Proline residue: B 618 - end of helix Processing helix chain 'B' and resid 628 through 645 removed outlier: 3.920A pdb=" N ILE B 632 " --> pdb=" O GLU B 628 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 661 removed outlier: 3.662A pdb=" N ASP B 659 " --> pdb=" O GLU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.654A pdb=" N CYS B 665 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 666 " --> pdb=" O PHE B 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 662 through 666' Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.819A pdb=" N GLY B 674 " --> pdb=" O TRP B 670 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 676 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY B 677 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 681 " --> pdb=" O GLY B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 694 removed outlier: 3.889A pdb=" N TYR B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 699 removed outlier: 3.981A pdb=" N TYR B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 694 through 699' Processing helix chain 'B' and resid 716 through 720 removed outlier: 3.543A pdb=" N VAL B 719 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 720 " --> pdb=" O LEU B 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 716 through 720' Processing helix chain 'B' and resid 725 through 733 removed outlier: 3.554A pdb=" N TYR B 731 " --> pdb=" O SER B 727 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 733 " --> pdb=" O PHE B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 753 Processing helix chain 'B' and resid 764 through 777 removed outlier: 3.504A pdb=" N ALA B 768 " --> pdb=" O ASP B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 790 Processing helix chain 'B' and resid 790 through 809 removed outlier: 3.528A pdb=" N GLN B 807 " --> pdb=" O ASN B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 813 removed outlier: 3.742A pdb=" N SER B 813 " --> pdb=" O LEU B 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 810 through 813' Processing helix chain 'B' and resid 821 through 825 Processing helix chain 'B' and resid 940 through 966 removed outlier: 3.630A pdb=" N GLN B 945 " --> pdb=" O LYS B 941 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 966 " --> pdb=" O LYS B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1025 removed outlier: 3.904A pdb=" N LYS B1024 " --> pdb=" O ASN B1021 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET B1025 " --> pdb=" O SER B1022 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1021 through 1025' Processing helix chain 'B' and resid 1138 through 1142 removed outlier: 3.569A pdb=" N SER B1141 " --> pdb=" O ASP B1138 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B1142 " --> pdb=" O LEU B1139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1138 through 1142' Processing helix chain 'B' and resid 1272 through 1276 Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.722A pdb=" N LYS C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 Processing helix chain 'C' and resid 111 through 128 Processing helix chain 'C' and resid 137 through 170 removed outlier: 3.898A pdb=" N ASP C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 265 removed outlier: 3.699A pdb=" N GLN C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N MET C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 218 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 219 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARG C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 303 removed outlier: 3.573A pdb=" N GLU C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE C 303 " --> pdb=" O TRP C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 299 through 303' Processing helix chain 'C' and resid 306 through 311 removed outlier: 3.765A pdb=" N VAL C 311 " --> pdb=" O TRP C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 322 removed outlier: 4.109A pdb=" N ALA C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS C 320 " --> pdb=" O ALA C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 355 through 362 removed outlier: 3.510A pdb=" N PHE C 359 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE C 360 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP C 362 " --> pdb=" O PHE C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.782A pdb=" N VAL C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 371 " --> pdb=" O HIS C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'C' and resid 375 through 381 removed outlier: 4.120A pdb=" N PHE C 379 " --> pdb=" O CYS C 375 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 381 " --> pdb=" O GLN C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 426 removed outlier: 3.659A pdb=" N TRP C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 426 " --> pdb=" O GLU C 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 421 through 426' Processing helix chain 'C' and resid 429 through 439 removed outlier: 4.589A pdb=" N LEU C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 434 " --> pdb=" O LYS C 430 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY C 439 " --> pdb=" O ASN C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 removed outlier: 3.605A pdb=" N ASN C 449 " --> pdb=" O GLN C 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 45 removed outlier: 3.626A pdb=" N HIS D 44 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 192 through 226 removed outlier: 3.638A pdb=" N ARG D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 289 removed outlier: 3.878A pdb=" N LYS D 243 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 247 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN D 287 " --> pdb=" O HIS D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 324 removed outlier: 4.173A pdb=" N LEU D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 324 " --> pdb=" O GLN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 328 Processing helix chain 'D' and resid 359 through 364 removed outlier: 3.706A pdb=" N ALA D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 378 removed outlier: 3.868A pdb=" N ALA D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.658A pdb=" N THR D 404 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 433 Processing helix chain 'D' and resid 434 through 440 removed outlier: 3.707A pdb=" N TYR D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.839A pdb=" N LYS D 455 " --> pdb=" O PRO D 452 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D 456 " --> pdb=" O ASN D 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 79 through 84 removed outlier: 5.643A pdb=" N SER F 84 " --> pdb=" O ARG F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 90 removed outlier: 3.539A pdb=" N TYR F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 122 removed outlier: 3.560A pdb=" N PHE F 108 " --> pdb=" O ASN F 104 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 141 removed outlier: 4.694A pdb=" N ASN F 139 " --> pdb=" O ASP F 136 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG F 141 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 155 removed outlier: 3.718A pdb=" N ALA F 148 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN F 155 " --> pdb=" O TYR F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 181 Processing sheet with id=AA1, first strand: chain 'B' and resid 818 through 820 removed outlier: 4.826A pdb=" N VAL A 224 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N LYS A 6 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N GLY A 232 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N HIS A 8 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 9 " --> pdb=" O ARG B 829 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 removed outlier: 6.564A pdb=" N VAL A 106 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR A 126 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 108 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLY A 124 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 110 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N THR A 126 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS A 144 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 10.409A pdb=" N SER A 128 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 12.124A pdb=" N ASP A 142 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET A 215 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR A 216 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU A 26 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET A 218 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL A 19 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 21 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 89 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER A 25 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP A 87 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA5, first strand: chain 'A' and resid 591 through 592 removed outlier: 3.993A pdb=" N GLY A 680 " --> pdb=" O LYS A 636 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 673 " --> pdb=" O PHE A 681 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 688 through 689 Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 34 removed outlier: 6.209A pdb=" N TYR B 28 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LYS B 44 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS B 30 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA B 98 " --> pdb=" O LYS B 93 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS B 93 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 102 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS B 89 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.544A pdb=" N ASP B 108 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 176 removed outlier: 5.842A pdb=" N LEU B 175 " --> pdb=" O VAL B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 999 through 1001 removed outlier: 3.512A pdb=" N TYR B1038 " --> pdb=" O VAL B1017 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B1036 " --> pdb=" O ILE B1019 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1045 through 1050 removed outlier: 3.766A pdb=" N SER B1061 " --> pdb=" O ALA B1065 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA B1065 " --> pdb=" O SER B1061 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1097 through 1103 removed outlier: 3.687A pdb=" N ASP B1100 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B1122 " --> pdb=" O TYR B1114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B1116 " --> pdb=" O SER B1120 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER B1120 " --> pdb=" O THR B1116 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP B1133 " --> pdb=" O GLY B1123 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASP B1125 " --> pdb=" O ASN B1131 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASN B1131 " --> pdb=" O ASP B1125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1144 through 1146 removed outlier: 7.153A pdb=" N GLY B1159 " --> pdb=" O THR B1145 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR B1164 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B1177 " --> pdb=" O CYS B1167 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP B1169 " --> pdb=" O PRO B1175 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1191 through 1192 removed outlier: 5.721A pdb=" N ASP B1214 " --> pdb=" O ARG B1220 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG B1220 " --> pdb=" O ASP B1214 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B1299 " --> pdb=" O ARG B1221 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1242 through 1247 removed outlier: 4.233A pdb=" N GLY B1244 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B1259 " --> pdb=" O GLY B1244 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU B1256 " --> pdb=" O TRP B1268 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR B1258 " --> pdb=" O ARG B1266 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG B1266 " --> pdb=" O THR B1258 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLY B1260 " --> pdb=" O LYS B1264 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LYS B1264 " --> pdb=" O GLY B1260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1332 through 1339 removed outlier: 3.500A pdb=" N ILE B1345 " --> pdb=" O TRP B1357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 16 through 17 Processing sheet with id=AB9, first strand: chain 'C' and resid 276 through 279 Processing sheet with id=AC1, first strand: chain 'C' and resid 328 through 331 Processing sheet with id=AC2, first strand: chain 'C' and resid 394 through 397 Processing sheet with id=AC3, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.858A pdb=" N TYR D 161 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 86 through 87 removed outlier: 6.813A pdb=" N PHE D 113 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LYS D 132 " --> pdb=" O PHE D 113 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL D 115 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLU D 130 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE D 117 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 331 through 332 Processing sheet with id=AC6, first strand: chain 'D' and resid 394 through 396 Processing sheet with id=AC7, first strand: chain 'F' and resid 56 through 63 removed outlier: 3.630A pdb=" N GLN F 60 " --> pdb=" O PHE F 71 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA F 95 " --> pdb=" O GLN F 20 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LYS F 22 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE F 97 " --> pdb=" O LYS F 22 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL F 24 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL F 99 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU F 26 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N ASP F 101 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU F 158 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY F 132 " --> pdb=" O MET F 160 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2901 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: 4.50 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7857 1.34 - 1.46: 5008 1.46 - 1.58: 11484 1.58 - 1.70: 8 1.70 - 1.82: 186 Bond restraints: 24543 Sorted by residual: bond pdb=" C ASP B 700 " pdb=" N PRO B 701 " ideal model delta sigma weight residual 1.326 1.369 -0.043 1.44e-02 4.82e+03 8.93e+00 bond pdb=" N ASN B 457 " pdb=" CA ASN B 457 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.90e-02 2.77e+03 4.87e+00 bond pdb=" N ASN A 264 " pdb=" CA ASN A 264 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 4.02e+00 bond pdb=" C PHE B 273 " pdb=" N PRO B 274 " ideal model delta sigma weight residual 1.338 1.374 -0.036 1.90e-02 2.77e+03 3.64e+00 bond pdb=" C GLU A 263 " pdb=" N ASN A 264 " ideal model delta sigma weight residual 1.329 1.356 -0.027 1.40e-02 5.10e+03 3.62e+00 ... (remaining 24538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 32819 2.73 - 5.46: 293 5.46 - 8.19: 49 8.19 - 10.92: 10 10.92 - 13.65: 5 Bond angle restraints: 33176 Sorted by residual: angle pdb=" C HIS A 141 " pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 121.70 135.29 -13.59 1.80e+00 3.09e-01 5.70e+01 angle pdb=" C ILE B 456 " pdb=" N ASN B 457 " pdb=" CA ASN B 457 " ideal model delta sigma weight residual 121.70 135.07 -13.37 1.80e+00 3.09e-01 5.52e+01 angle pdb=" C GLU A 263 " pdb=" N ASN A 264 " pdb=" CA ASN A 264 " ideal model delta sigma weight residual 121.70 134.73 -13.03 1.80e+00 3.09e-01 5.24e+01 angle pdb=" C SER B 142 " pdb=" N GLY B 143 " pdb=" CA GLY B 143 " ideal model delta sigma weight residual 121.70 132.59 -10.89 1.80e+00 3.09e-01 3.66e+01 angle pdb=" CA TYR A 803 " pdb=" CB TYR A 803 " pdb=" CG TYR A 803 " ideal model delta sigma weight residual 113.90 122.34 -8.44 1.80e+00 3.09e-01 2.20e+01 ... (remaining 33171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.45: 14481 30.45 - 60.90: 378 60.90 - 91.35: 65 91.35 - 121.81: 1 121.81 - 152.26: 3 Dihedral angle restraints: 14928 sinusoidal: 6196 harmonic: 8732 Sorted by residual: dihedral pdb=" CA GLU A 263 " pdb=" C GLU A 263 " pdb=" N ASN A 264 " pdb=" CA ASN A 264 " ideal model delta harmonic sigma weight residual 0.00 38.60 -38.60 0 5.00e+00 4.00e-02 5.96e+01 dihedral pdb=" C8 GTP F 301 " pdb=" C1' GTP F 301 " pdb=" N9 GTP F 301 " pdb=" O4' GTP F 301 " ideal model delta sinusoidal sigma weight residual 104.59 -47.66 152.26 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" O2B GDP B1401 " pdb=" O3A GDP B1401 " pdb=" PB GDP B1401 " pdb=" PA GDP B1401 " ideal model delta sinusoidal sigma weight residual 180.00 43.44 136.56 1 2.00e+01 2.50e-03 4.14e+01 ... (remaining 14925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2968 0.053 - 0.106: 574 0.106 - 0.159: 132 0.159 - 0.212: 11 0.212 - 0.265: 2 Chirality restraints: 3687 Sorted by residual: chirality pdb=" CB ILE B 23 " pdb=" CA ILE B 23 " pdb=" CG1 ILE B 23 " pdb=" CG2 ILE B 23 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB THR B1049 " pdb=" CA THR B1049 " pdb=" OG1 THR B1049 " pdb=" CG2 THR B1049 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL B1098 " pdb=" N VAL B1098 " pdb=" C VAL B1098 " pdb=" CB VAL B1098 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.86e-01 ... (remaining 3684 not shown) Planarity restraints: 4248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 650 " 0.059 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO B 651 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 651 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 651 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 666 " -0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO B 667 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 667 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 667 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 179 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO B 180 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 180 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 180 " 0.037 5.00e-02 4.00e+02 ... (remaining 4245 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 232 2.64 - 3.21: 19650 3.21 - 3.77: 35272 3.77 - 4.34: 46629 4.34 - 4.90: 77019 Nonbonded interactions: 178802 Sorted by model distance: nonbonded pdb="MG MG F 300 " pdb=" O2A GTP F 301 " model vdw 2.076 2.170 nonbonded pdb="MG MG F 300 " pdb=" O1G GTP F 301 " model vdw 2.092 2.170 nonbonded pdb="MG MG F 300 " pdb=" O3G GTP F 301 " model vdw 2.115 2.170 nonbonded pdb=" O3A GDP B1401 " pdb="MG MG B1402 " model vdw 2.225 2.170 nonbonded pdb=" OG1 THR B 157 " pdb=" O TRP B 159 " model vdw 2.284 3.040 ... (remaining 178797 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=0.68 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: 6.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.800 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 : 0.003 0.083 24548 Z= 0.189 Angle : 0.859 45.228 33182 Z= 0.447 Chirality : 0.045 0.265 3687 Planarity : 0.006 0.088 4248 Dihedral : 14.627 152.258 9262 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.12 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.35 % 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 are not related in a simple way. whole: -1.50 (0.14), residues: 2947 helix: -1.01 (0.13), residues: 1222 sheet: -0.26 (0.28), residues: 335 loop : -1.05 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 210 TYR 0.036 0.002 TYR A 803 PHE 0.022 0.002 PHE D 113 TRP 0.025 0.001 TRP B 159 HIS 0.005 0.001 HIS B1103 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.18 (24543) covalent geometry : angle 0.76646 / 0.44 (33176) hydrogen bonds : bond 0.20695 / 12.86 ( 1018) hydrogen bonds : angle 6.54778 / 4.46 ( 2901) metal coordination : bond 0.05104 / 2.27 ( 4) metal coordination : angle 28.79290 / 17.12 ( 6) Misc. bond : bond 0.08256 / 4.35 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.8984 (tp) cc_final: 0.8530 (tp) REVERT: A 16 ASP cc_start: 0.9002 (t0) cc_final: 0.8544 (p0) REVERT: A 29 LYS cc_start: 0.9040 (mttt) cc_final: 0.8771 (ttmm) REVERT: A 33 LYS cc_start: 0.9335 (mmtt) cc_final: 0.9029 (mmmm) REVERT: A 39 LEU cc_start: 0.8929 (tp) cc_final: 0.8712 (mm) REVERT: A 191 ASP cc_start: 0.8870 (p0) cc_final: 0.8623 (p0) REVERT: A 267 GLU cc_start: 0.8464 (tp30) cc_final: 0.7960 (tm-30) REVERT: A 296 LEU cc_start: 0.9544 (mt) cc_final: 0.9248 (mp) REVERT: A 313 GLN cc_start: 0.8868 (mt0) cc_final: 0.8498 (mm-40) REVERT: A 358 MET cc_start: 0.8078 (mtt) cc_final: 0.7865 (mtm) REVERT: A 394 MET cc_start: 0.8715 (mmp) cc_final: 0.8038 (mmt) REVERT: A 396 LEU cc_start: 0.9166 (mt) cc_final: 0.8857 (mt) REVERT: A 401 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8294 (mm-40) REVERT: A 475 LEU cc_start: 0.9129 (mt) cc_final: 0.8893 (tt) REVERT: A 479 LEU cc_start: 0.9236 (mt) cc_final: 0.8775 (pp) REVERT: A 491 ASN cc_start: 0.9110 (m-40) cc_final: 0.8784 (t0) REVERT: A 494 TYR cc_start: 0.8950 (t80) cc_final: 0.8208 (t80) REVERT: A 495 TRP cc_start: 0.8761 (m100) cc_final: 0.8281 (m100) REVERT: A 496 TYR cc_start: 0.8596 (m-10) cc_final: 0.8031 (m-10) REVERT: A 523 ARG cc_start: 0.8652 (mtp180) cc_final: 0.8306 (mmt180) REVERT: A 538 MET cc_start: 0.8975 (mtm) cc_final: 0.8520 (mpp) REVERT: A 551 ARG cc_start: 0.9190 (mtt180) cc_final: 0.8852 (mtp180) REVERT: A 648 LEU cc_start: 0.9291 (mt) cc_final: 0.8960 (pp) REVERT: A 649 GLN cc_start: 0.8996 (tp40) cc_final: 0.8568 (tp-100) REVERT: A 650 ILE cc_start: 0.9355 (tp) cc_final: 0.9116 (pt) REVERT: A 653 LEU cc_start: 0.9644 (tp) cc_final: 0.9422 (pp) REVERT: A 654 MET cc_start: 0.9210 (ptp) cc_final: 0.8884 (ppp) REVERT: A 700 ILE cc_start: 0.9128 (tt) cc_final: 0.8274 (tp) REVERT: A 703 PHE cc_start: 0.8850 (t80) cc_final: 0.8336 (t80) REVERT: A 704 PHE cc_start: 0.8723 (m-10) cc_final: 0.7792 (m-80) REVERT: A 759 HIS cc_start: 0.8191 (m-70) cc_final: 0.7409 (m-70) REVERT: A 798 PHE cc_start: 0.9112 (t80) cc_final: 0.8522 (t80) REVERT: A 802 CYS cc_start: 0.8957 (m) cc_final: 0.8603 (m) REVERT: A 806 PHE cc_start: 0.9542 (t80) cc_final: 0.9119 (t80) REVERT: A 834 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8002 (mm-30) REVERT: A 854 GLU cc_start: 0.9320 (mt-10) cc_final: 0.9086 (mt-10) REVERT: A 858 TYR cc_start: 0.9423 (t80) cc_final: 0.9147 (t80) REVERT: A 859 MET cc_start: 0.9166 (ppp) cc_final: 0.8704 (ppp) REVERT: A 860 GLN cc_start: 0.9432 (mt0) cc_final: 0.9128 (mm110) REVERT: A 862 LEU cc_start: 0.9445 (mt) cc_final: 0.9031 (mt) REVERT: A 863 ILE cc_start: 0.9654 (mt) cc_final: 0.9429 (tt) REVERT: A 866 SER cc_start: 0.9364 (m) cc_final: 0.9029 (p) REVERT: B 155 MET cc_start: 0.7644 (mmm) cc_final: 0.7302 (mtp) REVERT: B 177 GLU cc_start: 0.8096 (tt0) cc_final: 0.7514 (mt-10) REVERT: B 197 ILE cc_start: 0.8337 (mt) cc_final: 0.7874 (tt) REVERT: B 328 MET cc_start: 0.8964 (mmm) cc_final: 0.8443 (mpp) REVERT: B 341 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8545 (mp0) REVERT: B 383 THR cc_start: 0.8181 (m) cc_final: 0.7912 (m) REVERT: B 503 LYS cc_start: 0.9239 (mttm) cc_final: 0.9026 (tppt) REVERT: B 587 ASP cc_start: 0.8720 (t0) cc_final: 0.8414 (t0) REVERT: B 615 ILE cc_start: 0.9467 (mt) cc_final: 0.9255 (tp) REVERT: B 703 ILE cc_start: 0.9086 (mm) cc_final: 0.8829 (pt) REVERT: B 720 LEU cc_start: 0.9516 (mt) cc_final: 0.9294 (mp) REVERT: B 730 ASP cc_start: 0.8979 (m-30) cc_final: 0.8773 (p0) REVERT: B 779 MET cc_start: 0.7890 (tmm) cc_final: 0.7678 (tmm) REVERT: B 801 LYS cc_start: 0.9140 (tmmt) cc_final: 0.8906 (tppt) REVERT: B 944 LEU cc_start: 0.9217 (mt) cc_final: 0.8900 (tp) REVERT: B 1025 MET cc_start: 0.1753 (mtp) cc_final: 0.1006 (tpt) REVERT: B 1100 ASP cc_start: 0.8170 (t0) cc_final: 0.7822 (t0) REVERT: B 1139 LEU cc_start: 0.9155 (mt) cc_final: 0.8537 (tp) REVERT: B 1210 VAL cc_start: 0.8533 (t) cc_final: 0.8188 (t) REVERT: B 1268 TRP cc_start: 0.8355 (m100) cc_final: 0.7903 (m100) REVERT: C 126 MET cc_start: 0.9011 (mtm) cc_final: 0.8730 (mtp) REVERT: C 162 TYR cc_start: 0.9221 (m-10) cc_final: 0.8777 (m-10) REVERT: C 240 GLN cc_start: 0.9388 (tt0) cc_final: 0.9155 (tm-30) REVERT: D 80 PHE cc_start: 0.8060 (t80) cc_final: 0.7147 (t80) REVERT: D 115 VAL cc_start: 0.9206 (t) cc_final: 0.8856 (m) REVERT: D 191 TYR cc_start: 0.8164 (t80) cc_final: 0.7897 (t80) REVERT: D 240 LEU cc_start: 0.9487 (mp) cc_final: 0.9201 (tp) REVERT: F 21 PHE cc_start: 0.7907 (m-80) cc_final: 0.7455 (m-10) REVERT: F 70 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8766 (tppt) REVERT: F 82 TYR cc_start: 0.8174 (m-80) cc_final: 0.7774 (m-10) REVERT: F 94 GLN cc_start: 0.8810 (mt0) cc_final: 0.8509 (mt0) REVERT: F 100 TYR cc_start: 0.8580 (p90) cc_final: 0.8285 (p90) REVERT: F 101 ASP cc_start: 0.8733 (t0) cc_final: 0.8337 (t0) REVERT: F 106 GLU cc_start: 0.9321 (mp0) cc_final: 0.8512 (mp0) REVERT: F 149 GLN cc_start: 0.9087 (tp40) cc_final: 0.8808 (tp-100) REVERT: F 153 ASP cc_start: 0.8960 (m-30) cc_final: 0.8672 (p0) REVERT: F 159 PHE cc_start: 0.8161 (t80) cc_final: 0.7023 (t80) outliers start: 0 outliers final: 0 residues processed: 559 average time/residue: 0.1822 time to fit residues: 150.1924 Evaluate side-chains 395 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS A 794 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 140 HIS B 457 ASN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1197 GLN ** B1302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 HIS F 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.116762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083809 restraints weight = 107607.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.085911 restraints weight = 55216.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.087290 restraints weight = 35704.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.088142 restraints weight = 26740.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.088752 restraints weight = 22126.416| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (14 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24548 Z= 0.136 Angle : 0.669 13.807 33182 Z= 0.337 Chirality : 0.043 0.230 3687 Planarity : 0.005 0.071 4248 Dihedral : 7.267 149.814 3260 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.46 % Favored : 96.47 % Rotamer: Outliers : 1.58 % Allowed : 11.40 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.15), residues: 2947 helix: 0.44 (0.14), residues: 1235 sheet: -0.13 (0.28), residues: 346 loop : -0.76 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 752 TYR 0.029 0.002 TYR A 803 PHE 0.030 0.001 PHE B 567 TRP 0.022 0.001 TRP B1213 HIS 0.009 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (24543) covalent geometry : angle 0.65839 / 0.34 (33176) hydrogen bonds : bond 0.04539 / 2.89 ( 1018) hydrogen bonds : angle 4.65298 / 3.16 ( 2901) metal coordination : bond 0.00895 / 0.44 ( 4) metal coordination : angle 9.00926 / 5.37 ( 6) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 419 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.8980 (tp) cc_final: 0.8621 (tp) REVERT: A 16 ASP cc_start: 0.8621 (t0) cc_final: 0.8204 (p0) REVERT: A 191 ASP cc_start: 0.8438 (p0) cc_final: 0.8201 (p0) REVERT: A 312 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8419 (mt-10) REVERT: A 335 LYS cc_start: 0.9495 (mttt) cc_final: 0.9279 (mtpt) REVERT: A 344 GLU cc_start: 0.7698 (tt0) cc_final: 0.7453 (tt0) REVERT: A 358 MET cc_start: 0.7480 (mtt) cc_final: 0.7178 (mtm) REVERT: A 372 THR cc_start: 0.8690 (p) cc_final: 0.8429 (t) REVERT: A 394 MET cc_start: 0.8696 (mmp) cc_final: 0.8005 (mmt) REVERT: A 396 LEU cc_start: 0.9066 (mt) cc_final: 0.8770 (mt) REVERT: A 401 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8456 (mm-40) REVERT: A 479 LEU cc_start: 0.9211 (mt) cc_final: 0.8765 (pp) REVERT: A 491 ASN cc_start: 0.8820 (m-40) cc_final: 0.8583 (t0) REVERT: A 523 ARG cc_start: 0.8683 (mtp180) cc_final: 0.8327 (mmt180) REVERT: A 538 MET cc_start: 0.8968 (mtm) cc_final: 0.8461 (mpp) REVERT: A 551 ARG cc_start: 0.9210 (mtt180) cc_final: 0.8960 (mtp180) REVERT: A 648 LEU cc_start: 0.9389 (mt) cc_final: 0.9033 (pp) REVERT: A 649 GLN cc_start: 0.8935 (tp40) cc_final: 0.8618 (tp-100) REVERT: A 650 ILE cc_start: 0.9394 (tp) cc_final: 0.9141 (pt) REVERT: A 700 ILE cc_start: 0.8978 (tt) cc_final: 0.8136 (tp) REVERT: A 703 PHE cc_start: 0.8392 (t80) cc_final: 0.8048 (t80) REVERT: A 704 PHE cc_start: 0.8479 (m-10) cc_final: 0.7680 (m-80) REVERT: A 722 MET cc_start: 0.8693 (ptp) cc_final: 0.8352 (ptp) REVERT: A 783 MET cc_start: 0.8348 (tpp) cc_final: 0.7770 (mmm) REVERT: A 795 TYR cc_start: 0.9172 (t80) cc_final: 0.8960 (t80) REVERT: A 798 PHE cc_start: 0.8857 (t80) cc_final: 0.8445 (t80) REVERT: A 802 CYS cc_start: 0.8681 (m) cc_final: 0.8368 (m) REVERT: A 806 PHE cc_start: 0.9470 (t80) cc_final: 0.9136 (t80) REVERT: A 834 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7656 (mm-30) REVERT: A 836 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7077 (p0) REVERT: A 854 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8817 (mt-10) REVERT: A 858 TYR cc_start: 0.9196 (t80) cc_final: 0.8910 (t80) REVERT: A 859 MET cc_start: 0.9152 (ppp) cc_final: 0.8550 (ppp) REVERT: A 860 GLN cc_start: 0.9241 (mt0) cc_final: 0.8962 (mm110) REVERT: A 863 ILE cc_start: 0.9593 (mt) cc_final: 0.9328 (mt) REVERT: B 58 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7720 (mm-40) REVERT: B 155 MET cc_start: 0.7884 (mmm) cc_final: 0.7418 (mtp) REVERT: B 162 VAL cc_start: 0.8948 (t) cc_final: 0.8554 (p) REVERT: B 383 THR cc_start: 0.8646 (m) cc_final: 0.8364 (m) REVERT: B 393 ASP cc_start: 0.8617 (m-30) cc_final: 0.8340 (m-30) REVERT: B 696 MET cc_start: 0.8801 (tpp) cc_final: 0.8390 (tpp) REVERT: B 703 ILE cc_start: 0.9016 (mm) cc_final: 0.8812 (pt) REVERT: B 720 LEU cc_start: 0.9500 (mt) cc_final: 0.9287 (mp) REVERT: B 801 LYS cc_start: 0.9122 (tmmt) cc_final: 0.8856 (tppt) REVERT: B 951 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8136 (pttm) REVERT: B 1044 ARG cc_start: 0.8840 (mmp80) cc_final: 0.8514 (mmp80) REVERT: B 1100 ASP cc_start: 0.7511 (t0) cc_final: 0.7137 (t0) REVERT: B 1139 LEU cc_start: 0.9169 (mt) cc_final: 0.8549 (tp) REVERT: B 1156 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8806 (tp) REVERT: B 1213 TRP cc_start: 0.7135 (m100) cc_final: 0.6587 (m100) REVERT: B 1257 LEU cc_start: 0.8253 (tp) cc_final: 0.8009 (tp) REVERT: B 1268 TRP cc_start: 0.8278 (m100) cc_final: 0.7885 (m100) REVERT: C 125 ILE cc_start: 0.9228 (tt) cc_final: 0.8996 (pt) REVERT: C 126 MET cc_start: 0.8540 (mtm) cc_final: 0.7916 (mmt) REVERT: C 158 GLU cc_start: 0.8738 (tp30) cc_final: 0.8476 (tp30) REVERT: C 161 ASN cc_start: 0.9193 (m-40) cc_final: 0.8976 (m110) REVERT: C 195 ILE cc_start: 0.9233 (mm) cc_final: 0.9014 (pt) REVERT: D 115 VAL cc_start: 0.9076 (t) cc_final: 0.8870 (m) REVERT: F 101 ASP cc_start: 0.8193 (t0) cc_final: 0.7811 (t0) REVERT: F 149 GLN cc_start: 0.8636 (tp40) cc_final: 0.8027 (tp-100) REVERT: F 153 ASP cc_start: 0.8700 (m-30) cc_final: 0.8134 (m-30) REVERT: F 171 ASN cc_start: 0.8904 (t0) cc_final: 0.8516 (t0) REVERT: F 175 MET cc_start: 0.8616 (ptt) cc_final: 0.8140 (ptt) outliers start: 42 outliers final: 19 residues processed: 443 average time/residue: 0.1568 time to fit residues: 105.1140 Evaluate side-chains 370 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 348 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 951 LYS Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1197 GLN Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 167 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 256 optimal weight: 10.0000 chunk 23 optimal weight: 0.0980 chunk 204 optimal weight: 9.9990 chunk 277 optimal weight: 0.0030 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 266 optimal weight: 9.9990 chunk 152 optimal weight: 0.9990 overall best weight: 1.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 GLN ** B1137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1179 HIS ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1253 ASN C 23 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.122644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.090166 restraints weight = 133808.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.090346 restraints weight = 78173.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.090502 restraints weight = 53795.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.090376 restraints weight = 41199.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.090445 restraints weight = 38149.075| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24548 Z= 0.150 Angle : 0.661 13.785 33182 Z= 0.329 Chirality : 0.043 0.200 3687 Planarity : 0.004 0.067 4248 Dihedral : 7.166 148.357 3260 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.27 % Rotamer: Outliers : 1.70 % Allowed : 13.47 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.35 % 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 are not related in a simple way. whole: 0.10 (0.15), residues: 2947 helix: 0.92 (0.15), residues: 1242 sheet: -0.01 (0.28), residues: 340 loop : -0.65 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 572 TYR 0.021 0.001 TYR A 803 PHE 0.023 0.001 PHE F 145 TRP 0.018 0.002 TRP A 355 HIS 0.007 0.001 HIS B 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (24543) covalent geometry : angle 0.65157 / 0.33 (33176) hydrogen bonds : bond 0.04216 / 2.71 ( 1018) hydrogen bonds : angle 4.45465 / 3.05 ( 2901) metal coordination : bond 0.00805 / 0.40 ( 4) metal coordination : angle 8.23535 / 4.88 ( 6) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 363 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.8977 (tp) cc_final: 0.8670 (tp) REVERT: A 16 ASP cc_start: 0.8500 (t0) cc_final: 0.8176 (p0) REVERT: A 344 GLU cc_start: 0.7705 (tt0) cc_final: 0.7456 (tt0) REVERT: A 372 THR cc_start: 0.8634 (p) cc_final: 0.8360 (t) REVERT: A 396 LEU cc_start: 0.9058 (mt) cc_final: 0.8723 (mt) REVERT: A 401 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8494 (mm-40) REVERT: A 479 LEU cc_start: 0.9184 (mt) cc_final: 0.8810 (pp) REVERT: A 491 ASN cc_start: 0.9030 (m-40) cc_final: 0.8502 (t0) REVERT: A 495 TRP cc_start: 0.8854 (m100) cc_final: 0.8186 (m100) REVERT: A 523 ARG cc_start: 0.8705 (mtp180) cc_final: 0.8293 (mmt180) REVERT: A 538 MET cc_start: 0.8998 (mtm) cc_final: 0.8573 (mpp) REVERT: A 648 LEU cc_start: 0.9422 (mt) cc_final: 0.9070 (pp) REVERT: A 653 LEU cc_start: 0.9585 (pp) cc_final: 0.9353 (pp) REVERT: A 700 ILE cc_start: 0.9029 (tt) cc_final: 0.8312 (tp) REVERT: A 703 PHE cc_start: 0.8989 (t80) cc_final: 0.8529 (t80) REVERT: A 704 PHE cc_start: 0.8914 (m-10) cc_final: 0.8162 (m-80) REVERT: A 722 MET cc_start: 0.8726 (ptp) cc_final: 0.8379 (ptp) REVERT: A 759 HIS cc_start: 0.8241 (m-70) cc_final: 0.7831 (m-70) REVERT: A 783 MET cc_start: 0.8471 (tpp) cc_final: 0.7929 (mmm) REVERT: A 798 PHE cc_start: 0.9034 (t80) cc_final: 0.8474 (t80) REVERT: A 802 CYS cc_start: 0.8705 (m) cc_final: 0.8418 (m) REVERT: A 806 PHE cc_start: 0.9479 (t80) cc_final: 0.9107 (t80) REVERT: A 834 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7789 (mm-30) REVERT: A 840 LYS cc_start: 0.9299 (ttpt) cc_final: 0.9037 (tppt) REVERT: A 859 MET cc_start: 0.9226 (ppp) cc_final: 0.8677 (ppp) REVERT: A 860 GLN cc_start: 0.9334 (mt0) cc_final: 0.8978 (mm110) REVERT: B 58 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7770 (mm-40) REVERT: B 162 VAL cc_start: 0.8971 (t) cc_final: 0.8604 (p) REVERT: B 383 THR cc_start: 0.8704 (m) cc_final: 0.8391 (m) REVERT: B 393 ASP cc_start: 0.8583 (m-30) cc_final: 0.8360 (m-30) REVERT: B 587 ASP cc_start: 0.8450 (t0) cc_final: 0.8143 (t0) REVERT: B 696 MET cc_start: 0.8747 (tpp) cc_final: 0.8453 (tpp) REVERT: B 703 ILE cc_start: 0.9032 (mm) cc_final: 0.8830 (pt) REVERT: B 756 LEU cc_start: 0.8966 (mm) cc_final: 0.8734 (pp) REVERT: B 801 LYS cc_start: 0.9119 (tmmt) cc_final: 0.8797 (tppt) REVERT: B 944 LEU cc_start: 0.8887 (tp) cc_final: 0.8596 (tp) REVERT: B 959 ARG cc_start: 0.8964 (mtt-85) cc_final: 0.8715 (mtm-85) REVERT: B 1011 CYS cc_start: 0.4791 (OUTLIER) cc_final: 0.4580 (t) REVERT: B 1100 ASP cc_start: 0.7812 (t0) cc_final: 0.7516 (t0) REVERT: B 1112 LEU cc_start: 0.9045 (mp) cc_final: 0.8841 (mm) REVERT: B 1213 TRP cc_start: 0.7224 (m100) cc_final: 0.6883 (m100) REVERT: B 1257 LEU cc_start: 0.8566 (tp) cc_final: 0.8359 (tp) REVERT: B 1268 TRP cc_start: 0.8194 (m100) cc_final: 0.7837 (m100) REVERT: C 158 GLU cc_start: 0.8789 (tp30) cc_final: 0.8424 (tp30) REVERT: D 115 VAL cc_start: 0.9101 (t) cc_final: 0.8890 (m) REVERT: D 162 TYR cc_start: 0.8593 (m-80) cc_final: 0.8253 (m-10) REVERT: D 240 LEU cc_start: 0.9280 (tp) cc_final: 0.8984 (tp) REVERT: F 70 LYS cc_start: 0.8271 (mmmt) cc_final: 0.7905 (tppt) REVERT: F 101 ASP cc_start: 0.8307 (t0) cc_final: 0.8007 (t0) REVERT: F 149 GLN cc_start: 0.8472 (tp40) cc_final: 0.8224 (tp-100) REVERT: F 159 PHE cc_start: 0.7738 (t80) cc_final: 0.7482 (t80) REVERT: F 171 ASN cc_start: 0.8891 (t160) cc_final: 0.8570 (t0) REVERT: F 175 MET cc_start: 0.8632 (ptt) cc_final: 0.7957 (ptt) outliers start: 45 outliers final: 25 residues processed: 392 average time/residue: 0.1523 time to fit residues: 91.1521 Evaluate side-chains 356 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 330 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1197 GLN Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 256 TYR Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 167 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 266 optimal weight: 7.9990 chunk 185 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 chunk 232 optimal weight: 30.0000 chunk 105 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 201 optimal weight: 0.0980 chunk 124 optimal weight: 0.7980 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 HIS ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 HIS B 3 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 GLN B 954 GLN ** B1137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1236 GLN B1253 ASN C 157 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.122289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.091809 restraints weight = 133536.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.091591 restraints weight = 88188.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.090482 restraints weight = 52811.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.090169 restraints weight = 45126.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.090489 restraints weight = 41253.137| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24548 Z= 0.135 Angle : 0.661 12.987 33182 Z= 0.323 Chirality : 0.043 0.324 3687 Planarity : 0.004 0.064 4248 Dihedral : 7.031 147.472 3260 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 2.04 % Allowed : 14.49 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.35 % 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 are not related in a simple way. whole: 0.32 (0.16), residues: 2947 helix: 1.16 (0.15), residues: 1248 sheet: -0.13 (0.28), residues: 342 loop : -0.52 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 141 TYR 0.021 0.001 TYR B 307 PHE 0.029 0.001 PHE B 323 TRP 0.010 0.001 TRP B1213 HIS 0.009 0.001 HIS A 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (24543) covalent geometry : angle 0.65450 / 0.32 (33176) hydrogen bonds : bond 0.03931 / 2.57 ( 1018) hydrogen bonds : angle 4.30550 / 2.96 ( 2901) metal coordination : bond 0.00631 / 0.32 ( 4) metal coordination : angle 6.92495 / 4.09 ( 6) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 358 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.8967 (tp) cc_final: 0.8647 (tp) REVERT: A 16 ASP cc_start: 0.8451 (t0) cc_final: 0.8151 (p0) REVERT: A 191 ASP cc_start: 0.8293 (p0) cc_final: 0.7849 (p0) REVERT: A 287 LYS cc_start: 0.8828 (tptt) cc_final: 0.8613 (tptp) REVERT: A 372 THR cc_start: 0.8585 (p) cc_final: 0.8329 (t) REVERT: A 394 MET cc_start: 0.8797 (mmm) cc_final: 0.8150 (mmm) REVERT: A 396 LEU cc_start: 0.9012 (mt) cc_final: 0.8694 (mt) REVERT: A 401 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8473 (mm-40) REVERT: A 479 LEU cc_start: 0.9171 (mt) cc_final: 0.8825 (pp) REVERT: A 491 ASN cc_start: 0.8911 (m-40) cc_final: 0.8513 (t0) REVERT: A 495 TRP cc_start: 0.8885 (m100) cc_final: 0.8230 (m100) REVERT: A 523 ARG cc_start: 0.8720 (mtp180) cc_final: 0.8381 (mmt180) REVERT: A 648 LEU cc_start: 0.9425 (mt) cc_final: 0.9124 (pp) REVERT: A 664 ASP cc_start: 0.8389 (t0) cc_final: 0.7647 (p0) REVERT: A 673 LEU cc_start: 0.9070 (tp) cc_final: 0.8783 (tt) REVERT: A 700 ILE cc_start: 0.9004 (tt) cc_final: 0.8164 (tp) REVERT: A 703 PHE cc_start: 0.8484 (t80) cc_final: 0.8153 (t80) REVERT: A 704 PHE cc_start: 0.8549 (m-10) cc_final: 0.7799 (m-80) REVERT: A 722 MET cc_start: 0.8627 (ptp) cc_final: 0.8329 (ptp) REVERT: A 759 HIS cc_start: 0.8671 (m90) cc_final: 0.8090 (m-70) REVERT: A 798 PHE cc_start: 0.8909 (t80) cc_final: 0.8400 (t80) REVERT: A 806 PHE cc_start: 0.9431 (t80) cc_final: 0.9104 (t80) REVERT: A 834 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7746 (mm-30) REVERT: A 840 LYS cc_start: 0.9297 (ttpt) cc_final: 0.9045 (tppt) REVERT: A 859 MET cc_start: 0.9162 (ppp) cc_final: 0.8523 (ppp) REVERT: A 860 GLN cc_start: 0.9278 (mt0) cc_final: 0.8941 (mm110) REVERT: B 58 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7763 (mm-40) REVERT: B 108 ASP cc_start: 0.8164 (m-30) cc_final: 0.7463 (t0) REVERT: B 162 VAL cc_start: 0.8972 (t) cc_final: 0.8616 (p) REVERT: B 306 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8461 (p0) REVERT: B 347 ARG cc_start: 0.8871 (tmm-80) cc_final: 0.8595 (ttp80) REVERT: B 383 THR cc_start: 0.8758 (m) cc_final: 0.8452 (m) REVERT: B 393 ASP cc_start: 0.8535 (m-30) cc_final: 0.8305 (m-30) REVERT: B 587 ASP cc_start: 0.8509 (t0) cc_final: 0.8243 (t0) REVERT: B 590 ASP cc_start: 0.7804 (t0) cc_final: 0.7572 (t0) REVERT: B 696 MET cc_start: 0.8703 (tpp) cc_final: 0.8498 (tpp) REVERT: B 756 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8726 (pp) REVERT: B 801 LYS cc_start: 0.9111 (tmmt) cc_final: 0.8801 (tppt) REVERT: B 944 LEU cc_start: 0.8923 (tp) cc_final: 0.8615 (tp) REVERT: B 965 MET cc_start: 0.8534 (mmp) cc_final: 0.8297 (mmm) REVERT: B 1011 CYS cc_start: 0.4200 (OUTLIER) cc_final: 0.3676 (t) REVERT: B 1025 MET cc_start: 0.3608 (mtp) cc_final: 0.2346 (tpt) REVERT: B 1100 ASP cc_start: 0.7578 (t0) cc_final: 0.7224 (t0) REVERT: B 1213 TRP cc_start: 0.7028 (m100) cc_final: 0.6623 (m100) REVERT: B 1257 LEU cc_start: 0.8699 (tp) cc_final: 0.8493 (tp) REVERT: B 1268 TRP cc_start: 0.8336 (m100) cc_final: 0.7933 (m100) REVERT: B 1292 ARG cc_start: 0.8803 (ttm110) cc_final: 0.8158 (mtt180) REVERT: C 126 MET cc_start: 0.8448 (mtp) cc_final: 0.8148 (mtp) REVERT: C 161 ASN cc_start: 0.8843 (m110) cc_final: 0.8590 (p0) REVERT: D 115 VAL cc_start: 0.9091 (t) cc_final: 0.8884 (m) REVERT: D 162 TYR cc_start: 0.8581 (m-80) cc_final: 0.8319 (m-10) REVERT: D 240 LEU cc_start: 0.9260 (tp) cc_final: 0.8995 (tt) REVERT: F 70 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8138 (tppt) REVERT: F 101 ASP cc_start: 0.8302 (t0) cc_final: 0.8041 (t0) REVERT: F 105 GLU cc_start: 0.8651 (pm20) cc_final: 0.8429 (pm20) REVERT: F 141 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7988 (tmm-80) REVERT: F 153 ASP cc_start: 0.8780 (m-30) cc_final: 0.8511 (p0) REVERT: F 175 MET cc_start: 0.8614 (ptt) cc_final: 0.7810 (ptt) outliers start: 54 outliers final: 30 residues processed: 395 average time/residue: 0.1639 time to fit residues: 98.5899 Evaluate side-chains 366 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 333 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1197 GLN Chi-restraints excluded: chain B residue 1263 MET Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 256 TYR Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 167 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 108 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 263 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 280 optimal weight: 0.4980 chunk 274 optimal weight: 0.4980 chunk 159 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 HIS ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 554 GLN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1137 HIS ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1197 GLN ** B1253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.116164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083252 restraints weight = 107751.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.085332 restraints weight = 55316.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.086748 restraints weight = 35755.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.087545 restraints weight = 26730.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088137 restraints weight = 22238.221| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24548 Z= 0.116 Angle : 0.663 13.788 33182 Z= 0.322 Chirality : 0.042 0.268 3687 Planarity : 0.004 0.062 4248 Dihedral : 6.812 146.299 3260 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.27 % Rotamer: Outliers : 1.74 % Allowed : 15.58 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.35 % 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 are not related in a simple way. whole: 0.46 (0.16), residues: 2947 helix: 1.27 (0.15), residues: 1257 sheet: -0.05 (0.28), residues: 333 loop : -0.45 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 141 TYR 0.026 0.001 TYR A 858 PHE 0.027 0.001 PHE F 145 TRP 0.010 0.001 TRP B1155 HIS 0.008 0.001 HIS A 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (24543) covalent geometry : angle 0.65857 / 0.32 (33176) hydrogen bonds : bond 0.03589 / 2.34 ( 1018) hydrogen bonds : angle 4.15324 / 2.85 ( 2901) metal coordination : bond 0.00504 / 0.26 ( 4) metal coordination : angle 5.81496 / 3.43 ( 6) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 352 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.8999 (tp) cc_final: 0.8645 (tp) REVERT: A 16 ASP cc_start: 0.8551 (t0) cc_final: 0.8173 (p0) REVERT: A 287 LYS cc_start: 0.8870 (tptt) cc_final: 0.8625 (tptp) REVERT: A 361 GLU cc_start: 0.8467 (mp0) cc_final: 0.8230 (mp0) REVERT: A 362 ASP cc_start: 0.7482 (t0) cc_final: 0.7120 (t0) REVERT: A 394 MET cc_start: 0.8991 (mmm) cc_final: 0.8475 (mmm) REVERT: A 396 LEU cc_start: 0.8969 (mt) cc_final: 0.8652 (mt) REVERT: A 401 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8427 (mm-40) REVERT: A 479 LEU cc_start: 0.9212 (mt) cc_final: 0.8921 (pp) REVERT: A 491 ASN cc_start: 0.8808 (m-40) cc_final: 0.8476 (t0) REVERT: A 495 TRP cc_start: 0.8858 (m100) cc_final: 0.8180 (m100) REVERT: A 523 ARG cc_start: 0.8795 (mtp180) cc_final: 0.8446 (mmt180) REVERT: A 560 GLN cc_start: 0.8435 (pp30) cc_final: 0.8187 (pp30) REVERT: A 648 LEU cc_start: 0.9431 (mt) cc_final: 0.9111 (pp) REVERT: A 664 ASP cc_start: 0.8320 (t0) cc_final: 0.7550 (p0) REVERT: A 700 ILE cc_start: 0.9000 (tt) cc_final: 0.8169 (tp) REVERT: A 703 PHE cc_start: 0.8396 (t80) cc_final: 0.8104 (t80) REVERT: A 704 PHE cc_start: 0.8472 (m-10) cc_final: 0.7773 (m-80) REVERT: A 722 MET cc_start: 0.8623 (ptp) cc_final: 0.8334 (ptp) REVERT: A 759 HIS cc_start: 0.8605 (m90) cc_final: 0.8104 (m-70) REVERT: A 798 PHE cc_start: 0.8875 (t80) cc_final: 0.8566 (t80) REVERT: A 834 GLU cc_start: 0.8580 (mt-10) cc_final: 0.7719 (mm-30) REVERT: A 859 MET cc_start: 0.9193 (ppp) cc_final: 0.8756 (ppp) REVERT: A 860 GLN cc_start: 0.9316 (mt0) cc_final: 0.8950 (mm-40) REVERT: B 58 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7751 (mm-40) REVERT: B 155 MET cc_start: 0.8830 (mmm) cc_final: 0.8226 (mpp) REVERT: B 162 VAL cc_start: 0.8930 (t) cc_final: 0.8584 (p) REVERT: B 347 ARG cc_start: 0.8917 (tmm-80) cc_final: 0.8650 (ttp80) REVERT: B 587 ASP cc_start: 0.8558 (t0) cc_final: 0.8176 (t0) REVERT: B 590 ASP cc_start: 0.7820 (t0) cc_final: 0.7235 (t0) REVERT: B 696 MET cc_start: 0.8634 (tpp) cc_final: 0.8400 (tpp) REVERT: B 801 LYS cc_start: 0.9119 (tmmt) cc_final: 0.8820 (tppt) REVERT: B 951 LYS cc_start: 0.8722 (pttm) cc_final: 0.8284 (pttm) REVERT: B 1011 CYS cc_start: 0.2194 (OUTLIER) cc_final: 0.1024 (t) REVERT: B 1025 MET cc_start: 0.1087 (mtp) cc_final: 0.0326 (tpt) REVERT: B 1049 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7337 (p) REVERT: B 1056 TYR cc_start: 0.6688 (m-80) cc_final: 0.6417 (m-80) REVERT: B 1100 ASP cc_start: 0.7130 (t0) cc_final: 0.6899 (t0) REVERT: B 1139 LEU cc_start: 0.9144 (mp) cc_final: 0.8578 (tp) REVERT: C 254 MET cc_start: 0.7040 (mmt) cc_final: 0.6725 (mmt) REVERT: D 115 VAL cc_start: 0.9121 (t) cc_final: 0.8913 (m) REVERT: D 240 LEU cc_start: 0.9276 (tp) cc_final: 0.9067 (tt) REVERT: F 70 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8197 (mmmt) REVERT: F 101 ASP cc_start: 0.8362 (t0) cc_final: 0.8125 (t0) REVERT: F 106 GLU cc_start: 0.8957 (pm20) cc_final: 0.8622 (mp0) REVERT: F 141 ARG cc_start: 0.8320 (ttp80) cc_final: 0.8072 (tmm-80) REVERT: F 153 ASP cc_start: 0.8619 (m-30) cc_final: 0.8348 (p0) REVERT: F 171 ASN cc_start: 0.8669 (t0) cc_final: 0.7972 (t0) REVERT: F 175 MET cc_start: 0.8508 (ptt) cc_final: 0.8060 (ptt) outliers start: 46 outliers final: 25 residues processed: 381 average time/residue: 0.1617 time to fit residues: 94.2557 Evaluate side-chains 351 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 324 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1197 GLN Chi-restraints excluded: chain B residue 1263 MET Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 58 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 201 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 224 optimal weight: 50.0000 chunk 157 optimal weight: 8.9990 chunk 125 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 GLN ** B 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 946 GLN B 954 GLN ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1240 HIS B1253 ASN ** B1302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN F 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.119242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.083507 restraints weight = 133126.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081175 restraints weight = 81868.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.081755 restraints weight = 54483.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082550 restraints weight = 43634.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.082830 restraints weight = 36875.816| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24548 Z= 0.237 Angle : 0.752 14.703 33182 Z= 0.374 Chirality : 0.045 0.210 3687 Planarity : 0.005 0.062 4248 Dihedral : 7.269 151.196 3260 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 2.45 % Allowed : 15.89 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.35 % 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 are not related in a simple way. whole: 0.23 (0.16), residues: 2947 helix: 1.09 (0.15), residues: 1260 sheet: -0.37 (0.26), residues: 363 loop : -0.54 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 225 TYR 0.043 0.002 TYR A 58 PHE 0.030 0.002 PHE A 64 TRP 0.027 0.002 TRP B1213 HIS 0.011 0.001 HIS F 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.24 (24543) covalent geometry : angle 0.74528 / 0.37 (33176) hydrogen bonds : bond 0.04731 / 3.12 ( 1018) hydrogen bonds : angle 4.50090 / 3.10 ( 2901) metal coordination : bond 0.00734 / 0.37 ( 4) metal coordination : angle 7.34810 / 4.29 ( 6) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 338 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.9020 (tp) cc_final: 0.8638 (tp) REVERT: A 16 ASP cc_start: 0.8501 (t0) cc_final: 0.8155 (p0) REVERT: A 361 GLU cc_start: 0.8588 (mp0) cc_final: 0.8320 (mp0) REVERT: A 394 MET cc_start: 0.9095 (mmm) cc_final: 0.8757 (mmm) REVERT: A 396 LEU cc_start: 0.8969 (mt) cc_final: 0.8657 (mt) REVERT: A 479 LEU cc_start: 0.9239 (mt) cc_final: 0.8946 (pp) REVERT: A 491 ASN cc_start: 0.8956 (m-40) cc_final: 0.8615 (t0) REVERT: A 495 TRP cc_start: 0.8981 (m100) cc_final: 0.8321 (m100) REVERT: A 523 ARG cc_start: 0.8878 (mtp180) cc_final: 0.8534 (mmt180) REVERT: A 648 LEU cc_start: 0.9462 (mt) cc_final: 0.9125 (pp) REVERT: A 654 MET cc_start: 0.8953 (tpt) cc_final: 0.8523 (tmm) REVERT: A 664 ASP cc_start: 0.8560 (t0) cc_final: 0.7989 (p0) REVERT: A 682 MET cc_start: 0.8523 (tpt) cc_final: 0.8183 (tpt) REVERT: A 700 ILE cc_start: 0.9000 (tt) cc_final: 0.8193 (tp) REVERT: A 703 PHE cc_start: 0.8583 (t80) cc_final: 0.8279 (t80) REVERT: A 704 PHE cc_start: 0.8662 (m-10) cc_final: 0.7939 (m-80) REVERT: A 722 MET cc_start: 0.8705 (ptp) cc_final: 0.8434 (ptp) REVERT: A 756 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7896 (tptm) REVERT: A 759 HIS cc_start: 0.8783 (m90) cc_final: 0.8190 (m-70) REVERT: A 798 PHE cc_start: 0.8922 (t80) cc_final: 0.8599 (t80) REVERT: A 806 PHE cc_start: 0.9438 (t80) cc_final: 0.9134 (t80) REVERT: A 834 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8010 (mm-30) REVERT: A 840 LYS cc_start: 0.9305 (ttpt) cc_final: 0.8786 (tptp) REVERT: A 859 MET cc_start: 0.9185 (ppp) cc_final: 0.8728 (ppp) REVERT: A 860 GLN cc_start: 0.9339 (mt0) cc_final: 0.8952 (mm-40) REVERT: A 862 LEU cc_start: 0.9260 (mt) cc_final: 0.8848 (mt) REVERT: B 58 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7754 (mm-40) REVERT: B 106 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8602 (m) REVERT: B 155 MET cc_start: 0.8689 (mmm) cc_final: 0.8386 (mmm) REVERT: B 306 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8587 (p0) REVERT: B 328 MET cc_start: 0.9053 (tpp) cc_final: 0.8466 (mpp) REVERT: B 383 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8598 (m) REVERT: B 801 LYS cc_start: 0.9105 (tmmt) cc_final: 0.8789 (tppt) REVERT: B 945 GLN cc_start: 0.7458 (tm-30) cc_final: 0.7159 (tm-30) REVERT: B 965 MET cc_start: 0.8783 (mmm) cc_final: 0.8302 (tpp) REVERT: B 998 ARG cc_start: 0.6970 (mmm160) cc_final: 0.6630 (mmm160) REVERT: B 1011 CYS cc_start: 0.4492 (OUTLIER) cc_final: 0.4272 (t) REVERT: B 1025 MET cc_start: 0.4426 (mtp) cc_final: 0.3303 (tpt) REVERT: B 1100 ASP cc_start: 0.7811 (t0) cc_final: 0.7509 (t0) REVERT: B 1139 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8749 (tp) REVERT: B 1268 TRP cc_start: 0.8315 (m100) cc_final: 0.7878 (m100) REVERT: C 214 LYS cc_start: 0.9529 (tttt) cc_final: 0.9209 (tptp) REVERT: D 240 LEU cc_start: 0.9305 (tp) cc_final: 0.9070 (tt) REVERT: D 291 GLU cc_start: 0.9114 (mp0) cc_final: 0.8127 (pm20) REVERT: F 70 LYS cc_start: 0.8477 (mmmt) cc_final: 0.8000 (tppt) REVERT: F 101 ASP cc_start: 0.8229 (t0) cc_final: 0.7979 (t0) REVERT: F 105 GLU cc_start: 0.8466 (pm20) cc_final: 0.8134 (pm20) REVERT: F 118 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8173 (mt) REVERT: F 153 ASP cc_start: 0.8795 (m-30) cc_final: 0.8302 (p0) REVERT: F 171 ASN cc_start: 0.8639 (t0) cc_final: 0.8066 (t0) REVERT: F 175 MET cc_start: 0.8400 (ptt) cc_final: 0.8038 (ptt) outliers start: 65 outliers final: 36 residues processed: 382 average time/residue: 0.1603 time to fit residues: 93.4603 Evaluate side-chains 352 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 682 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 959 ARG Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1147 PHE Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1263 MET Chi-restraints excluded: chain B residue 1347 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 113 ASN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 167 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 104 optimal weight: 2.9990 chunk 227 optimal weight: 0.3980 chunk 112 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1197 GLN B1240 HIS ** B1302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN F 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.113754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.081047 restraints weight = 109979.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.083066 restraints weight = 56454.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084352 restraints weight = 36453.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085218 restraints weight = 27409.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085469 restraints weight = 22681.622| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24548 Z= 0.131 Angle : 0.693 15.349 33182 Z= 0.339 Chirality : 0.043 0.290 3687 Planarity : 0.004 0.061 4248 Dihedral : 6.934 145.830 3260 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.80 % Favored : 96.13 % Rotamer: Outliers : 1.74 % Allowed : 17.36 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.35 % 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 are not related in a simple way. whole: 0.37 (0.16), residues: 2947 helix: 1.27 (0.15), residues: 1257 sheet: -0.32 (0.26), residues: 359 loop : -0.52 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 198 TYR 0.027 0.001 TYR A 58 PHE 0.044 0.001 PHE F 145 TRP 0.035 0.001 TRP B1213 HIS 0.011 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (24543) covalent geometry : angle 0.68862 / 0.34 (33176) hydrogen bonds : bond 0.03893 / 2.54 ( 1018) hydrogen bonds : angle 4.19776 / 2.88 ( 2901) metal coordination : bond 0.00488 / 0.24 ( 4) metal coordination : angle 5.97426 / 3.46 ( 6) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 327 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.9048 (tp) cc_final: 0.8677 (tp) REVERT: A 16 ASP cc_start: 0.8559 (t0) cc_final: 0.8273 (p0) REVERT: A 198 PHE cc_start: 0.8273 (m-80) cc_final: 0.7847 (m-80) REVERT: A 361 GLU cc_start: 0.8520 (mp0) cc_final: 0.8253 (mp0) REVERT: A 372 THR cc_start: 0.8603 (p) cc_final: 0.8345 (t) REVERT: A 394 MET cc_start: 0.8986 (mmm) cc_final: 0.8623 (mmm) REVERT: A 396 LEU cc_start: 0.8951 (mt) cc_final: 0.8658 (mt) REVERT: A 479 LEU cc_start: 0.9232 (mt) cc_final: 0.8944 (pp) REVERT: A 491 ASN cc_start: 0.8822 (m-40) cc_final: 0.8565 (t0) REVERT: A 495 TRP cc_start: 0.8925 (m100) cc_final: 0.8260 (m100) REVERT: A 521 MET cc_start: 0.9102 (ppp) cc_final: 0.8718 (ppp) REVERT: A 523 ARG cc_start: 0.8860 (mtp180) cc_final: 0.8481 (mmt180) REVERT: A 663 LEU cc_start: 0.8582 (mm) cc_final: 0.8346 (mm) REVERT: A 682 MET cc_start: 0.8020 (tpt) cc_final: 0.7774 (tpt) REVERT: A 700 ILE cc_start: 0.9001 (tt) cc_final: 0.8164 (tp) REVERT: A 703 PHE cc_start: 0.8427 (t80) cc_final: 0.8169 (t80) REVERT: A 704 PHE cc_start: 0.8494 (m-10) cc_final: 0.7810 (m-80) REVERT: A 722 MET cc_start: 0.8647 (ptp) cc_final: 0.8396 (ptp) REVERT: A 756 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7930 (tptm) REVERT: A 759 HIS cc_start: 0.8615 (m90) cc_final: 0.8060 (m-70) REVERT: A 798 PHE cc_start: 0.8917 (t80) cc_final: 0.8585 (t80) REVERT: A 806 PHE cc_start: 0.9451 (t80) cc_final: 0.9134 (t80) REVERT: A 834 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7967 (mm-30) REVERT: A 859 MET cc_start: 0.9213 (ppp) cc_final: 0.8686 (ppp) REVERT: A 860 GLN cc_start: 0.9335 (mt0) cc_final: 0.8931 (mm-40) REVERT: B 58 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7761 (mm-40) REVERT: B 141 LYS cc_start: 0.8457 (mmtm) cc_final: 0.8240 (mmtm) REVERT: B 155 MET cc_start: 0.8704 (mmm) cc_final: 0.8241 (mmm) REVERT: B 162 VAL cc_start: 0.8951 (t) cc_final: 0.8625 (p) REVERT: B 306 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8635 (p0) REVERT: B 328 MET cc_start: 0.9110 (tpp) cc_final: 0.8513 (mpp) REVERT: B 347 ARG cc_start: 0.8943 (tmm-80) cc_final: 0.8662 (ttp80) REVERT: B 587 ASP cc_start: 0.8361 (t0) cc_final: 0.8120 (t0) REVERT: B 696 MET cc_start: 0.8524 (tpp) cc_final: 0.8026 (mpp) REVERT: B 801 LYS cc_start: 0.9113 (tmmt) cc_final: 0.8804 (tppt) REVERT: B 945 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6839 (tm-30) REVERT: B 951 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.7764 (ptpt) REVERT: B 954 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8208 (pp30) REVERT: B 1011 CYS cc_start: 0.2612 (OUTLIER) cc_final: 0.1447 (t) REVERT: B 1025 MET cc_start: 0.1297 (mtp) cc_final: 0.0562 (tpt) REVERT: B 1048 LEU cc_start: 0.9126 (tp) cc_final: 0.8114 (pp) REVERT: B 1100 ASP cc_start: 0.7371 (t0) cc_final: 0.7102 (t0) REVERT: B 1139 LEU cc_start: 0.9187 (mp) cc_final: 0.8706 (tp) REVERT: B 1212 MET cc_start: 0.8019 (mmp) cc_final: 0.7737 (mmp) REVERT: B 1268 TRP cc_start: 0.8185 (m100) cc_final: 0.7871 (m100) REVERT: C 214 LYS cc_start: 0.9477 (tttt) cc_final: 0.9170 (tptp) REVERT: C 254 MET cc_start: 0.7169 (mmt) cc_final: 0.6900 (mmm) REVERT: C 396 MET cc_start: -0.3037 (OUTLIER) cc_final: -0.3587 (ttm) REVERT: D 240 LEU cc_start: 0.9266 (tp) cc_final: 0.9013 (tt) REVERT: F 70 LYS cc_start: 0.8486 (mmmt) cc_final: 0.7993 (tppt) REVERT: F 101 ASP cc_start: 0.8305 (t0) cc_final: 0.8083 (t0) REVERT: F 146 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8396 (tp-100) REVERT: F 149 GLN cc_start: 0.8848 (pt0) cc_final: 0.8298 (tp-100) REVERT: F 171 ASN cc_start: 0.8774 (t0) cc_final: 0.8260 (t0) REVERT: F 175 MET cc_start: 0.8744 (ptt) cc_final: 0.8166 (ptt) outliers start: 46 outliers final: 30 residues processed: 354 average time/residue: 0.1557 time to fit residues: 85.0767 Evaluate side-chains 353 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 318 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 951 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1147 PHE Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain B residue 1174 LEU Chi-restraints excluded: chain B residue 1263 MET Chi-restraints excluded: chain B residue 1347 THR Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 256 TYR Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 167 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 17 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 242 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 283 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 288 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 206 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 GLN B 954 GLN ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.113147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080376 restraints weight = 110729.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082339 restraints weight = 57198.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083645 restraints weight = 37235.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.084358 restraints weight = 28056.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.084886 restraints weight = 23646.153| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24548 Z= 0.154 Angle : 0.704 13.759 33182 Z= 0.347 Chirality : 0.044 0.300 3687 Planarity : 0.004 0.060 4248 Dihedral : 6.936 145.139 3260 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.66 % Rotamer: Outliers : 1.77 % Allowed : 17.81 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.35 % 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 are not related in a simple way. whole: 0.36 (0.16), residues: 2947 helix: 1.25 (0.15), residues: 1252 sheet: -0.32 (0.26), residues: 357 loop : -0.52 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 20 TYR 0.025 0.001 TYR A 58 PHE 0.026 0.001 PHE B1222 TRP 0.043 0.001 TRP B1213 HIS 0.009 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (24543) covalent geometry : angle 0.69907 / 0.35 (33176) hydrogen bonds : bond 0.04043 / 2.66 ( 1018) hydrogen bonds : angle 4.24270 / 2.92 ( 2901) metal coordination : bond 0.00457 / 0.23 ( 4) metal coordination : angle 6.05832 / 3.51 ( 6) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 326 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.9054 (tp) cc_final: 0.8671 (tp) REVERT: A 16 ASP cc_start: 0.8566 (t0) cc_final: 0.8219 (p0) REVERT: A 198 PHE cc_start: 0.8303 (m-80) cc_final: 0.7881 (m-80) REVERT: A 344 GLU cc_start: 0.7735 (tt0) cc_final: 0.7320 (tt0) REVERT: A 358 MET cc_start: 0.7361 (mtt) cc_final: 0.7031 (mtt) REVERT: A 361 GLU cc_start: 0.8553 (mp0) cc_final: 0.8276 (mp0) REVERT: A 396 LEU cc_start: 0.8977 (mt) cc_final: 0.8674 (mt) REVERT: A 479 LEU cc_start: 0.9232 (mt) cc_final: 0.8930 (pp) REVERT: A 480 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8749 (pt) REVERT: A 491 ASN cc_start: 0.8826 (m-40) cc_final: 0.8590 (t0) REVERT: A 495 TRP cc_start: 0.8950 (m100) cc_final: 0.8321 (m100) REVERT: A 523 ARG cc_start: 0.8891 (mtp180) cc_final: 0.8640 (mmt180) REVERT: A 583 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.6714 (mpp) REVERT: A 648 LEU cc_start: 0.9418 (mm) cc_final: 0.9101 (pp) REVERT: A 654 MET cc_start: 0.8872 (tpt) cc_final: 0.8443 (tmm) REVERT: A 663 LEU cc_start: 0.8756 (mm) cc_final: 0.8532 (mm) REVERT: A 682 MET cc_start: 0.8011 (tpt) cc_final: 0.7756 (tpt) REVERT: A 704 PHE cc_start: 0.8478 (m-10) cc_final: 0.8210 (m-80) REVERT: A 722 MET cc_start: 0.8692 (ptp) cc_final: 0.8414 (ptp) REVERT: A 756 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7880 (tptm) REVERT: A 759 HIS cc_start: 0.8595 (m90) cc_final: 0.7928 (m-70) REVERT: A 795 TYR cc_start: 0.9233 (t80) cc_final: 0.8875 (t80) REVERT: A 798 PHE cc_start: 0.8904 (t80) cc_final: 0.8571 (t80) REVERT: A 806 PHE cc_start: 0.9453 (t80) cc_final: 0.9136 (t80) REVERT: A 834 GLU cc_start: 0.8610 (mt-10) cc_final: 0.7985 (mm-30) REVERT: A 840 LYS cc_start: 0.9215 (ttpt) cc_final: 0.8875 (tptp) REVERT: A 859 MET cc_start: 0.9215 (ppp) cc_final: 0.8676 (ppp) REVERT: A 860 GLN cc_start: 0.9328 (mt0) cc_final: 0.8927 (mm-40) REVERT: B 58 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7792 (mm-40) REVERT: B 155 MET cc_start: 0.8648 (mmm) cc_final: 0.8188 (mmm) REVERT: B 162 VAL cc_start: 0.8953 (t) cc_final: 0.8626 (p) REVERT: B 306 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8624 (p0) REVERT: B 328 MET cc_start: 0.9158 (tpp) cc_final: 0.8566 (mpp) REVERT: B 347 ARG cc_start: 0.8960 (tmm-80) cc_final: 0.8681 (ttp80) REVERT: B 383 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8495 (m) REVERT: B 587 ASP cc_start: 0.8372 (t0) cc_final: 0.8168 (t0) REVERT: B 696 MET cc_start: 0.8497 (tpp) cc_final: 0.8020 (mpp) REVERT: B 801 LYS cc_start: 0.9120 (tmmt) cc_final: 0.8815 (tppt) REVERT: B 945 GLN cc_start: 0.7264 (tm-30) cc_final: 0.6936 (tm-30) REVERT: B 950 GLN cc_start: 0.8870 (tp40) cc_final: 0.8591 (tp40) REVERT: B 951 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8589 (pttm) REVERT: B 1011 CYS cc_start: 0.2553 (OUTLIER) cc_final: 0.1438 (t) REVERT: B 1025 MET cc_start: 0.1359 (mtp) cc_final: 0.0601 (tpt) REVERT: B 1048 LEU cc_start: 0.9113 (tp) cc_final: 0.7970 (pp) REVERT: B 1057 LEU cc_start: 0.8509 (tp) cc_final: 0.8301 (pt) REVERT: B 1139 LEU cc_start: 0.9207 (mp) cc_final: 0.8769 (tp) REVERT: B 1212 MET cc_start: 0.8019 (mmp) cc_final: 0.7544 (mmp) REVERT: B 1268 TRP cc_start: 0.8185 (m100) cc_final: 0.7879 (m100) REVERT: B 1292 ARG cc_start: 0.8433 (ttm110) cc_final: 0.8121 (mtt-85) REVERT: C 211 ASN cc_start: 0.9359 (t0) cc_final: 0.9126 (t0) REVERT: C 214 LYS cc_start: 0.9470 (tttt) cc_final: 0.9166 (tptp) REVERT: C 254 MET cc_start: 0.7195 (mmt) cc_final: 0.6872 (mmm) REVERT: C 396 MET cc_start: -0.2929 (OUTLIER) cc_final: -0.3442 (ttm) REVERT: D 240 LEU cc_start: 0.9258 (tp) cc_final: 0.9017 (tt) REVERT: F 101 ASP cc_start: 0.8382 (t0) cc_final: 0.8127 (t0) REVERT: F 145 PHE cc_start: 0.8480 (t80) cc_final: 0.8219 (t80) REVERT: F 146 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8382 (tp-100) REVERT: F 149 GLN cc_start: 0.8731 (pt0) cc_final: 0.8458 (tp-100) REVERT: F 171 ASN cc_start: 0.8741 (t0) cc_final: 0.8264 (t0) REVERT: F 175 MET cc_start: 0.8762 (ptt) cc_final: 0.8176 (ptt) outliers start: 47 outliers final: 31 residues processed: 354 average time/residue: 0.1647 time to fit residues: 89.5484 Evaluate side-chains 345 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 307 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 951 LYS Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1147 PHE Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain B residue 1174 LEU Chi-restraints excluded: chain B residue 1243 HIS Chi-restraints excluded: chain B residue 1263 MET Chi-restraints excluded: chain B residue 1347 THR Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain C residue 396 MET Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 167 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 2.9990 chunk 174 optimal weight: 0.0170 chunk 176 optimal weight: 0.7980 chunk 151 optimal weight: 0.3980 chunk 191 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 649 GLN ** B1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.113963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.081481 restraints weight = 108149.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.083472 restraints weight = 54898.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.084685 restraints weight = 35478.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085597 restraints weight = 26825.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086120 restraints weight = 22292.197| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24548 Z= 0.135 Angle : 0.721 17.206 33182 Z= 0.351 Chirality : 0.043 0.283 3687 Planarity : 0.004 0.067 4248 Dihedral : 6.815 144.707 3260 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 1.51 % Allowed : 18.64 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.35 % 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 are not related in a simple way. whole: 0.40 (0.16), residues: 2947 helix: 1.26 (0.15), residues: 1251 sheet: -0.22 (0.26), residues: 353 loop : -0.49 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1044 TYR 0.019 0.001 TYR A 58 PHE 0.020 0.001 PHE B 130 TRP 0.044 0.001 TRP B1213 HIS 0.008 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (24543) covalent geometry : angle 0.71690 / 0.35 (33176) hydrogen bonds : bond 0.03917 / 2.58 ( 1018) hydrogen bonds : angle 4.21145 / 2.88 ( 2901) metal coordination : bond 0.00406 / 0.20 ( 4) metal coordination : angle 5.54544 / 3.22 ( 6) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 317 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.9044 (tp) cc_final: 0.8705 (tp) REVERT: A 16 ASP cc_start: 0.8532 (t0) cc_final: 0.8247 (p0) REVERT: A 198 PHE cc_start: 0.8217 (m-80) cc_final: 0.7796 (m-80) REVERT: A 344 GLU cc_start: 0.7777 (tt0) cc_final: 0.7378 (tt0) REVERT: A 358 MET cc_start: 0.7364 (mtt) cc_final: 0.7158 (mtm) REVERT: A 361 GLU cc_start: 0.8490 (mp0) cc_final: 0.8226 (mp0) REVERT: A 396 LEU cc_start: 0.8921 (mt) cc_final: 0.8628 (mt) REVERT: A 479 LEU cc_start: 0.9223 (mt) cc_final: 0.8971 (pp) REVERT: A 491 ASN cc_start: 0.8782 (m-40) cc_final: 0.8576 (t0) REVERT: A 493 LEU cc_start: 0.9486 (tt) cc_final: 0.9253 (pp) REVERT: A 495 TRP cc_start: 0.8918 (m100) cc_final: 0.8265 (m100) REVERT: A 521 MET cc_start: 0.9080 (ppp) cc_final: 0.8672 (ppp) REVERT: A 523 ARG cc_start: 0.8885 (mtp180) cc_final: 0.8587 (mmt180) REVERT: A 583 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.6595 (mpp) REVERT: A 648 LEU cc_start: 0.9399 (mm) cc_final: 0.9092 (pp) REVERT: A 663 LEU cc_start: 0.8773 (mm) cc_final: 0.8556 (mm) REVERT: A 682 MET cc_start: 0.7960 (tpt) cc_final: 0.7739 (tpt) REVERT: A 722 MET cc_start: 0.8670 (ptp) cc_final: 0.8383 (ptp) REVERT: A 756 LYS cc_start: 0.8253 (mmtt) cc_final: 0.7936 (tptm) REVERT: A 798 PHE cc_start: 0.8892 (t80) cc_final: 0.8575 (t80) REVERT: A 806 PHE cc_start: 0.9435 (t80) cc_final: 0.9112 (t80) REVERT: A 834 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7982 (mm-30) REVERT: A 840 LYS cc_start: 0.9205 (ttpt) cc_final: 0.8844 (tptp) REVERT: A 858 TYR cc_start: 0.9182 (t80) cc_final: 0.8908 (t80) REVERT: A 859 MET cc_start: 0.9239 (ppp) cc_final: 0.8556 (ppp) REVERT: A 860 GLN cc_start: 0.9289 (mt0) cc_final: 0.8937 (mm-40) REVERT: B 58 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7826 (mm-40) REVERT: B 155 MET cc_start: 0.8641 (mmm) cc_final: 0.8211 (mmm) REVERT: B 162 VAL cc_start: 0.8939 (t) cc_final: 0.8633 (p) REVERT: B 306 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8628 (p0) REVERT: B 328 MET cc_start: 0.9163 (tpp) cc_final: 0.8580 (mpp) REVERT: B 347 ARG cc_start: 0.8930 (tmm-80) cc_final: 0.8721 (ttp80) REVERT: B 383 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8500 (m) REVERT: B 581 MET cc_start: 0.8102 (mmm) cc_final: 0.7576 (mtt) REVERT: B 696 MET cc_start: 0.8475 (tpp) cc_final: 0.8024 (mpp) REVERT: B 801 LYS cc_start: 0.9100 (tmmt) cc_final: 0.8808 (tppt) REVERT: B 945 GLN cc_start: 0.7193 (tm-30) cc_final: 0.6860 (tm-30) REVERT: B 950 GLN cc_start: 0.8832 (tp40) cc_final: 0.8403 (tp40) REVERT: B 951 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8008 (ptpt) REVERT: B 954 GLN cc_start: 0.8259 (pp30) cc_final: 0.7805 (pp30) REVERT: B 1011 CYS cc_start: 0.2395 (OUTLIER) cc_final: 0.1310 (t) REVERT: B 1025 MET cc_start: 0.1378 (mtp) cc_final: 0.0686 (tpt) REVERT: B 1048 LEU cc_start: 0.9081 (tp) cc_final: 0.7928 (pp) REVERT: B 1139 LEU cc_start: 0.9192 (mp) cc_final: 0.8763 (tp) REVERT: B 1292 ARG cc_start: 0.8340 (ttm110) cc_final: 0.8118 (mtt-85) REVERT: C 211 ASN cc_start: 0.9344 (t0) cc_final: 0.9093 (t0) REVERT: C 214 LYS cc_start: 0.9461 (tttt) cc_final: 0.9167 (tptp) REVERT: C 254 MET cc_start: 0.7149 (mmt) cc_final: 0.6838 (mmm) REVERT: F 101 ASP cc_start: 0.8360 (t0) cc_final: 0.8132 (t0) REVERT: F 145 PHE cc_start: 0.8401 (t80) cc_final: 0.8157 (t80) REVERT: F 149 GLN cc_start: 0.8686 (pt0) cc_final: 0.8453 (tp-100) REVERT: F 171 ASN cc_start: 0.8734 (t0) cc_final: 0.8339 (t0) REVERT: F 175 MET cc_start: 0.8751 (ptt) cc_final: 0.8108 (ptt) outliers start: 40 outliers final: 31 residues processed: 341 average time/residue: 0.1639 time to fit residues: 85.5001 Evaluate side-chains 339 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 303 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 951 LYS Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1147 PHE Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain B residue 1174 LEU Chi-restraints excluded: chain B residue 1243 HIS Chi-restraints excluded: chain B residue 1263 MET Chi-restraints excluded: chain B residue 1347 THR Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 144 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN A 649 GLN B 554 GLN B 954 GLN ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.119493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.086279 restraints weight = 134200.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.086364 restraints weight = 78822.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.086383 restraints weight = 54565.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.086279 restraints weight = 45434.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.086500 restraints weight = 40015.500| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24548 Z= 0.185 Angle : 0.785 16.282 33182 Z= 0.383 Chirality : 0.045 0.284 3687 Planarity : 0.004 0.059 4248 Dihedral : 6.958 145.352 3260 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.82 % Favored : 95.11 % Rotamer: Outliers : 1.74 % Allowed : 19.02 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.35 % 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 are not related in a simple way. whole: 0.27 (0.16), residues: 2947 helix: 1.18 (0.15), residues: 1250 sheet: -0.42 (0.26), residues: 359 loop : -0.54 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 221 TYR 0.025 0.002 TYR A 58 PHE 0.045 0.002 PHE A 704 TRP 0.053 0.002 TRP B1268 HIS 0.007 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (24543) covalent geometry : angle 0.78097 / 0.38 (33176) hydrogen bonds : bond 0.04243 / 2.80 ( 1018) hydrogen bonds : angle 4.38233 / 3.00 ( 2901) metal coordination : bond 0.00497 / 0.25 ( 4) metal coordination : angle 6.01557 / 3.49 ( 6) Misc. bond : bond 0.00022 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 310 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.9054 (tp) cc_final: 0.8719 (tp) REVERT: A 16 ASP cc_start: 0.8481 (t0) cc_final: 0.8181 (p0) REVERT: A 187 MET cc_start: 0.7897 (ppp) cc_final: 0.7435 (ppp) REVERT: A 198 PHE cc_start: 0.8488 (m-80) cc_final: 0.8026 (m-80) REVERT: A 344 GLU cc_start: 0.7850 (tt0) cc_final: 0.7482 (pt0) REVERT: A 358 MET cc_start: 0.7415 (mtt) cc_final: 0.7177 (mtt) REVERT: A 361 GLU cc_start: 0.8530 (mp0) cc_final: 0.8261 (mp0) REVERT: A 396 LEU cc_start: 0.8971 (mt) cc_final: 0.8668 (mt) REVERT: A 401 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8692 (mm-40) REVERT: A 479 LEU cc_start: 0.9258 (mt) cc_final: 0.9020 (pp) REVERT: A 491 ASN cc_start: 0.9029 (m-40) cc_final: 0.8684 (t0) REVERT: A 495 TRP cc_start: 0.8960 (m100) cc_final: 0.8366 (m100) REVERT: A 523 ARG cc_start: 0.9005 (mtp180) cc_final: 0.8654 (mmt180) REVERT: A 648 LEU cc_start: 0.9429 (mm) cc_final: 0.9111 (pp) REVERT: A 663 LEU cc_start: 0.8974 (mm) cc_final: 0.8753 (pp) REVERT: A 682 MET cc_start: 0.8688 (tpt) cc_final: 0.8433 (tpt) REVERT: A 722 MET cc_start: 0.8678 (ptp) cc_final: 0.8334 (ptp) REVERT: A 756 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7888 (tptm) REVERT: A 798 PHE cc_start: 0.8999 (t80) cc_final: 0.8632 (t80) REVERT: A 806 PHE cc_start: 0.9465 (t80) cc_final: 0.9139 (t80) REVERT: A 834 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8028 (mm-30) REVERT: A 840 LYS cc_start: 0.9233 (ttpt) cc_final: 0.8803 (tptp) REVERT: A 859 MET cc_start: 0.9257 (ppp) cc_final: 0.8757 (ppp) REVERT: A 860 GLN cc_start: 0.9316 (mt0) cc_final: 0.8906 (mm-40) REVERT: B 108 ASP cc_start: 0.8304 (m-30) cc_final: 0.7510 (t0) REVERT: B 155 MET cc_start: 0.8596 (mmm) cc_final: 0.8183 (mmm) REVERT: B 162 VAL cc_start: 0.8955 (t) cc_final: 0.8648 (p) REVERT: B 306 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8597 (p0) REVERT: B 328 MET cc_start: 0.9164 (tpp) cc_final: 0.8588 (mpp) REVERT: B 347 ARG cc_start: 0.8953 (tmm-80) cc_final: 0.8743 (ttp80) REVERT: B 383 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8548 (m) REVERT: B 581 MET cc_start: 0.8104 (mmm) cc_final: 0.7680 (mtt) REVERT: B 696 MET cc_start: 0.8591 (tpp) cc_final: 0.8124 (mpp) REVERT: B 801 LYS cc_start: 0.9122 (tmmt) cc_final: 0.8804 (tppt) REVERT: B 945 GLN cc_start: 0.7381 (tm-30) cc_final: 0.7041 (tm-30) REVERT: B 950 GLN cc_start: 0.8912 (tp40) cc_final: 0.8500 (tp40) REVERT: B 951 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8038 (ptpt) REVERT: B 954 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7911 (pp30) REVERT: B 1008 PHE cc_start: 0.8234 (m-80) cc_final: 0.7747 (m-80) REVERT: B 1011 CYS cc_start: 0.4554 (OUTLIER) cc_final: 0.4266 (t) REVERT: B 1025 MET cc_start: 0.4707 (mtp) cc_final: 0.3527 (tpt) REVERT: B 1048 LEU cc_start: 0.8864 (tp) cc_final: 0.8068 (pp) REVERT: B 1139 LEU cc_start: 0.9229 (mp) cc_final: 0.8824 (tp) REVERT: B 1292 ARG cc_start: 0.8987 (ttm110) cc_final: 0.8497 (mtt-85) REVERT: C 211 ASN cc_start: 0.9404 (t0) cc_final: 0.9158 (t0) REVERT: C 214 LYS cc_start: 0.9522 (tttt) cc_final: 0.9207 (tptp) REVERT: F 101 ASP cc_start: 0.8365 (t0) cc_final: 0.8150 (t0) REVERT: F 145 PHE cc_start: 0.8603 (t80) cc_final: 0.8306 (t80) REVERT: F 149 GLN cc_start: 0.8744 (pt0) cc_final: 0.8494 (tp-100) REVERT: F 171 ASN cc_start: 0.8704 (t0) cc_final: 0.8308 (t0) REVERT: F 175 MET cc_start: 0.8636 (ptt) cc_final: 0.8104 (ptt) outliers start: 46 outliers final: 36 residues processed: 337 average time/residue: 0.1605 time to fit residues: 83.0751 Evaluate side-chains 341 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 300 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 725 TYR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 557 MET Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 951 LYS Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 970 TRP Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1147 PHE Chi-restraints excluded: chain B residue 1152 HIS Chi-restraints excluded: chain B residue 1174 LEU Chi-restraints excluded: chain B residue 1243 HIS Chi-restraints excluded: chain B residue 1263 MET Chi-restraints excluded: chain B residue 1347 THR Chi-restraints excluded: chain C residue 203 LYS Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 230 optimal weight: 0.0570 chunk 235 optimal weight: 50.0000 chunk 196 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 276 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 HIS ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.119528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086147 restraints weight = 132948.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.086107 restraints weight = 79152.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.085750 restraints weight = 54264.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.085950 restraints weight = 46387.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.085833 restraints weight = 40400.480| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.303 24548 Z= 0.278 Angle : 1.027 59.199 33182 Z= 0.584 Chirality : 0.046 0.536 3687 Planarity : 0.005 0.112 4248 Dihedral : 6.962 145.337 3260 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.15 % Rotamer: Outliers : 1.70 % Allowed : 19.13 % Favored : 79.17 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.35 % 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 are not related in a simple way. whole: 0.26 (0.16), residues: 2947 helix: 1.17 (0.15), residues: 1250 sheet: -0.42 (0.26), residues: 359 loop : -0.54 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 221 TYR 0.021 0.002 TYR A 58 PHE 0.025 0.002 PHE A 704 TRP 0.042 0.002 TRP B1268 HIS 0.007 0.001 HIS A 808 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.28 (24543) covalent geometry : angle 1.02391 / 0.58 (33176) hydrogen bonds : bond 0.04238 / 2.79 ( 1018) hydrogen bonds : angle 4.39224 / 3.00 ( 2901) metal coordination : bond 0.00449 / 0.23 ( 4) metal coordination : angle 5.98453 / 3.47 ( 6) Misc. bond : bond 0.00030 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5360.45 seconds wall clock time: 92 minutes 38.01 seconds (5558.01 seconds total)