Starting phenix.real_space_refine on Wed May 21 06:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yg1_39233/05_2025/8yg1_39233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yg1_39233/05_2025/8yg1_39233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yg1_39233/05_2025/8yg1_39233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yg1_39233/05_2025/8yg1_39233.map" model { file = "/net/cci-nas-00/data/ceres_data/8yg1_39233/05_2025/8yg1_39233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yg1_39233/05_2025/8yg1_39233.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 13596 2.51 5 N 3396 2.21 5 O 3956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21026 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 8285 Classifications: {'peptide': 995} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 975} Chain: "B" Number of atoms: 8285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 8285 Classifications: {'peptide': 995} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 975} Chain: "C" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2220 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain: "D" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2236 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 10, 'TRANS': 263} Time building chain proxies: 12.47, per 1000 atoms: 0.59 Number of scatterers: 21026 At special positions: 0 Unit cell: (107.07, 131.97, 187.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3956 8.00 N 3396 7.00 C 13596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.80 Conformation dependent library (CDL) restraints added in 2.6 seconds 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4816 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 8 sheets defined 65.8% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 23 through 39 removed outlier: 3.528A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.990A pdb=" N LEU A 70 " --> pdb=" O TYR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 95 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.578A pdb=" N GLY A 102 " --> pdb=" O MET A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.734A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.555A pdb=" N ASP A 157 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 158 " --> pdb=" O GLU A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.538A pdb=" N SER A 201 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 236 removed outlier: 3.505A pdb=" N GLN A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.843A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.757A pdb=" N GLU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 326 through 334 removed outlier: 4.031A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N HIS A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.764A pdb=" N PHE A 361 " --> pdb=" O MET A 357 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 375 through 391 removed outlier: 4.411A pdb=" N GLU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N PHE A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 426 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.631A pdb=" N LEU A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 468 through 496 removed outlier: 3.513A pdb=" N TYR A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 525 through 531 removed outlier: 4.400A pdb=" N ASN A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'A' and resid 554 through 572 removed outlier: 3.999A pdb=" N ASN A 563 " --> pdb=" O PHE A 559 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.725A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.648A pdb=" N HIS A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 640 Processing helix chain 'A' and resid 648 through 659 removed outlier: 3.511A pdb=" N PHE A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 705 through 723 removed outlier: 3.819A pdb=" N THR A 710 " --> pdb=" O VAL A 706 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 718 " --> pdb=" O SER A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.705A pdb=" N LEU A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 734 " --> pdb=" O GLU A 730 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 736 " --> pdb=" O GLY A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 765 removed outlier: 3.558A pdb=" N LYS A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 4.132A pdb=" N ILE A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.868A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 removed outlier: 3.636A pdb=" N SER A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 823 " --> pdb=" O ARG A 819 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 841 removed outlier: 3.524A pdb=" N LEU A 841 " --> pdb=" O PHE A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 856 removed outlier: 3.526A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 872 removed outlier: 3.538A pdb=" N ARG A 870 " --> pdb=" O MET A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 903 removed outlier: 3.501A pdb=" N GLU A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 922 Processing helix chain 'A' and resid 927 through 934 removed outlier: 3.747A pdb=" N MET A 930 " --> pdb=" O ASN A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 removed outlier: 3.681A pdb=" N LYS A 953 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 961 Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 975 through 991 removed outlier: 4.733A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1003 removed outlier: 4.344A pdb=" N LEU A 997 " --> pdb=" O ASP A 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 23 through 39 removed outlier: 3.535A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 28 " --> pdb=" O ASN B 24 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 4.003A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 3.582A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 96 removed outlier: 4.157A pdb=" N GLN B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.626A pdb=" N ILE B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.901A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 155 through 161 removed outlier: 3.847A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 3.601A pdb=" N ASN B 192 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 211 removed outlier: 3.956A pdb=" N SER B 201 " --> pdb=" O TYR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 235 removed outlier: 3.504A pdb=" N MET B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 228 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 235 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.674A pdb=" N ILE B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.612A pdb=" N ARG B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.927A pdb=" N VAL B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 309 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 321 removed outlier: 3.744A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 326 through 335 removed outlier: 4.665A pdb=" N LYS B 331 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 335 " --> pdb=" O HIS B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 366 removed outlier: 3.956A pdb=" N PHE B 361 " --> pdb=" O MET B 357 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.918A pdb=" N LYS B 372 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 392 removed outlier: 3.594A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.782A pdb=" N HIS B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 426 removed outlier: 3.887A pdb=" N MET B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 446 Processing helix chain 'B' and resid 447 through 463 Processing helix chain 'B' and resid 468 through 496 Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.629A pdb=" N LEU B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 546 removed outlier: 4.457A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 546 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 559 removed outlier: 3.686A pdb=" N PHE B 559 " --> pdb=" O THR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' Processing helix chain 'B' and resid 566 through 572 removed outlier: 3.612A pdb=" N SER B 570 " --> pdb=" O ARG B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 598 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.872A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 629 removed outlier: 3.754A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 619 " --> pdb=" O SER B 615 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE B 620 " --> pdb=" O MET B 616 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 621 " --> pdb=" O SER B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 639 removed outlier: 4.119A pdb=" N SER B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 638 " --> pdb=" O LEU B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.740A pdb=" N LYS B 675 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 676 " --> pdb=" O ILE B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 672 through 676' Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.739A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 722 removed outlier: 3.962A pdb=" N GLN B 711 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 743 removed outlier: 3.865A pdb=" N LYS B 735 " --> pdb=" O GLU B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 762 removed outlier: 3.823A pdb=" N TYR B 755 " --> pdb=" O ILE B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 801 through 812 removed outlier: 3.935A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 removed outlier: 4.010A pdb=" N CYS B 826 " --> pdb=" O GLU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 839 Processing helix chain 'B' and resid 840 through 842 No H-bonds generated for 'chain 'B' and resid 840 through 842' Processing helix chain 'B' and resid 846 through 855 Processing helix chain 'B' and resid 861 through 871 removed outlier: 3.900A pdb=" N ASN B 867 " --> pdb=" O ASN B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 903 Processing helix chain 'B' and resid 911 through 922 Processing helix chain 'B' and resid 927 through 933 removed outlier: 4.097A pdb=" N GLU B 931 " --> pdb=" O ASN B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 955 through 962 Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 975 through 991 removed outlier: 4.430A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.503A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 39 removed outlier: 3.754A pdb=" N ASN C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 removed outlier: 4.057A pdb=" N LEU C 53 " --> pdb=" O GLY C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.896A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 95 Proline residue: C 88 - end of helix removed outlier: 3.682A pdb=" N PHE C 91 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 115 through 123 removed outlier: 4.262A pdb=" N ASP C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 154 through 160 removed outlier: 4.195A pdb=" N VAL C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 160' Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 223 through 228 removed outlier: 3.564A pdb=" N LEU C 228 " --> pdb=" O ASN C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 235 removed outlier: 3.729A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 265 Processing helix chain 'C' and resid 281 through 296 removed outlier: 3.550A pdb=" N ARG C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 39 Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.708A pdb=" N SER D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.853A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.777A pdb=" N LEU D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.680A pdb=" N PHE D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.517A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.603A pdb=" N VAL D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 192 removed outlier: 3.536A pdb=" N TYR D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.529A pdb=" N HIS D 211 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 236 through 240 removed outlier: 3.921A pdb=" N PHE D 240 " --> pdb=" O LYS D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.696A pdb=" N SER D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.355A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU A 42 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 244 through 247 removed outlier: 6.470A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 340 removed outlier: 3.700A pdb=" N VAL A 346 " --> pdb=" O CYS A 395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.573A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU B 42 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE B 245 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 152 removed outlier: 3.683A pdb=" N VAL C 129 " --> pdb=" O TYR C 166 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 168 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS C 128 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE C 245 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.084A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL D 129 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 43 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE D 216 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N PHE D 45 " --> pdb=" O ILE D 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 244 through 247 removed outlier: 3.531A pdb=" N ARG D 247 " --> pdb=" O ILE D 269 " (cutoff:3.500A) 981 hydrogen bonds defined for protein. 2832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.86 Time building geometry restraints manager: 5.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6677 1.34 - 1.46: 5417 1.46 - 1.58: 9292 1.58 - 1.70: 2 1.70 - 1.82: 132 Bond restraints: 21520 Sorted by residual: bond pdb=" CB PRO B 768 " pdb=" CG PRO B 768 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.37e+00 bond pdb=" CG PRO A 113 " pdb=" CD PRO A 113 " ideal model delta sigma weight residual 1.503 1.573 -0.070 3.40e-02 8.65e+02 4.24e+00 bond pdb=" CB PRO A 113 " pdb=" CG PRO A 113 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.34e+00 bond pdb=" C SER A 317 " pdb=" N PRO A 318 " ideal model delta sigma weight residual 1.337 1.351 -0.015 9.80e-03 1.04e+04 2.28e+00 bond pdb=" SD MET D 290 " pdb=" CE MET D 290 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.73e+00 ... (remaining 21515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 28676 2.57 - 5.14: 300 5.14 - 7.71: 37 7.71 - 10.28: 9 10.28 - 12.85: 4 Bond angle restraints: 29026 Sorted by residual: angle pdb=" CA PRO B 768 " pdb=" N PRO B 768 " pdb=" CD PRO B 768 " ideal model delta sigma weight residual 112.00 100.94 11.06 1.40e+00 5.10e-01 6.24e+01 angle pdb=" N VAL B 565 " pdb=" CA VAL B 565 " pdb=" C VAL B 565 " ideal model delta sigma weight residual 113.20 107.86 5.34 9.60e-01 1.09e+00 3.10e+01 angle pdb=" CA PRO A 113 " pdb=" N PRO A 113 " pdb=" CD PRO A 113 " ideal model delta sigma weight residual 112.00 104.50 7.50 1.40e+00 5.10e-01 2.87e+01 angle pdb=" N VAL C 50 " pdb=" CA VAL C 50 " pdb=" C VAL C 50 " ideal model delta sigma weight residual 112.80 107.10 5.70 1.15e+00 7.56e-01 2.46e+01 angle pdb=" CB MET C 290 " pdb=" CG MET C 290 " pdb=" SD MET C 290 " ideal model delta sigma weight residual 112.70 125.55 -12.85 3.00e+00 1.11e-01 1.84e+01 ... (remaining 29021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 10760 17.89 - 35.79: 1507 35.79 - 53.68: 429 53.68 - 71.57: 80 71.57 - 89.47: 40 Dihedral angle restraints: 12816 sinusoidal: 5302 harmonic: 7514 Sorted by residual: dihedral pdb=" CA GLN B 297 " pdb=" C GLN B 297 " pdb=" N GLU B 298 " pdb=" CA GLU B 298 " ideal model delta harmonic sigma weight residual 180.00 147.61 32.39 0 5.00e+00 4.00e-02 4.20e+01 dihedral pdb=" CA GLY C 40 " pdb=" C GLY C 40 " pdb=" N LYS C 41 " pdb=" CA LYS C 41 " ideal model delta harmonic sigma weight residual -180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ASN A 299 " pdb=" C ASN A 299 " pdb=" N LYS A 300 " pdb=" CA LYS A 300 " ideal model delta harmonic sigma weight residual -180.00 -158.96 -21.04 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 12813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2657 0.059 - 0.118: 395 0.118 - 0.177: 28 0.177 - 0.236: 1 0.236 - 0.295: 1 Chirality restraints: 3082 Sorted by residual: chirality pdb=" CA ASN B 125 " pdb=" N ASN B 125 " pdb=" C ASN B 125 " pdb=" CB ASN B 125 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB ILE A 541 " pdb=" CA ILE A 541 " pdb=" CG1 ILE A 541 " pdb=" CG2 ILE A 541 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CG LEU C 235 " pdb=" CB LEU C 235 " pdb=" CD1 LEU C 235 " pdb=" CD2 LEU C 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 3079 not shown) Planarity restraints: 3712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 767 " -0.114 5.00e-02 4.00e+02 1.64e-01 4.30e+01 pdb=" N PRO B 768 " 0.283 5.00e-02 4.00e+02 pdb=" CA PRO B 768 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO B 768 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 143 " -0.034 2.00e-02 2.50e+03 3.52e-02 3.09e+01 pdb=" CG TRP D 143 " 0.095 2.00e-02 2.50e+03 pdb=" CD1 TRP D 143 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP D 143 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 143 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 143 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 143 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 143 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 60 " 0.021 2.00e-02 2.50e+03 2.21e-02 1.22e+01 pdb=" CG TRP D 60 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP D 60 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 60 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 60 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 60 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 60 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 60 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 60 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP D 60 " -0.004 2.00e-02 2.50e+03 ... (remaining 3709 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 364 2.69 - 3.24: 20666 3.24 - 3.79: 31523 3.79 - 4.35: 40662 4.35 - 4.90: 65957 Nonbonded interactions: 159172 Sorted by model distance: nonbonded pdb=" OG1 THR D 131 " pdb=" OD1 ASN D 133 " model vdw 2.134 3.040 nonbonded pdb=" O LEU A 842 " pdb=" NZ LYS A 850 " model vdw 2.157 3.120 nonbonded pdb=" OG SER B 150 " pdb=" O ARG B 165 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR B 414 " pdb=" OD1 ASN B 654 " model vdw 2.168 3.040 nonbonded pdb=" O PRO B 318 " pdb=" OH TYR B 539 " model vdw 2.181 3.040 ... (remaining 159167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 26 through 297) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 45.240 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 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 0.126 21520 Z= 0.156 Angle : 0.691 12.855 29026 Z= 0.389 Chirality : 0.041 0.295 3082 Planarity : 0.005 0.164 3712 Dihedral : 18.372 89.468 8000 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.97 % Favored : 93.79 % Rotamer: Outliers : 0.73 % Allowed : 26.53 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2528 helix: 0.64 (0.14), residues: 1401 sheet: -1.06 (0.52), residues: 88 loop : -1.52 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.003 TRP D 143 HIS 0.005 0.001 HIS B 67 PHE 0.043 0.002 PHE B 240 TYR 0.030 0.002 TYR C 56 ARG 0.009 0.001 ARG B 747 Details of bonding type rmsd hydrogen bonds : bond 0.17694 ( 981) hydrogen bonds : angle 6.01081 ( 2832) covalent geometry : bond 0.00346 (21520) covalent geometry : angle 0.69079 (29026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 495 time to evaluate : 2.135 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: A 17 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: A 408 GLU cc_start: 0.7163 (tp30) cc_final: 0.6954 (tp30) REVERT: A 448 TRP cc_start: 0.7692 (m-10) cc_final: 0.7167 (m-10) REVERT: A 540 LYS cc_start: 0.8510 (tptm) cc_final: 0.8166 (tppt) REVERT: A 974 LYS cc_start: 0.9168 (ttpt) cc_final: 0.8704 (tmmt) REVERT: A 977 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8036 (ttpp) REVERT: B 181 GLU cc_start: 0.7521 (pt0) cc_final: 0.7185 (mt-10) REVERT: B 295 GLU cc_start: 0.7681 (tt0) cc_final: 0.7381 (tp30) REVERT: C 128 HIS cc_start: 0.8291 (m-70) cc_final: 0.8005 (m90) REVERT: C 224 ASN cc_start: 0.7853 (t0) cc_final: 0.7521 (t0) REVERT: D 83 GLU cc_start: 0.6071 (mm-30) cc_final: 0.4717 (mt-10) REVERT: D 169 LYS cc_start: 0.8633 (mttm) cc_final: 0.8379 (mttp) outliers start: 17 outliers final: 9 residues processed: 499 average time/residue: 0.3603 time to fit residues: 271.8427 Evaluate side-chains 497 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 486 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 977 LYS Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain D residue 136 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.5980 chunk 191 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 128 optimal weight: 0.0050 chunk 102 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 147 optimal weight: 9.9990 chunk 228 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN B 67 HIS ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 HIS C 133 ASN D 58 GLN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.156966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122759 restraints weight = 32654.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126854 restraints weight = 17247.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129594 restraints weight = 11311.442| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21520 Z= 0.142 Angle : 0.583 11.021 29026 Z= 0.311 Chirality : 0.041 0.181 3082 Planarity : 0.004 0.095 3712 Dihedral : 5.382 57.640 2824 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.54 % Favored : 94.22 % Rotamer: Outliers : 3.33 % Allowed : 23.51 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2528 helix: 0.75 (0.14), residues: 1458 sheet: -1.08 (0.58), residues: 65 loop : -1.48 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 143 HIS 0.006 0.001 HIS D 67 PHE 0.034 0.002 PHE A 933 TYR 0.021 0.002 TYR A 552 ARG 0.005 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.04711 ( 981) hydrogen bonds : angle 4.70142 ( 2832) covalent geometry : bond 0.00317 (21520) covalent geometry : angle 0.58320 (29026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 507 time to evaluate : 2.121 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: A 41 LYS cc_start: 0.7993 (mttt) cc_final: 0.7661 (mttm) REVERT: A 117 ILE cc_start: 0.6907 (mm) cc_final: 0.6706 (mm) REVERT: A 131 THR cc_start: 0.8421 (m) cc_final: 0.8136 (t) REVERT: A 280 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6656 (m-80) REVERT: A 286 TYR cc_start: 0.7412 (m-80) cc_final: 0.7189 (m-10) REVERT: A 391 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7749 (t0) REVERT: A 393 VAL cc_start: 0.6770 (OUTLIER) cc_final: 0.6386 (p) REVERT: A 448 TRP cc_start: 0.7819 (m-10) cc_final: 0.7434 (m-10) REVERT: A 516 GLU cc_start: 0.7919 (tp30) cc_final: 0.7536 (tp30) REVERT: A 760 ARG cc_start: 0.7660 (mtp-110) cc_final: 0.7460 (mtp-110) REVERT: A 823 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7966 (mp) REVERT: A 829 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: A 882 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: A 916 PHE cc_start: 0.8309 (m-80) cc_final: 0.7971 (m-80) REVERT: A 933 PHE cc_start: 0.7904 (m-80) cc_final: 0.7643 (m-10) REVERT: A 969 LYS cc_start: 0.8488 (tptm) cc_final: 0.8204 (tptm) REVERT: A 974 LYS cc_start: 0.9063 (ttpt) cc_final: 0.8731 (tmmt) REVERT: B 181 GLU cc_start: 0.7347 (pt0) cc_final: 0.7107 (mt-10) REVERT: B 291 ASP cc_start: 0.7670 (m-30) cc_final: 0.7419 (m-30) REVERT: B 304 LYS cc_start: 0.8216 (mmtm) cc_final: 0.7990 (mmtm) REVERT: B 335 GLU cc_start: 0.7565 (mp0) cc_final: 0.7339 (mp0) REVERT: B 569 MET cc_start: 0.2426 (mtp) cc_final: 0.2047 (mtp) REVERT: B 595 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7448 (mt) REVERT: B 669 ARG cc_start: 0.7212 (tpp80) cc_final: 0.6672 (tpp80) REVERT: B 818 LYS cc_start: 0.8463 (tppt) cc_final: 0.7830 (mmmt) REVERT: C 224 ASN cc_start: 0.7973 (t0) cc_final: 0.7726 (t0) REVERT: C 236 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7260 (mt0) REVERT: D 71 TYR cc_start: 0.6344 (m-80) cc_final: 0.5820 (m-80) REVERT: D 83 GLU cc_start: 0.6051 (mm-30) cc_final: 0.4795 (mt-10) REVERT: D 120 LYS cc_start: 0.8302 (pttt) cc_final: 0.7277 (pmtt) REVERT: D 155 GLU cc_start: 0.6295 (mm-30) cc_final: 0.5941 (mm-30) REVERT: D 197 TYR cc_start: 0.7616 (m-80) cc_final: 0.7139 (m-80) REVERT: D 208 ILE cc_start: 0.8727 (mt) cc_final: 0.8463 (tt) outliers start: 77 outliers final: 31 residues processed: 546 average time/residue: 0.3297 time to fit residues: 271.2062 Evaluate side-chains 521 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 482 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 290 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 196 optimal weight: 3.9990 chunk 245 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 44 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 181 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 175 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 ASN C 109 GLN C 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.156817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122540 restraints weight = 32622.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126670 restraints weight = 17192.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129472 restraints weight = 11246.266| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21520 Z= 0.133 Angle : 0.566 11.176 29026 Z= 0.298 Chirality : 0.041 0.172 3082 Planarity : 0.004 0.084 3712 Dihedral : 5.042 53.283 2808 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.34 % Favored : 94.46 % Rotamer: Outliers : 3.54 % Allowed : 24.16 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2528 helix: 0.86 (0.14), residues: 1459 sheet: -1.30 (0.58), residues: 65 loop : -1.45 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP D 143 HIS 0.005 0.001 HIS D 67 PHE 0.019 0.001 PHE A 933 TYR 0.018 0.001 TYR A 552 ARG 0.005 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 981) hydrogen bonds : angle 4.50664 ( 2832) covalent geometry : bond 0.00298 (21520) covalent geometry : angle 0.56587 (29026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 495 time to evaluate : 2.110 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: A 41 LYS cc_start: 0.7896 (mttt) cc_final: 0.7692 (mttm) REVERT: A 107 PHE cc_start: 0.7912 (m-80) cc_final: 0.7704 (m-80) REVERT: A 131 THR cc_start: 0.8384 (m) cc_final: 0.8128 (t) REVERT: A 280 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6683 (m-80) REVERT: A 286 TYR cc_start: 0.7465 (m-80) cc_final: 0.7230 (m-10) REVERT: A 350 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7920 (mmtt) REVERT: A 391 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7869 (t0) REVERT: A 393 VAL cc_start: 0.6751 (OUTLIER) cc_final: 0.6375 (p) REVERT: A 448 TRP cc_start: 0.7824 (m-10) cc_final: 0.7577 (m-10) REVERT: A 516 GLU cc_start: 0.7953 (tp30) cc_final: 0.7626 (tp30) REVERT: A 540 LYS cc_start: 0.8547 (tptm) cc_final: 0.8263 (tppt) REVERT: A 696 THR cc_start: 0.7602 (m) cc_final: 0.7333 (m) REVERT: A 823 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7906 (mp) REVERT: A 829 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7698 (tp40) REVERT: A 882 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8358 (mt-10) REVERT: A 916 PHE cc_start: 0.8343 (m-80) cc_final: 0.7972 (m-80) REVERT: A 969 LYS cc_start: 0.8619 (tptm) cc_final: 0.8307 (tptm) REVERT: B 181 GLU cc_start: 0.7340 (pt0) cc_final: 0.7035 (mt-10) REVERT: B 291 ASP cc_start: 0.7662 (m-30) cc_final: 0.7271 (m-30) REVERT: B 304 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7829 (mmtm) REVERT: B 329 ASP cc_start: 0.7428 (t0) cc_final: 0.7029 (t0) REVERT: B 354 PHE cc_start: 0.7856 (t80) cc_final: 0.7557 (t80) REVERT: B 559 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7215 (t80) REVERT: B 569 MET cc_start: 0.3036 (mtp) cc_final: 0.2498 (mtp) REVERT: B 669 ARG cc_start: 0.7208 (tpp80) cc_final: 0.6679 (tpp80) REVERT: B 818 LYS cc_start: 0.8456 (tppt) cc_final: 0.7844 (mmmt) REVERT: B 986 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7773 (tm-30) REVERT: C 224 ASN cc_start: 0.8034 (t0) cc_final: 0.7636 (t0) REVERT: C 235 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7270 (pp) REVERT: C 249 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6420 (m-30) REVERT: D 83 GLU cc_start: 0.6017 (mm-30) cc_final: 0.4819 (mt-10) REVERT: D 120 LYS cc_start: 0.8301 (pttt) cc_final: 0.7469 (pmtt) REVERT: D 144 LYS cc_start: 0.8044 (mttt) cc_final: 0.7828 (tptt) REVERT: D 208 ILE cc_start: 0.8719 (mt) cc_final: 0.8446 (tt) REVERT: D 222 ASP cc_start: 0.7350 (t0) cc_final: 0.7023 (t0) outliers start: 82 outliers final: 41 residues processed: 539 average time/residue: 0.3273 time to fit residues: 267.1284 Evaluate side-chains 539 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 489 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 290 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 175 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 GLN A 939 GLN B 67 HIS ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** D 128 HIS ** 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 = 0.3954 r_free = 0.3954 target = 0.153693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119090 restraints weight = 33301.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123118 restraints weight = 17556.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125868 restraints weight = 11539.546| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 21520 Z= 0.224 Angle : 0.611 9.632 29026 Z= 0.325 Chirality : 0.044 0.208 3082 Planarity : 0.004 0.077 3712 Dihedral : 4.973 49.102 2805 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.21 % Favored : 93.59 % Rotamer: Outliers : 4.49 % Allowed : 23.51 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2528 helix: 0.75 (0.14), residues: 1471 sheet: -1.51 (0.57), residues: 65 loop : -1.55 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP D 143 HIS 0.008 0.001 HIS D 67 PHE 0.050 0.002 PHE B 240 TYR 0.034 0.002 TYR A 649 ARG 0.005 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.05117 ( 981) hydrogen bonds : angle 4.56647 ( 2832) covalent geometry : bond 0.00517 (21520) covalent geometry : angle 0.61105 (29026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 506 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7106 (tm-30) REVERT: A 42 LEU cc_start: 0.8675 (tp) cc_final: 0.8381 (tt) REVERT: A 45 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7052 (t80) REVERT: A 75 LYS cc_start: 0.8499 (tppt) cc_final: 0.7829 (ttmm) REVERT: A 109 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7414 (tm-30) REVERT: A 131 THR cc_start: 0.8445 (m) cc_final: 0.8187 (t) REVERT: A 176 LYS cc_start: 0.8730 (mtmm) cc_final: 0.8440 (mtmm) REVERT: A 280 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6767 (m-80) REVERT: A 297 GLN cc_start: 0.8165 (mp10) cc_final: 0.7895 (mp10) REVERT: A 310 ASP cc_start: 0.7200 (m-30) cc_final: 0.6802 (t0) REVERT: A 391 ASN cc_start: 0.8335 (t0) cc_final: 0.8076 (t0) REVERT: A 393 VAL cc_start: 0.6729 (OUTLIER) cc_final: 0.6416 (p) REVERT: A 408 GLU cc_start: 0.7198 (tp30) cc_final: 0.6966 (tp30) REVERT: A 448 TRP cc_start: 0.7879 (m-10) cc_final: 0.7674 (m-10) REVERT: A 516 GLU cc_start: 0.8044 (tp30) cc_final: 0.7710 (tp30) REVERT: A 531 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7130 (mmm) REVERT: A 540 LYS cc_start: 0.8559 (tptm) cc_final: 0.8332 (tppt) REVERT: A 696 THR cc_start: 0.7677 (m) cc_final: 0.7421 (m) REVERT: A 809 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8428 (mmtt) REVERT: A 823 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7923 (mp) REVERT: A 829 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7823 (tp40) REVERT: A 881 HIS cc_start: 0.8231 (OUTLIER) cc_final: 0.7983 (m90) REVERT: A 882 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: A 916 PHE cc_start: 0.8420 (m-80) cc_final: 0.8002 (m-80) REVERT: A 969 LYS cc_start: 0.8727 (tptm) cc_final: 0.8380 (tptm) REVERT: A 974 LYS cc_start: 0.8859 (tmmt) cc_final: 0.8603 (tmmt) REVERT: B 291 ASP cc_start: 0.7738 (m-30) cc_final: 0.7252 (m-30) REVERT: B 304 LYS cc_start: 0.8200 (mmtm) cc_final: 0.7853 (mmtm) REVERT: B 329 ASP cc_start: 0.7484 (t0) cc_final: 0.7011 (t0) REVERT: B 531 MET cc_start: 0.8239 (mmm) cc_final: 0.7738 (mmm) REVERT: B 541 ILE cc_start: 0.8400 (mm) cc_final: 0.7994 (mm) REVERT: B 565 VAL cc_start: 0.3116 (OUTLIER) cc_final: 0.2857 (t) REVERT: B 595 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7609 (mt) REVERT: B 622 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6711 (tptm) REVERT: B 669 ARG cc_start: 0.7298 (tpp80) cc_final: 0.6820 (tpp80) REVERT: B 686 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6858 (mm-30) REVERT: B 818 LYS cc_start: 0.8472 (tppt) cc_final: 0.7891 (mmmt) REVERT: B 986 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7792 (tm-30) REVERT: C 224 ASN cc_start: 0.8186 (t0) cc_final: 0.7828 (t160) REVERT: C 235 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7342 (pp) REVERT: C 249 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6531 (m-30) REVERT: D 83 GLU cc_start: 0.6193 (mm-30) cc_final: 0.4983 (mt-10) REVERT: D 120 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7249 (pmtt) REVERT: D 140 THR cc_start: 0.8498 (p) cc_final: 0.7917 (p) REVERT: D 203 LEU cc_start: 0.8296 (tp) cc_final: 0.7930 (tt) REVERT: D 208 ILE cc_start: 0.8764 (mt) cc_final: 0.8506 (tt) REVERT: D 222 ASP cc_start: 0.7534 (t0) cc_final: 0.7176 (t0) outliers start: 104 outliers final: 54 residues processed: 559 average time/residue: 0.3510 time to fit residues: 295.8250 Evaluate side-chains 565 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 497 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 881 HIS Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 665 LYS Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 251 optimal weight: 2.9990 chunk 10 optimal weight: 0.0020 chunk 191 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN B 67 HIS ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.154891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120379 restraints weight = 32785.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.124450 restraints weight = 17283.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.127212 restraints weight = 11339.219| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21520 Z= 0.149 Angle : 0.567 9.729 29026 Z= 0.301 Chirality : 0.041 0.183 3082 Planarity : 0.004 0.073 3712 Dihedral : 4.758 37.964 2803 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.54 % Favored : 94.26 % Rotamer: Outliers : 4.11 % Allowed : 24.24 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2528 helix: 0.88 (0.14), residues: 1468 sheet: -1.56 (0.57), residues: 65 loop : -1.56 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP D 143 HIS 0.006 0.001 HIS D 67 PHE 0.060 0.002 PHE B 240 TYR 0.018 0.001 TYR A 649 ARG 0.006 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 981) hydrogen bonds : angle 4.40878 ( 2832) covalent geometry : bond 0.00342 (21520) covalent geometry : angle 0.56748 (29026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 500 time to evaluate : 2.129 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: A 35 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7109 (tm-30) REVERT: A 45 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.6820 (m-80) REVERT: A 109 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 131 THR cc_start: 0.8383 (m) cc_final: 0.8045 (t) REVERT: A 155 GLU cc_start: 0.7568 (tp30) cc_final: 0.7344 (tp30) REVERT: A 176 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8393 (mtmm) REVERT: A 297 GLN cc_start: 0.8167 (mp10) cc_final: 0.7929 (mp10) REVERT: A 316 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8148 (tt) REVERT: A 329 ASP cc_start: 0.7321 (t0) cc_final: 0.7055 (t0) REVERT: A 350 LYS cc_start: 0.8292 (mmtt) cc_final: 0.8000 (mmtm) REVERT: A 391 ASN cc_start: 0.8339 (t0) cc_final: 0.8061 (t0) REVERT: A 393 VAL cc_start: 0.6690 (OUTLIER) cc_final: 0.6388 (p) REVERT: A 448 TRP cc_start: 0.7774 (m-10) cc_final: 0.7548 (m-10) REVERT: A 516 GLU cc_start: 0.8034 (tp30) cc_final: 0.7610 (tp30) REVERT: A 531 MET cc_start: 0.7432 (mmm) cc_final: 0.7176 (mmm) REVERT: A 540 LYS cc_start: 0.8522 (tptm) cc_final: 0.8284 (tppt) REVERT: A 809 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8400 (mmtt) REVERT: A 823 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7897 (mp) REVERT: A 829 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7796 (tp-100) REVERT: A 878 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.7572 (p) REVERT: A 882 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8370 (mt-10) REVERT: A 916 PHE cc_start: 0.8386 (m-80) cc_final: 0.7988 (m-80) REVERT: A 969 LYS cc_start: 0.8809 (tptm) cc_final: 0.8287 (tptp) REVERT: A 974 LYS cc_start: 0.8810 (tmmt) cc_final: 0.8543 (tmmt) REVERT: B 125 ASN cc_start: 0.8263 (p0) cc_final: 0.7913 (p0) REVERT: B 291 ASP cc_start: 0.7736 (m-30) cc_final: 0.7157 (m-30) REVERT: B 304 LYS cc_start: 0.8207 (mmtm) cc_final: 0.7906 (mmtm) REVERT: B 329 ASP cc_start: 0.7438 (t0) cc_final: 0.7054 (t70) REVERT: B 357 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6058 (tmm) REVERT: B 538 LYS cc_start: 0.8562 (mttm) cc_final: 0.8212 (mtmt) REVERT: B 541 ILE cc_start: 0.8377 (mm) cc_final: 0.7805 (mm) REVERT: B 595 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7540 (mt) REVERT: B 622 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6566 (mmmt) REVERT: B 625 TYR cc_start: 0.6827 (t80) cc_final: 0.6522 (t80) REVERT: B 686 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6838 (mm-30) REVERT: B 724 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7367 (pttm) REVERT: B 818 LYS cc_start: 0.8470 (tppt) cc_final: 0.7892 (mmmt) REVERT: B 986 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7754 (tm-30) REVERT: C 117 ILE cc_start: 0.8328 (mm) cc_final: 0.7998 (tt) REVERT: C 193 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7630 (t80) REVERT: C 224 ASN cc_start: 0.8207 (t0) cc_final: 0.7949 (t0) REVERT: C 235 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7235 (pp) REVERT: C 248 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7694 (p) REVERT: C 249 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6554 (m-30) REVERT: C 254 GLU cc_start: 0.5885 (OUTLIER) cc_final: 0.5439 (tp30) REVERT: D 83 GLU cc_start: 0.6114 (mm-30) cc_final: 0.5000 (mt-10) REVERT: D 120 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7594 (pmtt) REVERT: D 144 LYS cc_start: 0.8091 (tptt) cc_final: 0.7831 (tptt) REVERT: D 222 ASP cc_start: 0.7515 (t0) cc_final: 0.7163 (t0) outliers start: 95 outliers final: 53 residues processed: 549 average time/residue: 0.3329 time to fit residues: 275.9599 Evaluate side-chains 564 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 494 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 665 LYS Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 724 LYS Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 19 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 chunk 148 optimal weight: 0.0060 chunk 56 optimal weight: 30.0000 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 163 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 67 HIS B 297 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.155264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120639 restraints weight = 32667.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124669 restraints weight = 17308.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.127472 restraints weight = 11387.257| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21520 Z= 0.132 Angle : 0.558 10.175 29026 Z= 0.295 Chirality : 0.041 0.192 3082 Planarity : 0.004 0.072 3712 Dihedral : 4.600 39.738 2801 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.66 % Favored : 94.15 % Rotamer: Outliers : 4.02 % Allowed : 25.06 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 2528 helix: 1.00 (0.14), residues: 1468 sheet: -1.66 (0.57), residues: 65 loop : -1.55 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP D 143 HIS 0.008 0.001 HIS A 881 PHE 0.038 0.001 PHE B 240 TYR 0.024 0.001 TYR A 56 ARG 0.006 0.000 ARG A 760 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 981) hydrogen bonds : angle 4.27922 ( 2832) covalent geometry : bond 0.00300 (21520) covalent geometry : angle 0.55828 (29026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 500 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7099 (tm-30) REVERT: A 45 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.6804 (m-80) REVERT: A 109 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7532 (tm-30) REVERT: A 131 THR cc_start: 0.8368 (m) cc_final: 0.8038 (t) REVERT: A 135 ASP cc_start: 0.7923 (t0) cc_final: 0.7644 (t0) REVERT: A 176 LYS cc_start: 0.8702 (mtmm) cc_final: 0.8378 (mtmm) REVERT: A 248 THR cc_start: 0.8200 (p) cc_final: 0.7987 (p) REVERT: A 280 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: A 297 GLN cc_start: 0.8188 (mp10) cc_final: 0.7976 (mp10) REVERT: A 329 ASP cc_start: 0.7352 (t0) cc_final: 0.7044 (t0) REVERT: A 391 ASN cc_start: 0.8337 (t0) cc_final: 0.8069 (t0) REVERT: A 393 VAL cc_start: 0.6661 (OUTLIER) cc_final: 0.6362 (p) REVERT: A 448 TRP cc_start: 0.7781 (m-10) cc_final: 0.7559 (m-10) REVERT: A 516 GLU cc_start: 0.8013 (tp30) cc_final: 0.7589 (tp30) REVERT: A 540 LYS cc_start: 0.8520 (tptm) cc_final: 0.8292 (tppt) REVERT: A 681 GLN cc_start: 0.6893 (mt0) cc_final: 0.6389 (mm-40) REVERT: A 760 ARG cc_start: 0.7567 (mtp-110) cc_final: 0.7250 (mtp-110) REVERT: A 823 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7878 (mp) REVERT: A 829 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7803 (tp40) REVERT: A 882 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: A 916 PHE cc_start: 0.8360 (m-80) cc_final: 0.7890 (m-80) REVERT: A 958 TRP cc_start: 0.7804 (m-10) cc_final: 0.7576 (m-10) REVERT: A 969 LYS cc_start: 0.8858 (tptm) cc_final: 0.8507 (tptm) REVERT: A 974 LYS cc_start: 0.8860 (tmmt) cc_final: 0.8593 (tmmt) REVERT: B 125 ASN cc_start: 0.8330 (p0) cc_final: 0.8053 (p0) REVERT: B 203 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8249 (tt) REVERT: B 291 ASP cc_start: 0.7745 (m-30) cc_final: 0.7176 (m-30) REVERT: B 297 GLN cc_start: 0.5431 (OUTLIER) cc_final: 0.4505 (tp40) REVERT: B 304 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7933 (mmtm) REVERT: B 329 ASP cc_start: 0.7427 (t0) cc_final: 0.6810 (t0) REVERT: B 357 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.5931 (tmm) REVERT: B 426 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: B 538 LYS cc_start: 0.8529 (mttm) cc_final: 0.8219 (mttt) REVERT: B 541 ILE cc_start: 0.8403 (mm) cc_final: 0.7832 (mm) REVERT: B 569 MET cc_start: 0.1175 (mtp) cc_final: 0.0654 (mtp) REVERT: B 595 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7628 (mt) REVERT: B 622 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6620 (tptp) REVERT: B 625 TYR cc_start: 0.7017 (t80) cc_final: 0.6513 (t80) REVERT: B 686 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6858 (mm-30) REVERT: B 818 LYS cc_start: 0.8462 (tppt) cc_final: 0.7878 (mmmt) REVERT: B 986 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7731 (tm-30) REVERT: C 117 ILE cc_start: 0.8299 (mm) cc_final: 0.7987 (tt) REVERT: C 193 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7602 (t80) REVERT: C 224 ASN cc_start: 0.8303 (t0) cc_final: 0.8075 (t0) REVERT: C 235 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7265 (pp) REVERT: C 248 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7713 (p) REVERT: C 249 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6515 (m-30) REVERT: C 254 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.5362 (tp30) REVERT: D 83 GLU cc_start: 0.6083 (mm-30) cc_final: 0.5041 (mt-10) REVERT: D 120 LYS cc_start: 0.8426 (pttt) cc_final: 0.7414 (pmtt) REVERT: D 144 LYS cc_start: 0.8055 (tptt) cc_final: 0.7794 (tptt) REVERT: D 222 ASP cc_start: 0.7510 (t0) cc_final: 0.7145 (t0) REVERT: D 283 LEU cc_start: 0.8645 (tp) cc_final: 0.8439 (tp) outliers start: 93 outliers final: 53 residues processed: 549 average time/residue: 0.3343 time to fit residues: 276.0903 Evaluate side-chains 562 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 492 time to evaluate : 2.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 665 LYS Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 85 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 186 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 34 optimal weight: 0.0010 chunk 131 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 HIS B 297 GLN B 377 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.153338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118830 restraints weight = 32697.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122883 restraints weight = 17344.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.125636 restraints weight = 11390.802| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 21520 Z= 0.194 Angle : 0.602 11.294 29026 Z= 0.317 Chirality : 0.042 0.189 3082 Planarity : 0.004 0.068 3712 Dihedral : 4.687 37.699 2801 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.29 % Favored : 93.51 % Rotamer: Outliers : 3.93 % Allowed : 25.76 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2528 helix: 0.90 (0.14), residues: 1473 sheet: -1.75 (0.56), residues: 65 loop : -1.58 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP D 143 HIS 0.007 0.001 HIS D 67 PHE 0.045 0.002 PHE B 240 TYR 0.025 0.002 TYR A 649 ARG 0.010 0.001 ARG A 760 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 981) hydrogen bonds : angle 4.33752 ( 2832) covalent geometry : bond 0.00449 (21520) covalent geometry : angle 0.60218 (29026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 503 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7145 (tm-30) REVERT: A 45 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: A 109 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7633 (tm-30) REVERT: A 131 THR cc_start: 0.8426 (m) cc_final: 0.8069 (t) REVERT: A 176 LYS cc_start: 0.8711 (mtmm) cc_final: 0.8403 (mtmm) REVERT: A 280 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.7006 (m-80) REVERT: A 294 ILE cc_start: 0.8481 (tp) cc_final: 0.8230 (tt) REVERT: A 297 GLN cc_start: 0.8209 (mp10) cc_final: 0.8007 (mp10) REVERT: A 310 ASP cc_start: 0.7511 (t0) cc_final: 0.7039 (t0) REVERT: A 329 ASP cc_start: 0.7408 (t0) cc_final: 0.7144 (t0) REVERT: A 350 LYS cc_start: 0.8338 (mmtt) cc_final: 0.8090 (mmtm) REVERT: A 391 ASN cc_start: 0.8390 (t0) cc_final: 0.8119 (t0) REVERT: A 393 VAL cc_start: 0.6672 (OUTLIER) cc_final: 0.6392 (p) REVERT: A 408 GLU cc_start: 0.7110 (tp30) cc_final: 0.6878 (tp30) REVERT: A 448 TRP cc_start: 0.7803 (m-10) cc_final: 0.7578 (m-10) REVERT: A 516 GLU cc_start: 0.8061 (tp30) cc_final: 0.7622 (tp30) REVERT: A 540 LYS cc_start: 0.8530 (tptm) cc_final: 0.8267 (tppt) REVERT: A 681 GLN cc_start: 0.7011 (mt0) cc_final: 0.6451 (mm-40) REVERT: A 823 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7875 (mp) REVERT: A 829 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7809 (tp-100) REVERT: A 882 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: A 916 PHE cc_start: 0.8380 (m-80) cc_final: 0.7977 (m-80) REVERT: A 958 TRP cc_start: 0.7847 (m-10) cc_final: 0.7593 (m-10) REVERT: A 969 LYS cc_start: 0.8877 (tptm) cc_final: 0.8502 (tptm) REVERT: A 974 LYS cc_start: 0.8886 (tmmt) cc_final: 0.8611 (tmmt) REVERT: A 985 LYS cc_start: 0.8477 (mtmm) cc_final: 0.8246 (mttm) REVERT: B 125 ASN cc_start: 0.8390 (p0) cc_final: 0.8109 (p0) REVERT: B 291 ASP cc_start: 0.7766 (m-30) cc_final: 0.7173 (m-30) REVERT: B 304 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7919 (mmtm) REVERT: B 329 ASP cc_start: 0.7430 (t0) cc_final: 0.6944 (t0) REVERT: B 357 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.5945 (tmm) REVERT: B 426 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: B 538 LYS cc_start: 0.8582 (mttm) cc_final: 0.8244 (mttt) REVERT: B 595 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7667 (mt) REVERT: B 625 TYR cc_start: 0.7322 (t80) cc_final: 0.6750 (t80) REVERT: B 686 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6900 (mm-30) REVERT: B 818 LYS cc_start: 0.8495 (tppt) cc_final: 0.7957 (mmmt) REVERT: B 986 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7709 (tm-30) REVERT: C 120 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7552 (ttmt) REVERT: C 193 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7681 (t80) REVERT: C 224 ASN cc_start: 0.8352 (t0) cc_final: 0.8142 (t0) REVERT: C 235 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7294 (pp) REVERT: C 248 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7752 (p) REVERT: C 249 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6603 (m-30) REVERT: C 254 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.5395 (tp30) REVERT: D 66 TYR cc_start: 0.7765 (m-80) cc_final: 0.6497 (m-80) REVERT: D 83 GLU cc_start: 0.6262 (mm-30) cc_final: 0.5135 (mt-10) REVERT: D 95 LYS cc_start: 0.7247 (mmtt) cc_final: 0.6940 (mmtt) REVERT: D 120 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7847 (pmtt) REVERT: D 144 LYS cc_start: 0.8072 (tptt) cc_final: 0.7809 (tptt) REVERT: D 222 ASP cc_start: 0.7563 (t0) cc_final: 0.7205 (t0) REVERT: D 264 LYS cc_start: 0.8001 (tppp) cc_final: 0.7633 (ttmt) REVERT: D 283 LEU cc_start: 0.8670 (tp) cc_final: 0.8463 (tp) outliers start: 91 outliers final: 53 residues processed: 552 average time/residue: 0.3425 time to fit residues: 287.6545 Evaluate side-chains 566 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 497 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 665 LYS Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 136 ASN Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 171 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 73 optimal weight: 0.0060 chunk 202 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 ASN B 67 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.154905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120431 restraints weight = 32733.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.124518 restraints weight = 17275.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127262 restraints weight = 11275.052| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21520 Z= 0.140 Angle : 0.579 11.549 29026 Z= 0.305 Chirality : 0.041 0.184 3082 Planarity : 0.004 0.066 3712 Dihedral : 4.580 39.301 2801 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.46 % Favored : 94.34 % Rotamer: Outliers : 3.28 % Allowed : 26.66 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.17), residues: 2528 helix: 1.03 (0.14), residues: 1473 sheet: -1.83 (0.56), residues: 65 loop : -1.53 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP D 143 HIS 0.006 0.001 HIS D 67 PHE 0.035 0.001 PHE B 240 TYR 0.017 0.001 TYR A 649 ARG 0.008 0.000 ARG B 747 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 981) hydrogen bonds : angle 4.24029 ( 2832) covalent geometry : bond 0.00324 (21520) covalent geometry : angle 0.57933 (29026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 501 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7156 (tm-30) REVERT: A 45 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.6741 (m-80) REVERT: A 109 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 131 THR cc_start: 0.8387 (m) cc_final: 0.8074 (t) REVERT: A 135 ASP cc_start: 0.7857 (t0) cc_final: 0.7632 (p0) REVERT: A 155 GLU cc_start: 0.7603 (tp30) cc_final: 0.7326 (tp30) REVERT: A 176 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8376 (mtmm) REVERT: A 280 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.7015 (m-80) REVERT: A 294 ILE cc_start: 0.8444 (tp) cc_final: 0.8187 (tt) REVERT: A 297 GLN cc_start: 0.8214 (mp10) cc_final: 0.8007 (mp10) REVERT: A 310 ASP cc_start: 0.7508 (t0) cc_final: 0.7047 (t0) REVERT: A 329 ASP cc_start: 0.7410 (t0) cc_final: 0.7094 (t0) REVERT: A 350 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8102 (mmtm) REVERT: A 376 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8243 (ttpp) REVERT: A 393 VAL cc_start: 0.6651 (OUTLIER) cc_final: 0.6386 (p) REVERT: A 448 TRP cc_start: 0.7727 (m-10) cc_final: 0.7499 (m-10) REVERT: A 516 GLU cc_start: 0.8044 (tp30) cc_final: 0.7599 (tp30) REVERT: A 540 LYS cc_start: 0.8530 (tptm) cc_final: 0.8260 (tppt) REVERT: A 560 GLU cc_start: 0.7905 (tt0) cc_final: 0.7333 (tp30) REVERT: A 681 GLN cc_start: 0.6941 (mt0) cc_final: 0.6401 (mm-40) REVERT: A 823 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7860 (mp) REVERT: A 829 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7785 (tp-100) REVERT: A 877 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6878 (t80) REVERT: A 882 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: A 916 PHE cc_start: 0.8363 (m-80) cc_final: 0.7929 (m-80) REVERT: A 958 TRP cc_start: 0.7887 (m-10) cc_final: 0.7558 (m-10) REVERT: A 969 LYS cc_start: 0.8910 (tptm) cc_final: 0.8392 (tptp) REVERT: A 974 LYS cc_start: 0.8872 (tmmt) cc_final: 0.8592 (tmmt) REVERT: A 985 LYS cc_start: 0.8477 (mtmm) cc_final: 0.8224 (mttm) REVERT: B 203 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8235 (tt) REVERT: B 291 ASP cc_start: 0.7773 (m-30) cc_final: 0.7175 (m-30) REVERT: B 304 LYS cc_start: 0.8198 (mmtm) cc_final: 0.7910 (mmtm) REVERT: B 329 ASP cc_start: 0.7370 (t0) cc_final: 0.7055 (t70) REVERT: B 357 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.5853 (tmm) REVERT: B 426 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: B 538 LYS cc_start: 0.8515 (mttm) cc_final: 0.8202 (mttt) REVERT: B 541 ILE cc_start: 0.8489 (mm) cc_final: 0.7863 (mm) REVERT: B 569 MET cc_start: 0.1008 (mtp) cc_final: 0.0696 (mtp) REVERT: B 595 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7659 (mt) REVERT: B 686 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6853 (mm-30) REVERT: B 818 LYS cc_start: 0.8470 (tppt) cc_final: 0.7940 (mmmt) REVERT: C 120 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7534 (ttmt) REVERT: C 193 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7590 (t80) REVERT: C 225 ILE cc_start: 0.8027 (mm) cc_final: 0.7778 (mm) REVERT: C 235 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7252 (pp) REVERT: C 248 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7708 (p) REVERT: C 249 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6613 (m-30) REVERT: C 254 GLU cc_start: 0.5798 (OUTLIER) cc_final: 0.5347 (tp30) REVERT: D 83 GLU cc_start: 0.6167 (mm-30) cc_final: 0.5049 (mt-10) REVERT: D 95 LYS cc_start: 0.7215 (mmtt) cc_final: 0.6884 (mmtt) REVERT: D 120 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7689 (pmtt) REVERT: D 144 LYS cc_start: 0.8035 (tptt) cc_final: 0.7765 (tptt) REVERT: D 150 SER cc_start: 0.8210 (m) cc_final: 0.7968 (m) REVERT: D 222 ASP cc_start: 0.7553 (t0) cc_final: 0.7164 (t0) outliers start: 76 outliers final: 50 residues processed: 541 average time/residue: 0.3300 time to fit residues: 269.0729 Evaluate side-chains 554 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 486 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 131 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 174 optimal weight: 0.0870 chunk 199 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 236 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 = 0.3974 r_free = 0.3974 target = 0.154952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120695 restraints weight = 32701.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124617 restraints weight = 17321.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127467 restraints weight = 11432.418| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21520 Z= 0.137 Angle : 0.585 12.699 29026 Z= 0.305 Chirality : 0.041 0.174 3082 Planarity : 0.003 0.064 3712 Dihedral : 4.530 40.066 2801 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.58 % Favored : 94.22 % Rotamer: Outliers : 3.33 % Allowed : 26.92 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.17), residues: 2528 helix: 1.06 (0.14), residues: 1475 sheet: -1.91 (0.55), residues: 65 loop : -1.51 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP D 143 HIS 0.006 0.001 HIS D 67 PHE 0.037 0.001 PHE B 240 TYR 0.017 0.001 TYR A 56 ARG 0.009 0.000 ARG B 747 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 981) hydrogen bonds : angle 4.20825 ( 2832) covalent geometry : bond 0.00316 (21520) covalent geometry : angle 0.58463 (29026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 498 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7147 (tm-30) REVERT: A 45 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: A 109 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7658 (tp-100) REVERT: A 131 THR cc_start: 0.8369 (m) cc_final: 0.8088 (t) REVERT: A 155 GLU cc_start: 0.7586 (tp30) cc_final: 0.7296 (tp30) REVERT: A 176 LYS cc_start: 0.8717 (mtmm) cc_final: 0.8362 (mtmm) REVERT: A 280 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.7069 (m-80) REVERT: A 294 ILE cc_start: 0.8364 (tp) cc_final: 0.8102 (tt) REVERT: A 310 ASP cc_start: 0.7517 (t0) cc_final: 0.7057 (t0) REVERT: A 329 ASP cc_start: 0.7376 (t0) cc_final: 0.7112 (t0) REVERT: A 350 LYS cc_start: 0.8407 (mmtt) cc_final: 0.8129 (mmtm) REVERT: A 364 LYS cc_start: 0.7543 (ttmm) cc_final: 0.7173 (tttt) REVERT: A 376 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8240 (ttpp) REVERT: A 393 VAL cc_start: 0.6648 (OUTLIER) cc_final: 0.6373 (p) REVERT: A 448 TRP cc_start: 0.7709 (m-10) cc_final: 0.7477 (m-10) REVERT: A 516 GLU cc_start: 0.8059 (tp30) cc_final: 0.7615 (tp30) REVERT: A 540 LYS cc_start: 0.8512 (tptm) cc_final: 0.8251 (tppt) REVERT: A 560 GLU cc_start: 0.7914 (tt0) cc_final: 0.7323 (tp30) REVERT: A 675 LYS cc_start: 0.8466 (tttt) cc_final: 0.7440 (ttmm) REVERT: A 681 GLN cc_start: 0.6876 (mt0) cc_final: 0.6325 (mm-40) REVERT: A 823 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7852 (mp) REVERT: A 829 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7776 (tp-100) REVERT: A 877 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6879 (t80) REVERT: A 882 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: A 916 PHE cc_start: 0.8320 (m-80) cc_final: 0.7890 (m-80) REVERT: A 958 TRP cc_start: 0.8288 (m-10) cc_final: 0.7463 (m100) REVERT: A 965 LYS cc_start: 0.8545 (mmtm) cc_final: 0.8337 (tppt) REVERT: A 969 LYS cc_start: 0.8912 (tptm) cc_final: 0.8381 (tptp) REVERT: A 974 LYS cc_start: 0.8940 (tmmt) cc_final: 0.8684 (tmmt) REVERT: A 985 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8220 (mttm) REVERT: B 93 ASN cc_start: 0.8409 (t0) cc_final: 0.8170 (t0) REVERT: B 203 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8251 (tt) REVERT: B 291 ASP cc_start: 0.7769 (m-30) cc_final: 0.7185 (m-30) REVERT: B 304 LYS cc_start: 0.8203 (mmtm) cc_final: 0.7901 (mmtm) REVERT: B 324 TYR cc_start: 0.8007 (t80) cc_final: 0.7733 (t80) REVERT: B 329 ASP cc_start: 0.7371 (t0) cc_final: 0.7015 (t70) REVERT: B 357 MET cc_start: 0.6871 (tmm) cc_final: 0.5858 (tmm) REVERT: B 408 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: B 426 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: B 538 LYS cc_start: 0.8489 (mttm) cc_final: 0.8199 (mttt) REVERT: B 541 ILE cc_start: 0.8486 (mm) cc_final: 0.7801 (mm) REVERT: B 554 ASP cc_start: 0.6884 (t0) cc_final: 0.6345 (t0) REVERT: B 595 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7681 (mt) REVERT: B 686 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6841 (mm-30) REVERT: B 818 LYS cc_start: 0.8470 (tppt) cc_final: 0.7939 (mmmt) REVERT: C 75 LYS cc_start: 0.5237 (OUTLIER) cc_final: 0.3769 (pptt) REVERT: C 120 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7543 (ttmt) REVERT: C 193 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7586 (t80) REVERT: C 203 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8164 (tp) REVERT: C 235 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7282 (pp) REVERT: C 248 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7761 (p) REVERT: C 249 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6579 (m-30) REVERT: C 254 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5337 (tp30) REVERT: D 83 GLU cc_start: 0.6207 (mm-30) cc_final: 0.5092 (mt-10) REVERT: D 95 LYS cc_start: 0.7227 (mmtt) cc_final: 0.6898 (mmtt) REVERT: D 120 LYS cc_start: 0.8279 (pttt) cc_final: 0.7658 (pmtt) REVERT: D 144 LYS cc_start: 0.8027 (tptt) cc_final: 0.7741 (tptt) REVERT: D 150 SER cc_start: 0.8220 (m) cc_final: 0.7970 (m) REVERT: D 222 ASP cc_start: 0.7545 (t0) cc_final: 0.7213 (t0) outliers start: 77 outliers final: 47 residues processed: 543 average time/residue: 0.3370 time to fit residues: 276.6064 Evaluate side-chains 551 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 485 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 256 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 188 optimal weight: 30.0000 chunk 193 optimal weight: 0.7980 chunk 132 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 199 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** D 128 HIS ** 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 = 0.3964 r_free = 0.3964 target = 0.154228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120040 restraints weight = 32706.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124008 restraints weight = 17353.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126691 restraints weight = 11427.494| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21520 Z= 0.153 Angle : 0.600 12.349 29026 Z= 0.313 Chirality : 0.042 0.170 3082 Planarity : 0.004 0.064 3712 Dihedral : 4.556 39.316 2801 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.97 % Favored : 93.79 % Rotamer: Outliers : 3.15 % Allowed : 27.36 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.17), residues: 2528 helix: 1.07 (0.14), residues: 1473 sheet: -2.00 (0.54), residues: 65 loop : -1.47 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP D 143 HIS 0.007 0.001 HIS D 67 PHE 0.036 0.001 PHE B 240 TYR 0.019 0.002 TYR A 649 ARG 0.009 0.000 ARG B 747 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 981) hydrogen bonds : angle 4.20897 ( 2832) covalent geometry : bond 0.00357 (21520) covalent geometry : angle 0.60025 (29026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 496 time to evaluate : 2.309 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: A 35 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7163 (tm-30) REVERT: A 45 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.6796 (m-80) REVERT: A 109 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7657 (tp-100) REVERT: A 131 THR cc_start: 0.8388 (m) cc_final: 0.8058 (t) REVERT: A 176 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8369 (mtmm) REVERT: A 280 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.7128 (m-80) REVERT: A 294 ILE cc_start: 0.8326 (tp) cc_final: 0.8104 (tt) REVERT: A 310 ASP cc_start: 0.7566 (t0) cc_final: 0.7155 (t0) REVERT: A 329 ASP cc_start: 0.7364 (t0) cc_final: 0.7092 (t0) REVERT: A 350 LYS cc_start: 0.8413 (mmtt) cc_final: 0.8132 (mmtm) REVERT: A 364 LYS cc_start: 0.7586 (ttmm) cc_final: 0.7255 (tttt) REVERT: A 376 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8222 (ttpp) REVERT: A 393 VAL cc_start: 0.6645 (OUTLIER) cc_final: 0.6367 (p) REVERT: A 408 GLU cc_start: 0.7108 (tp30) cc_final: 0.6879 (tp30) REVERT: A 448 TRP cc_start: 0.7681 (m-10) cc_final: 0.7466 (m-10) REVERT: A 516 GLU cc_start: 0.8031 (tp30) cc_final: 0.7568 (tp30) REVERT: A 519 MET cc_start: 0.7351 (ttm) cc_final: 0.7119 (ttm) REVERT: A 540 LYS cc_start: 0.8502 (tptm) cc_final: 0.8256 (tppt) REVERT: A 560 GLU cc_start: 0.7937 (tt0) cc_final: 0.7305 (tp30) REVERT: A 675 LYS cc_start: 0.8468 (tttt) cc_final: 0.7447 (ttmm) REVERT: A 681 GLN cc_start: 0.6963 (mt0) cc_final: 0.6422 (mm-40) REVERT: A 823 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7871 (mp) REVERT: A 829 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7830 (tp-100) REVERT: A 877 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6910 (t80) REVERT: A 882 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: A 916 PHE cc_start: 0.8319 (m-80) cc_final: 0.7868 (m-80) REVERT: A 969 LYS cc_start: 0.8932 (tptm) cc_final: 0.8379 (tptp) REVERT: A 974 LYS cc_start: 0.8922 (tmmt) cc_final: 0.8694 (tmmt) REVERT: A 985 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8203 (mttm) REVERT: B 93 ASN cc_start: 0.8403 (t0) cc_final: 0.8141 (t0) REVERT: B 203 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8240 (tt) REVERT: B 291 ASP cc_start: 0.7781 (m-30) cc_final: 0.7194 (m-30) REVERT: B 304 LYS cc_start: 0.8203 (mmtm) cc_final: 0.7792 (mmtm) REVERT: B 324 TYR cc_start: 0.8022 (t80) cc_final: 0.7724 (t80) REVERT: B 329 ASP cc_start: 0.7367 (t0) cc_final: 0.7125 (t70) REVERT: B 357 MET cc_start: 0.6859 (tmm) cc_final: 0.5898 (tmm) REVERT: B 408 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: B 426 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: B 538 LYS cc_start: 0.8493 (mttm) cc_final: 0.8204 (mttt) REVERT: B 554 ASP cc_start: 0.6950 (t0) cc_final: 0.6429 (t0) REVERT: B 646 PHE cc_start: 0.6150 (m-80) cc_final: 0.5809 (m-10) REVERT: B 686 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6849 (mm-30) REVERT: B 727 LYS cc_start: 0.8069 (tptp) cc_final: 0.7805 (tptt) REVERT: B 818 LYS cc_start: 0.8465 (tppt) cc_final: 0.7935 (mmmt) REVERT: C 75 LYS cc_start: 0.5249 (OUTLIER) cc_final: 0.3785 (pptt) REVERT: C 120 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7576 (ttmt) REVERT: C 193 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.7576 (t80) REVERT: C 203 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8114 (tp) REVERT: C 248 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7800 (p) REVERT: C 249 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6635 (m-30) REVERT: C 254 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.5352 (tp30) REVERT: D 66 TYR cc_start: 0.7740 (m-80) cc_final: 0.6476 (m-80) REVERT: D 83 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5115 (mt-10) REVERT: D 120 LYS cc_start: 0.8265 (pttt) cc_final: 0.7718 (pmtt) REVERT: D 144 LYS cc_start: 0.8011 (tptt) cc_final: 0.7732 (tptt) REVERT: D 150 SER cc_start: 0.8239 (m) cc_final: 0.8008 (m) REVERT: D 222 ASP cc_start: 0.7571 (t0) cc_final: 0.7242 (t0) outliers start: 73 outliers final: 48 residues processed: 541 average time/residue: 0.3525 time to fit residues: 290.2269 Evaluate side-chains 554 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 489 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 408 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 256 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 3 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 231 optimal weight: 0.0570 chunk 88 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** 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 = 0.3967 r_free = 0.3967 target = 0.154666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.120189 restraints weight = 33091.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124116 restraints weight = 17509.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126970 restraints weight = 11568.664| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21520 Z= 0.151 Angle : 0.593 10.480 29026 Z= 0.311 Chirality : 0.042 0.185 3082 Planarity : 0.003 0.063 3712 Dihedral : 4.532 39.295 2800 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.66 % Favored : 94.11 % Rotamer: Outliers : 3.11 % Allowed : 27.36 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2528 helix: 1.11 (0.14), residues: 1465 sheet: -2.06 (0.55), residues: 65 loop : -1.41 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP D 143 HIS 0.006 0.001 HIS D 67 PHE 0.036 0.001 PHE B 240 TYR 0.019 0.002 TYR A 649 ARG 0.009 0.000 ARG B 747 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 981) hydrogen bonds : angle 4.18613 ( 2832) covalent geometry : bond 0.00353 (21520) covalent geometry : angle 0.59335 (29026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7448.86 seconds wall clock time: 131 minutes 7.56 seconds (7867.56 seconds total)