Starting phenix.real_space_refine on Wed Jun 18 09:47:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yg1_39233/06_2025/8yg1_39233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yg1_39233/06_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_39233/06_2025/8yg1_39233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yg1_39233/06_2025/8yg1_39233.map" model { file = "/net/cci-nas-00/data/ceres_data/8yg1_39233/06_2025/8yg1_39233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yg1_39233/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.53, per 1000 atoms: 0.60 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: 5.36 Conformation dependent library (CDL) restraints added in 2.8 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: 2.10 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: 7.44 Time building geometry restraints manager: 6.35 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 47.930 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.100 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.650 ------------------------------------------------------------------------------- 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 : 2.124 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: 0.3705 time to fit residues: 280.8332 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 : 2.165 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122759 restraints weight = 32654.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126863 restraints weight = 17272.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129604 restraints weight = 11311.811| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- 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 : 2.291 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: 0.7991 (mttt) cc_final: 0.7660 (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: 0.8134 (t) REVERT: A 280 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6657 (m-80) REVERT: A 286 TYR cc_start: 0.7411 (m-80) cc_final: 0.7189 (m-10) REVERT: A 391 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7750 (t0) REVERT: A 393 VAL cc_start: 0.6771 (OUTLIER) cc_final: 0.6387 (p) REVERT: A 448 TRP cc_start: 0.7819 (m-10) cc_final: 0.7435 (m-10) REVERT: A 516 GLU cc_start: 0.7919 (tp30) cc_final: 0.7536 (tp30) REVERT: A 760 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.7460 (mtp-110) REVERT: A 823 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7965 (mp) REVERT: A 829 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7736 (tp40) REVERT: A 882 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: A 916 PHE cc_start: 0.8307 (m-80) cc_final: 0.7971 (m-80) REVERT: A 933 PHE cc_start: 0.7905 (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: 0.9062 (ttpt) cc_final: 0.8730 (tmmt) REVERT: B 181 GLU cc_start: 0.7345 (pt0) cc_final: 0.7105 (mt-10) REVERT: B 291 ASP cc_start: 0.7670 (m-30) cc_final: 0.7419 (m-30) REVERT: B 304 LYS cc_start: 0.8215 (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: 0.2427 (mtp) cc_final: 0.2047 (mtp) REVERT: B 595 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7443 (mt) REVERT: B 669 ARG cc_start: 0.7212 (tpp80) cc_final: 0.6671 (tpp80) REVERT: B 818 LYS cc_start: 0.8463 (tppt) cc_final: 0.7831 (mmmt) REVERT: C 224 ASN cc_start: 0.7975 (t0) cc_final: 0.7727 (t0) REVERT: C 236 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7260 (mt0) REVERT: D 71 TYR cc_start: 0.6345 (m-80) cc_final: 0.5821 (m-80) REVERT: D 83 GLU cc_start: 0.6052 (mm-30) cc_final: 0.4796 (mt-10) REVERT: D 120 LYS cc_start: 0.8301 (pttt) cc_final: 0.7276 (pmtt) REVERT: D 155 GLU cc_start: 0.6296 (mm-30) cc_final: 0.5943 (mm-30) REVERT: D 197 TYR cc_start: 0.7615 (m-80) cc_final: 0.7140 (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: 0.3540 time to fit residues: 291.1803 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 : 2.183 ------------------------------------------------------------------------------- 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: 2.9990 chunk 245 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 181 optimal weight: 0.0270 chunk 4 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.156293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122012 restraints weight = 32641.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126005 restraints weight = 17192.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.128879 restraints weight = 11330.407| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21520 Z= 0.144 Angle : 0.572 11.430 29026 Z= 0.301 Chirality : 0.041 0.171 3082 Planarity : 0.004 0.083 3712 Dihedral : 5.050 52.613 2808 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.46 % Favored : 94.34 % Rotamer: Outliers : 3.67 % Allowed : 24.07 % Favored : 72.26 % 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: 0.84 (0.14), residues: 1459 sheet: -1.32 (0.57), residues: 65 loop : -1.46 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP D 143 HIS 0.009 0.001 HIS B 67 PHE 0.019 0.001 PHE A 933 TYR 0.018 0.001 TYR A 649 ARG 0.005 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 981) hydrogen bonds : angle 4.51801 ( 2832) covalent geometry : bond 0.00324 (21520) covalent geometry : angle 0.57171 (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 581 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 496 time to evaluate : 2.122 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: 0.7919 (mttt) cc_final: 0.7667 (mttm) REVERT: A 42 LEU cc_start: 0.8623 (tp) cc_final: 0.8386 (tt) REVERT: A 131 THR cc_start: 0.8389 (m) cc_final: 0.8113 (t) REVERT: A 280 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: A 286 TYR cc_start: 0.7481 (m-80) cc_final: 0.7273 (m-10) REVERT: A 350 LYS cc_start: 0.8225 (mmtt) cc_final: 0.7925 (mmtt) REVERT: A 391 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7884 (t0) REVERT: A 393 VAL cc_start: 0.6752 (OUTLIER) cc_final: 0.6379 (p) REVERT: A 448 TRP cc_start: 0.7827 (m-10) cc_final: 0.7588 (m-10) REVERT: A 516 GLU cc_start: 0.7973 (tp30) cc_final: 0.7657 (tp30) REVERT: A 540 LYS cc_start: 0.8570 (tptm) cc_final: 0.8305 (tppt) REVERT: A 696 THR cc_start: 0.7602 (m) cc_final: 0.7056 (p) REVERT: A 823 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7909 (mp) REVERT: A 829 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7726 (tp40) REVERT: A 882 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8372 (mt-10) REVERT: A 916 PHE cc_start: 0.8357 (m-80) cc_final: 0.7987 (m-80) REVERT: A 969 LYS cc_start: 0.8638 (tptm) cc_final: 0.8322 (tptm) REVERT: B 124 MET cc_start: 0.7793 (tpt) cc_final: 0.7509 (tpp) REVERT: B 291 ASP cc_start: 0.7667 (m-30) cc_final: 0.7275 (m-30) REVERT: B 304 LYS cc_start: 0.8257 (mmtm) cc_final: 0.7836 (mmtm) REVERT: B 329 ASP cc_start: 0.7452 (t0) cc_final: 0.7127 (t0) REVERT: B 338 TYR cc_start: 0.8211 (m-80) cc_final: 0.8010 (m-10) REVERT: B 354 PHE cc_start: 0.7851 (t80) cc_final: 0.7547 (t80) REVERT: B 559 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.7265 (t80) REVERT: B 569 MET cc_start: 0.3064 (mtp) cc_final: 0.2529 (mtp) REVERT: B 669 ARG cc_start: 0.7219 (tpp80) cc_final: 0.6709 (tpp80) REVERT: B 741 LEU cc_start: 0.7503 (mt) cc_final: 0.7227 (mt) REVERT: B 818 LYS cc_start: 0.8462 (tppt) cc_final: 0.7855 (mmmt) REVERT: B 986 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7786 (tm-30) REVERT: C 224 ASN cc_start: 0.8056 (t0) cc_final: 0.7681 (t0) REVERT: C 235 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7282 (pp) REVERT: C 249 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6494 (m-30) REVERT: D 83 GLU cc_start: 0.6051 (mm-30) cc_final: 0.4830 (mt-10) REVERT: D 120 LYS cc_start: 0.8306 (pttt) cc_final: 0.7468 (pmtt) REVERT: D 144 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7840 (tptt) REVERT: D 208 ILE cc_start: 0.8716 (mt) cc_final: 0.8459 (tt) REVERT: D 222 ASP cc_start: 0.7372 (t0) cc_final: 0.7053 (t0) outliers start: 85 outliers final: 42 residues processed: 540 average time/residue: 0.3435 time to fit residues: 280.2721 Evaluate side-chains 544 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 492 time to evaluate : 2.314 ------------------------------------------------------------------------------- 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 181 GLU Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 357 MET 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 959 LEU 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 144 LYS 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: 0.5980 chunk 207 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.153410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119257 restraints weight = 33237.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.123194 restraints weight = 17881.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125829 restraints weight = 11887.056| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1773 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= 0.223 Angle : 0.614 9.600 29026 Z= 0.326 Chirality : 0.044 0.208 3082 Planarity : 0.004 0.076 3712 Dihedral : 4.983 41.870 2805 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.25 % Favored : 93.55 % Rotamer: Outliers : 4.62 % Allowed : 23.34 % Favored : 72.04 % 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: -0.32 (0.17), residues: 2528 helix: 0.74 (0.14), residues: 1472 sheet: -1.42 (0.58), residues: 65 loop : -1.57 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP D 143 HIS 0.009 0.001 HIS D 67 PHE 0.049 0.002 PHE B 240 TYR 0.033 0.002 TYR A 649 ARG 0.008 0.001 ARG D 247 Details of bonding type rmsd hydrogen bonds : bond 0.05139 ( 981) hydrogen bonds : angle 4.56322 ( 2832) covalent geometry : bond 0.00512 (21520) covalent geometry : angle 0.61370 (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: 107 poor density : 503 time to evaluate : 2.140 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: 0.7495 (tm-30) cc_final: 0.7062 (tm-30) REVERT: A 41 LYS cc_start: 0.8014 (mttt) cc_final: 0.7811 (mttm) REVERT: A 42 LEU cc_start: 0.8686 (tp) cc_final: 0.8399 (tt) REVERT: A 45 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7107 (t80) REVERT: A 75 LYS cc_start: 0.8496 (tppt) cc_final: 0.7868 (ttmm) REVERT: A 109 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7376 (tm-30) REVERT: A 131 THR cc_start: 0.8425 (m) cc_final: 0.8187 (t) REVERT: A 176 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8419 (mtmm) REVERT: A 280 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: A 297 GLN cc_start: 0.8155 (mp10) cc_final: 0.7900 (mp10) REVERT: A 316 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8162 (tt) REVERT: A 393 VAL cc_start: 0.6804 (OUTLIER) cc_final: 0.6516 (p) REVERT: A 408 GLU cc_start: 0.7164 (tp30) cc_final: 0.6941 (tp30) REVERT: A 448 TRP cc_start: 0.7912 (m-10) cc_final: 0.7701 (m-10) REVERT: A 516 GLU cc_start: 0.8053 (tp30) cc_final: 0.7711 (tp30) REVERT: A 519 MET cc_start: 0.7212 (ttm) cc_final: 0.6861 (ttp) REVERT: A 540 LYS cc_start: 0.8527 (tptm) cc_final: 0.8317 (tppt) REVERT: A 696 THR cc_start: 0.7758 (m) cc_final: 0.7503 (m) REVERT: A 823 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7906 (mp) REVERT: A 829 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7819 (tp40) REVERT: A 881 HIS cc_start: 0.8153 (OUTLIER) cc_final: 0.7920 (m90) REVERT: A 882 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: A 916 PHE cc_start: 0.8376 (m-80) cc_final: 0.7982 (m-80) REVERT: A 969 LYS cc_start: 0.8767 (tptm) cc_final: 0.8450 (tptm) REVERT: A 974 LYS cc_start: 0.8800 (tmmt) cc_final: 0.8558 (tmmt) REVERT: B 181 GLU cc_start: 0.7275 (pt0) cc_final: 0.6926 (mt-10) REVERT: B 203 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8424 (tt) REVERT: B 291 ASP cc_start: 0.7661 (m-30) cc_final: 0.7194 (m-30) REVERT: B 304 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7869 (mmtm) REVERT: B 329 ASP cc_start: 0.7430 (t0) cc_final: 0.6916 (t0) REVERT: B 531 MET cc_start: 0.8211 (mmm) cc_final: 0.7702 (mmm) REVERT: B 541 ILE cc_start: 0.8302 (mm) cc_final: 0.7814 (mm) REVERT: B 565 VAL cc_start: 0.3136 (OUTLIER) cc_final: 0.2878 (t) REVERT: B 595 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7652 (mt) REVERT: B 622 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6725 (tptm) REVERT: B 686 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6846 (mm-30) REVERT: B 818 LYS cc_start: 0.8492 (tppt) cc_final: 0.7903 (mmmt) REVERT: B 986 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7778 (tm-30) REVERT: C 224 ASN cc_start: 0.8172 (t0) cc_final: 0.7836 (t160) REVERT: C 235 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7365 (pp) REVERT: C 249 ASP cc_start: 0.7010 (OUTLIER) cc_final: 0.6492 (m-30) REVERT: D 83 GLU cc_start: 0.6199 (mm-30) cc_final: 0.4990 (mt-10) REVERT: D 120 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7281 (pmtt) REVERT: D 144 LYS cc_start: 0.8093 (mttt) cc_final: 0.7876 (tptt) REVERT: D 203 LEU cc_start: 0.8334 (tp) cc_final: 0.7970 (tt) REVERT: D 208 ILE cc_start: 0.8791 (mt) cc_final: 0.8530 (tt) REVERT: D 222 ASP cc_start: 0.7534 (t0) cc_final: 0.7190 (t0) outliers start: 107 outliers final: 58 residues processed: 560 average time/residue: 0.3451 time to fit residues: 291.2321 Evaluate side-chains 565 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 492 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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 316 ILE 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 550 PHE 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 203 LEU 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 363 LEU Chi-restraints excluded: chain B residue 508 THR 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 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 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 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 Chi-restraints excluded: chain D residue 256 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.5980 chunk 212 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 225 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 251 optimal weight: 0.9990 chunk 10 optimal weight: 0.0050 chunk 191 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3976 r_free = 0.3976 target = 0.155283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120753 restraints weight = 32818.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124892 restraints weight = 17343.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127570 restraints weight = 11352.790| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1944 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= 0.133 Angle : 0.566 9.726 29026 Z= 0.300 Chirality : 0.041 0.180 3082 Planarity : 0.004 0.073 3712 Dihedral : 4.737 38.984 2803 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.54 % Favored : 94.26 % Rotamer: Outliers : 4.02 % Allowed : 24.94 % Favored : 71.05 % 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: -0.16 (0.17), residues: 2528 helix: 0.91 (0.14), residues: 1467 sheet: -1.52 (0.57), residues: 65 loop : -1.55 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP D 143 HIS 0.006 0.001 HIS D 67 PHE 0.056 0.001 PHE B 240 TYR 0.017 0.001 TYR B 721 ARG 0.006 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 981) hydrogen bonds : angle 4.38814 ( 2832) covalent geometry : bond 0.00302 (21520) covalent geometry : angle 0.56556 (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 591 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 498 time to evaluate : 2.107 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: 0.7515 (tm-30) cc_final: 0.7116 (tm-30) REVERT: A 41 LYS cc_start: 0.7969 (mttt) cc_final: 0.7755 (mttm) REVERT: A 42 LEU cc_start: 0.8700 (tp) cc_final: 0.8444 (tt) REVERT: A 45 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.6793 (m-80) REVERT: A 109 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 131 THR cc_start: 0.8387 (m) cc_final: 0.8040 (t) REVERT: A 176 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8394 (mtmm) REVERT: A 235 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7470 (mp) REVERT: A 248 THR cc_start: 0.8207 (p) cc_final: 0.7998 (p) REVERT: A 297 GLN cc_start: 0.8174 (mp10) cc_final: 0.7938 (mp10) REVERT: A 329 ASP cc_start: 0.7325 (t0) cc_final: 0.7050 (t0) REVERT: A 350 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7991 (mmtm) REVERT: A 393 VAL cc_start: 0.6738 (OUTLIER) cc_final: 0.6448 (p) REVERT: A 448 TRP cc_start: 0.7793 (m-10) cc_final: 0.7562 (m-10) REVERT: A 516 GLU cc_start: 0.8027 (tp30) cc_final: 0.7612 (tp30) REVERT: A 531 MET cc_start: 0.7378 (mmm) cc_final: 0.7085 (mmt) REVERT: A 540 LYS cc_start: 0.8521 (tptm) cc_final: 0.8281 (tppt) REVERT: A 647 MET cc_start: 0.6421 (mmp) cc_final: 0.6117 (mtp) REVERT: A 675 LYS cc_start: 0.8434 (mttt) cc_final: 0.7520 (ttmm) REVERT: A 809 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8388 (mmtt) REVERT: A 823 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7898 (mp) REVERT: A 829 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7783 (tp-100) REVERT: A 878 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.7570 (p) REVERT: A 882 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8360 (mt-10) REVERT: A 916 PHE cc_start: 0.8387 (m-80) cc_final: 0.7976 (m-80) REVERT: A 958 TRP cc_start: 0.7877 (m-10) cc_final: 0.7597 (m-10) REVERT: A 969 LYS cc_start: 0.8810 (tptm) cc_final: 0.8282 (tptp) REVERT: A 974 LYS cc_start: 0.8798 (tmmt) cc_final: 0.8546 (tmmt) REVERT: B 124 MET cc_start: 0.7913 (tpp) cc_final: 0.7656 (mtm) REVERT: B 181 GLU cc_start: 0.7313 (pt0) cc_final: 0.6971 (mt-10) REVERT: B 291 ASP cc_start: 0.7710 (m-30) cc_final: 0.7177 (m-30) REVERT: B 297 GLN cc_start: 0.5444 (OUTLIER) cc_final: 0.4467 (tp40) REVERT: B 304 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7904 (mmtm) REVERT: B 329 ASP cc_start: 0.7475 (t0) cc_final: 0.6987 (t70) REVERT: B 338 TYR cc_start: 0.8110 (m-80) cc_final: 0.7909 (m-10) REVERT: B 357 MET cc_start: 0.7191 (mmm) cc_final: 0.6876 (tmm) REVERT: B 538 LYS cc_start: 0.8548 (mttm) cc_final: 0.8199 (mtmt) REVERT: B 541 ILE cc_start: 0.8310 (mm) cc_final: 0.7750 (mm) REVERT: B 595 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7616 (mt) REVERT: B 622 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6538 (mmmt) REVERT: B 625 TYR cc_start: 0.6798 (t80) cc_final: 0.6491 (t80) REVERT: B 686 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6817 (mm-30) REVERT: B 724 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7346 (pttm) REVERT: B 818 LYS cc_start: 0.8469 (tppt) cc_final: 0.7889 (mmmt) REVERT: B 986 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7746 (tm-30) REVERT: C 193 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7597 (t80) REVERT: C 224 ASN cc_start: 0.8226 (t0) cc_final: 0.7987 (t0) REVERT: C 235 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7258 (pp) REVERT: C 248 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7666 (p) REVERT: C 249 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6573 (m-30) REVERT: C 254 GLU cc_start: 0.5875 (OUTLIER) cc_final: 0.5427 (tp30) REVERT: D 83 GLU cc_start: 0.6065 (mm-30) cc_final: 0.4948 (mt-10) REVERT: D 120 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7858 (pmtt) REVERT: D 222 ASP cc_start: 0.7508 (t0) cc_final: 0.7152 (t0) REVERT: D 283 LEU cc_start: 0.8643 (tp) cc_final: 0.8413 (tp) outliers start: 93 outliers final: 50 residues processed: 546 average time/residue: 0.3549 time to fit residues: 295.3923 Evaluate side-chains 562 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 495 time to evaluate : 2.122 ------------------------------------------------------------------------------- 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 235 LEU 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 678 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 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 284 GLU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 408 GLU 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 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 100 PHE 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 236 GLN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 19 optimal weight: 0.9980 chunk 245 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 23 optimal weight: 0.0670 chunk 71 optimal weight: 0.8980 chunk 10 optimal weight: 0.0670 chunk 240 optimal weight: 0.0770 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.156181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121586 restraints weight = 32774.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125598 restraints weight = 17341.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128438 restraints weight = 11425.850| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21520 Z= 0.114 Angle : 0.543 10.128 29026 Z= 0.287 Chirality : 0.040 0.184 3082 Planarity : 0.003 0.071 3712 Dihedral : 4.558 41.407 2801 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.62 % Favored : 94.19 % Rotamer: Outliers : 3.50 % Allowed : 25.32 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1471 sheet: -1.55 (0.58), residues: 65 loop : -1.53 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP D 143 HIS 0.006 0.001 HIS A 881 PHE 0.034 0.001 PHE B 240 TYR 0.021 0.001 TYR A 56 ARG 0.006 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 981) hydrogen bonds : angle 4.23820 ( 2832) covalent geometry : bond 0.00252 (21520) covalent geometry : angle 0.54278 (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 573 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 492 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7085 (tm-30) REVERT: A 41 LYS cc_start: 0.7956 (mttt) cc_final: 0.7718 (mttm) REVERT: A 42 LEU cc_start: 0.8699 (tp) cc_final: 0.8439 (tt) REVERT: A 45 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.6780 (m-80) REVERT: A 109 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7546 (tm-30) REVERT: A 131 THR cc_start: 0.8353 (m) cc_final: 0.8050 (t) REVERT: A 135 ASP cc_start: 0.7919 (t0) cc_final: 0.7434 (p0) REVERT: A 176 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8359 (mtmm) REVERT: A 235 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7468 (mp) REVERT: A 280 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: A 294 ILE cc_start: 0.8444 (tp) cc_final: 0.8190 (tt) REVERT: A 297 GLN cc_start: 0.8201 (mp10) cc_final: 0.7999 (mp10) REVERT: A 329 ASP cc_start: 0.7374 (t0) cc_final: 0.7100 (t0) REVERT: A 376 LYS cc_start: 0.8540 (ttpt) cc_final: 0.8225 (ttpp) REVERT: A 393 VAL cc_start: 0.6655 (OUTLIER) cc_final: 0.6365 (p) REVERT: A 448 TRP cc_start: 0.7773 (m-10) cc_final: 0.7530 (m-10) REVERT: A 516 GLU cc_start: 0.8006 (tp30) cc_final: 0.7609 (tp30) REVERT: A 519 MET cc_start: 0.7318 (ttm) cc_final: 0.7073 (mtm) REVERT: A 540 LYS cc_start: 0.8512 (tptm) cc_final: 0.8273 (tppt) REVERT: A 696 THR cc_start: 0.7766 (m) cc_final: 0.7484 (m) REVERT: A 820 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8532 (tt) REVERT: A 823 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7878 (mp) REVERT: A 829 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7780 (tp40) REVERT: A 882 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8313 (mt-10) REVERT: A 916 PHE cc_start: 0.8372 (m-80) cc_final: 0.7892 (m-80) REVERT: A 958 TRP cc_start: 0.7948 (m-10) cc_final: 0.7602 (m-10) REVERT: A 969 LYS cc_start: 0.8852 (tptm) cc_final: 0.8597 (tptm) REVERT: A 974 LYS cc_start: 0.8848 (tmmt) cc_final: 0.8582 (tmmt) REVERT: B 181 GLU cc_start: 0.7321 (pt0) cc_final: 0.6963 (mt-10) REVERT: B 291 ASP cc_start: 0.7692 (m-30) cc_final: 0.7143 (m-30) REVERT: B 304 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7945 (mmtm) REVERT: B 324 TYR cc_start: 0.8034 (t80) cc_final: 0.7703 (t80) REVERT: B 329 ASP cc_start: 0.7457 (t0) cc_final: 0.7019 (t70) REVERT: B 357 MET cc_start: 0.7159 (mmm) cc_final: 0.6771 (tmm) REVERT: B 538 LYS cc_start: 0.8440 (mttm) cc_final: 0.8153 (mttt) REVERT: B 541 ILE cc_start: 0.8320 (mm) cc_final: 0.7765 (mm) REVERT: B 569 MET cc_start: 0.0716 (mtp) cc_final: 0.0492 (mtp) REVERT: B 622 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6551 (tptp) REVERT: B 686 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6810 (mm-30) REVERT: B 818 LYS cc_start: 0.8444 (tppt) cc_final: 0.7852 (mmmt) REVERT: B 986 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7705 (tm-30) REVERT: C 228 LEU cc_start: 0.7962 (mt) cc_final: 0.7674 (mt) REVERT: C 235 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7200 (pp) REVERT: C 248 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7662 (p) REVERT: C 249 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6435 (m-30) REVERT: C 254 GLU cc_start: 0.5770 (OUTLIER) cc_final: 0.5319 (tp30) REVERT: D 83 GLU cc_start: 0.6007 (mm-30) cc_final: 0.4992 (mt-10) REVERT: D 120 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7257 (pmtt) REVERT: D 144 LYS cc_start: 0.8081 (tptt) cc_final: 0.7821 (tptt) REVERT: D 222 ASP cc_start: 0.7462 (t0) cc_final: 0.7112 (t0) REVERT: D 283 LEU cc_start: 0.8634 (tp) cc_final: 0.8428 (tp) outliers start: 81 outliers final: 50 residues processed: 534 average time/residue: 0.3403 time to fit residues: 274.0030 Evaluate side-chains 549 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 485 time to evaluate : 2.437 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 235 LEU 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 678 PHE Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 820 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 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 184 VAL 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 408 GLU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 622 LYS 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 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 44 PHE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 114 THR 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 85 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 34 optimal weight: 0.0060 chunk 131 optimal weight: 1.9990 chunk 168 optimal weight: 0.0040 chunk 125 optimal weight: 0.0370 overall best weight: 0.8090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 230 ASN ** 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 = 0.154513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120075 restraints weight = 32586.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124120 restraints weight = 17185.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126858 restraints weight = 11246.109| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21520 Z= 0.161 Angle : 0.576 10.724 29026 Z= 0.305 Chirality : 0.041 0.189 3082 Planarity : 0.004 0.067 3712 Dihedral : 4.585 39.497 2801 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.93 % Favored : 93.87 % Rotamer: Outliers : 3.67 % Allowed : 25.80 % Favored : 70.53 % 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: 0.99 (0.14), residues: 1475 sheet: -1.57 (0.58), residues: 65 loop : -1.56 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP D 143 HIS 0.007 0.001 HIS D 67 PHE 0.051 0.002 PHE B 240 TYR 0.019 0.002 TYR A 649 ARG 0.007 0.000 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 981) hydrogen bonds : angle 4.26668 ( 2832) covalent geometry : bond 0.00371 (21520) covalent geometry : angle 0.57621 (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 585 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 500 time to evaluate : 2.214 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: 0.7512 (tm-30) cc_final: 0.7119 (tm-30) REVERT: A 42 LEU cc_start: 0.8700 (tp) cc_final: 0.8436 (tt) REVERT: A 45 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.6724 (m-80) REVERT: A 109 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 131 THR cc_start: 0.8386 (m) cc_final: 0.8071 (t) REVERT: A 176 LYS cc_start: 0.8700 (mtmm) cc_final: 0.8375 (mtmm) REVERT: A 235 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7486 (mp) REVERT: A 280 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.6942 (m-80) REVERT: A 294 ILE cc_start: 0.8449 (tp) cc_final: 0.8204 (tt) REVERT: A 310 ASP cc_start: 0.7479 (t0) cc_final: 0.7018 (t0) REVERT: A 329 ASP cc_start: 0.7426 (t0) cc_final: 0.7091 (t0) REVERT: A 350 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8133 (mmtm) REVERT: A 376 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8243 (ttpp) REVERT: A 393 VAL cc_start: 0.6673 (OUTLIER) cc_final: 0.6391 (p) REVERT: A 419 ASP cc_start: 0.7128 (p0) cc_final: 0.6807 (p0) REVERT: A 448 TRP cc_start: 0.7793 (m-10) cc_final: 0.7548 (m-10) REVERT: A 516 GLU cc_start: 0.8060 (tp30) cc_final: 0.7646 (tp30) REVERT: A 540 LYS cc_start: 0.8517 (tptm) cc_final: 0.8266 (tppt) REVERT: A 560 GLU cc_start: 0.7893 (tt0) cc_final: 0.7335 (tp30) REVERT: A 675 LYS cc_start: 0.8453 (mttt) cc_final: 0.8252 (tttt) REVERT: A 823 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7879 (mp) REVERT: A 829 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7871 (tp40) REVERT: A 882 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8353 (mt-10) REVERT: A 916 PHE cc_start: 0.8378 (m-80) cc_final: 0.7946 (m-80) REVERT: A 958 TRP cc_start: 0.7956 (m-10) cc_final: 0.7569 (m-10) REVERT: A 969 LYS cc_start: 0.8890 (tptm) cc_final: 0.8610 (tptm) REVERT: A 974 LYS cc_start: 0.8867 (tmmt) cc_final: 0.8586 (tmmt) REVERT: B 125 ASN cc_start: 0.8303 (p0) cc_final: 0.7908 (p0) REVERT: B 155 GLU cc_start: 0.7301 (mp0) cc_final: 0.7040 (mp0) REVERT: B 181 GLU cc_start: 0.7328 (pt0) cc_final: 0.7000 (mt-10) REVERT: B 203 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8272 (tt) REVERT: B 291 ASP cc_start: 0.7785 (m-30) cc_final: 0.7183 (m-30) REVERT: B 304 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7942 (mmtm) REVERT: B 324 TYR cc_start: 0.8069 (t80) cc_final: 0.7691 (t80) REVERT: B 329 ASP cc_start: 0.7437 (t0) cc_final: 0.6933 (t0) REVERT: B 357 MET cc_start: 0.7030 (mmm) cc_final: 0.6187 (tmm) REVERT: B 426 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: B 538 LYS cc_start: 0.8566 (mttm) cc_final: 0.8213 (mtmt) REVERT: B 541 ILE cc_start: 0.8380 (mm) cc_final: 0.7892 (mm) REVERT: B 595 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7578 (mt) REVERT: B 686 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6878 (mm-30) REVERT: B 818 LYS cc_start: 0.8483 (tppt) cc_final: 0.7943 (mmmt) REVERT: B 986 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7707 (tm-30) REVERT: C 193 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7603 (t80) REVERT: C 235 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7236 (pp) REVERT: C 248 THR cc_start: 0.8114 (p) cc_final: 0.7730 (p) REVERT: C 249 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6520 (m-30) REVERT: C 254 GLU cc_start: 0.5796 (OUTLIER) cc_final: 0.5343 (tp30) REVERT: D 83 GLU cc_start: 0.6196 (mm-30) cc_final: 0.5097 (mt-10) REVERT: D 95 LYS cc_start: 0.7205 (mmtt) cc_final: 0.6902 (mmtt) REVERT: D 120 LYS cc_start: 0.8344 (pttt) cc_final: 0.7795 (pmtt) REVERT: D 144 LYS cc_start: 0.8084 (tptt) cc_final: 0.7806 (tptt) REVERT: D 222 ASP cc_start: 0.7525 (t0) cc_final: 0.7170 (t0) REVERT: D 254 GLU cc_start: 0.7473 (mp0) cc_final: 0.6252 (mt-10) REVERT: D 283 LEU cc_start: 0.8620 (tp) cc_final: 0.8407 (tp) REVERT: D 285 ARG cc_start: 0.7385 (mtp180) cc_final: 0.7002 (mtp180) outliers start: 85 outliers final: 53 residues processed: 545 average time/residue: 0.3408 time to fit residues: 280.4836 Evaluate side-chains 560 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 493 time to evaluate : 2.100 ------------------------------------------------------------------------------- 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 230 ASN Chi-restraints excluded: chain A residue 235 LEU 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 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 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 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 408 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 663 ASP 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 190 TYR Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 235 LEU 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 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 227 MET 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: 0.7980 chunk 8 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3958 r_free = 0.3958 target = 0.153634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119083 restraints weight = 33012.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123151 restraints weight = 17482.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125849 restraints weight = 11497.119| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21520 Z= 0.171 Angle : 0.592 12.325 29026 Z= 0.311 Chirality : 0.042 0.185 3082 Planarity : 0.004 0.065 3712 Dihedral : 4.601 38.560 2801 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.93 % Favored : 93.87 % Rotamer: Outliers : 3.59 % Allowed : 26.32 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.07 (0.17), residues: 2528 helix: 0.98 (0.14), residues: 1475 sheet: -1.62 (0.58), residues: 65 loop : -1.53 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP D 143 HIS 0.007 0.001 HIS D 67 PHE 0.047 0.002 PHE B 240 TYR 0.023 0.002 TYR A 649 ARG 0.013 0.001 ARG D 233 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 981) hydrogen bonds : angle 4.28506 ( 2832) covalent geometry : bond 0.00398 (21520) covalent geometry : angle 0.59199 (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 580 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 497 time to evaluate : 2.324 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: 0.7537 (tm-30) cc_final: 0.7138 (tm-30) REVERT: A 42 LEU cc_start: 0.8704 (tp) cc_final: 0.8422 (tt) REVERT: A 45 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.6761 (m-80) REVERT: A 109 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7623 (tm-30) REVERT: A 131 THR cc_start: 0.8401 (m) cc_final: 0.8059 (t) REVERT: A 176 LYS cc_start: 0.8713 (mtmm) cc_final: 0.8393 (mtmm) REVERT: A 229 LEU cc_start: 0.8226 (tp) cc_final: 0.8021 (tt) REVERT: A 235 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7519 (mp) REVERT: A 280 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.6995 (m-80) REVERT: A 294 ILE cc_start: 0.8455 (tp) cc_final: 0.8175 (tt) REVERT: A 310 ASP cc_start: 0.7518 (t0) cc_final: 0.7054 (t0) REVERT: A 329 ASP cc_start: 0.7388 (t0) cc_final: 0.7076 (t0) REVERT: A 350 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8050 (mmtm) REVERT: A 376 LYS cc_start: 0.8538 (ttpt) cc_final: 0.8242 (ttpp) REVERT: A 393 VAL cc_start: 0.6671 (OUTLIER) cc_final: 0.6396 (p) REVERT: A 408 GLU cc_start: 0.7105 (tp30) cc_final: 0.6874 (tp30) REVERT: A 419 ASP cc_start: 0.7171 (p0) cc_final: 0.6863 (p0) REVERT: A 448 TRP cc_start: 0.7742 (m-10) cc_final: 0.7511 (m-10) REVERT: A 516 GLU cc_start: 0.8077 (tp30) cc_final: 0.7655 (tp30) REVERT: A 540 LYS cc_start: 0.8523 (tptm) cc_final: 0.8256 (tppt) REVERT: A 560 GLU cc_start: 0.7923 (tt0) cc_final: 0.7339 (tp30) REVERT: A 675 LYS cc_start: 0.8453 (mttt) cc_final: 0.8227 (tttt) REVERT: A 681 GLN cc_start: 0.7001 (mt0) cc_final: 0.6428 (mm-40) REVERT: A 823 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7872 (mp) REVERT: A 829 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7789 (tp-100) REVERT: A 877 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6879 (t80) REVERT: A 882 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: A 916 PHE cc_start: 0.8344 (m-80) cc_final: 0.7969 (m-80) REVERT: A 958 TRP cc_start: 0.8359 (m-10) cc_final: 0.7536 (m100) REVERT: A 969 LYS cc_start: 0.8907 (tptm) cc_final: 0.8462 (tptp) REVERT: A 974 LYS cc_start: 0.8914 (tmmt) cc_final: 0.8678 (tmmt) REVERT: B 125 ASN cc_start: 0.8346 (p0) cc_final: 0.8019 (p0) REVERT: B 156 GLU cc_start: 0.7356 (mp0) cc_final: 0.7124 (mp0) REVERT: B 291 ASP cc_start: 0.7749 (m-30) cc_final: 0.7181 (m-30) REVERT: B 304 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7892 (mmtm) REVERT: B 324 TYR cc_start: 0.8060 (t80) cc_final: 0.7724 (t80) REVERT: B 329 ASP cc_start: 0.7433 (t0) cc_final: 0.6925 (t0) REVERT: B 426 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: B 538 LYS cc_start: 0.8567 (mttm) cc_final: 0.8245 (mttt) REVERT: B 541 ILE cc_start: 0.8401 (mm) cc_final: 0.7869 (mm) REVERT: B 569 MET cc_start: 0.0644 (mtp) cc_final: 0.0287 (mtp) REVERT: B 595 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7677 (mt) REVERT: B 686 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6876 (mm-30) REVERT: B 818 LYS cc_start: 0.8472 (tppt) cc_final: 0.7940 (mmmt) REVERT: C 75 LYS cc_start: 0.5293 (OUTLIER) cc_final: 0.3831 (pptt) REVERT: C 120 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7556 (ttmt) REVERT: C 193 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7592 (t80) REVERT: C 225 ILE cc_start: 0.8072 (mm) cc_final: 0.7833 (mm) REVERT: C 248 THR cc_start: 0.8164 (p) cc_final: 0.7765 (p) REVERT: C 249 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6565 (m-30) REVERT: C 254 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.5367 (tp30) REVERT: D 66 TYR cc_start: 0.7744 (m-80) cc_final: 0.6468 (m-80) REVERT: D 83 GLU cc_start: 0.6246 (mm-30) cc_final: 0.5126 (mt-10) REVERT: D 120 LYS cc_start: 0.8261 (pttt) cc_final: 0.7578 (pmtt) REVERT: D 144 LYS cc_start: 0.8087 (tptt) cc_final: 0.7804 (tptt) REVERT: D 150 SER cc_start: 0.8259 (m) cc_final: 0.8005 (m) REVERT: D 222 ASP cc_start: 0.7577 (t0) cc_final: 0.7208 (t0) REVERT: D 233 ARG cc_start: 0.6210 (OUTLIER) cc_final: 0.5984 (tmt-80) REVERT: D 254 GLU cc_start: 0.7518 (mp0) cc_final: 0.6361 (mt-10) outliers start: 83 outliers final: 55 residues processed: 545 average time/residue: 0.3448 time to fit residues: 284.6012 Evaluate side-chains 563 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 492 time to evaluate : 2.165 ------------------------------------------------------------------------------- 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 155 GLU Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 275 ILE 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 915 THR 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 408 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 595 LEU 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 75 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LYS 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 190 TYR Chi-restraints excluded: chain C residue 193 TYR 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 167 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 233 ARG 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: 0.9990 chunk 180 optimal weight: 7.9990 chunk 203 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.154121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119803 restraints weight = 32686.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123712 restraints weight = 17283.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126532 restraints weight = 11415.819| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21520 Z= 0.155 Angle : 0.587 12.527 29026 Z= 0.309 Chirality : 0.041 0.178 3082 Planarity : 0.004 0.063 3712 Dihedral : 4.570 39.066 2801 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.89 % Favored : 93.87 % Rotamer: Outliers : 3.37 % Allowed : 26.62 % Favored : 70.01 % 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: 1.03 (0.14), residues: 1474 sheet: -1.69 (0.57), residues: 65 loop : -1.46 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP D 143 HIS 0.006 0.001 HIS D 67 PHE 0.034 0.001 PHE B 240 TYR 0.019 0.002 TYR A 649 ARG 0.013 0.000 ARG D 233 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 981) hydrogen bonds : angle 4.22498 ( 2832) covalent geometry : bond 0.00358 (21520) covalent geometry : angle 0.58712 (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 579 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 501 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7156 (tm-30) REVERT: A 42 LEU cc_start: 0.8697 (tp) cc_final: 0.8383 (tt) REVERT: A 45 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.6763 (m-80) REVERT: A 109 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7585 (tm-30) REVERT: A 131 THR cc_start: 0.8398 (m) cc_final: 0.8066 (t) REVERT: A 135 ASP cc_start: 0.7438 (t0) cc_final: 0.6996 (t0) REVERT: A 176 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8371 (mtmm) REVERT: A 229 LEU cc_start: 0.8188 (tp) cc_final: 0.7973 (tt) REVERT: A 235 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7495 (mp) REVERT: A 280 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.7066 (m-80) REVERT: A 294 ILE cc_start: 0.8394 (tp) cc_final: 0.8128 (tt) REVERT: A 310 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7091 (t0) REVERT: A 329 ASP cc_start: 0.7368 (t0) cc_final: 0.7098 (t0) REVERT: A 350 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8112 (mmtm) REVERT: A 376 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8241 (ttpp) REVERT: A 393 VAL cc_start: 0.6667 (OUTLIER) cc_final: 0.6402 (p) REVERT: A 408 GLU cc_start: 0.7123 (tp30) cc_final: 0.6876 (tp30) REVERT: A 419 ASP cc_start: 0.7153 (p0) cc_final: 0.6859 (p0) REVERT: A 448 TRP cc_start: 0.7716 (m-10) cc_final: 0.7483 (m-10) REVERT: A 516 GLU cc_start: 0.8092 (tp30) cc_final: 0.7652 (tp30) REVERT: A 540 LYS cc_start: 0.8503 (tptm) cc_final: 0.8245 (tppt) REVERT: A 560 GLU cc_start: 0.7930 (tt0) cc_final: 0.7313 (tp30) REVERT: A 675 LYS cc_start: 0.8452 (mttt) cc_final: 0.8219 (tttt) REVERT: A 681 GLN cc_start: 0.6945 (mt0) cc_final: 0.6381 (mm-40) REVERT: A 823 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7880 (mp) REVERT: A 829 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7826 (tp-100) REVERT: A 877 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.6900 (t80) REVERT: A 882 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: A 916 PHE cc_start: 0.8292 (m-80) cc_final: 0.7876 (m-80) REVERT: A 958 TRP cc_start: 0.8387 (m-10) cc_final: 0.7525 (m100) REVERT: A 969 LYS cc_start: 0.8932 (tptm) cc_final: 0.8401 (tptp) REVERT: A 974 LYS cc_start: 0.8904 (tmmt) cc_final: 0.8651 (tmmt) REVERT: B 93 ASN cc_start: 0.8423 (t0) cc_final: 0.8174 (t0) REVERT: B 125 ASN cc_start: 0.8394 (p0) cc_final: 0.8133 (p0) REVERT: B 156 GLU cc_start: 0.7391 (mp0) cc_final: 0.7104 (mp0) REVERT: B 291 ASP cc_start: 0.7747 (m-30) cc_final: 0.7163 (m-30) REVERT: B 304 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7898 (mmtm) REVERT: B 324 TYR cc_start: 0.8031 (t80) cc_final: 0.7744 (t80) REVERT: B 329 ASP cc_start: 0.7399 (t0) cc_final: 0.7047 (t0) REVERT: B 357 MET cc_start: 0.7060 (mmm) cc_final: 0.6206 (tmm) REVERT: B 426 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: B 538 LYS cc_start: 0.8519 (mttm) cc_final: 0.8207 (mttt) REVERT: B 541 ILE cc_start: 0.8393 (mm) cc_final: 0.8121 (mt) REVERT: B 569 MET cc_start: 0.1047 (mtp) cc_final: 0.0437 (mtp) REVERT: B 595 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7643 (mt) REVERT: B 646 PHE cc_start: 0.6123 (m-80) cc_final: 0.5747 (m-10) REVERT: B 686 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6855 (mm-30) REVERT: B 818 LYS cc_start: 0.8472 (tppt) cc_final: 0.7941 (mmmt) REVERT: C 75 LYS cc_start: 0.5246 (OUTLIER) cc_final: 0.3757 (pptt) REVERT: C 120 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7574 (ttmt) REVERT: C 193 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7593 (t80) REVERT: C 248 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7794 (p) REVERT: C 249 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6618 (m-30) REVERT: C 254 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5353 (tp30) REVERT: D 66 TYR cc_start: 0.7749 (m-80) cc_final: 0.6501 (m-80) REVERT: D 83 GLU cc_start: 0.6209 (mm-30) cc_final: 0.5132 (mt-10) REVERT: D 112 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7478 (tptp) REVERT: D 120 LYS cc_start: 0.8246 (pttt) cc_final: 0.7660 (pmtt) REVERT: D 144 LYS cc_start: 0.8030 (tptt) cc_final: 0.7764 (tptt) REVERT: D 150 SER cc_start: 0.8275 (m) cc_final: 0.8023 (m) REVERT: D 222 ASP cc_start: 0.7564 (t0) cc_final: 0.7196 (t0) REVERT: D 233 ARG cc_start: 0.6306 (tmt-80) cc_final: 0.6103 (tmt-80) REVERT: D 254 GLU cc_start: 0.7541 (mp0) cc_final: 0.6464 (mt-10) outliers start: 78 outliers final: 53 residues processed: 544 average time/residue: 0.3442 time to fit residues: 283.9492 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 : 2.199 ------------------------------------------------------------------------------- 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 155 GLU Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 310 ASP 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 B residue 134 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE 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 653 VAL Chi-restraints excluded: chain B residue 663 ASP 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 75 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 LYS 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 190 TYR Chi-restraints excluded: chain C residue 193 TYR 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 167 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 241 HIS 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: 0.8980 chunk 132 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 199 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.153726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119290 restraints weight = 32952.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123353 restraints weight = 17520.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.126020 restraints weight = 11491.640| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21520 Z= 0.163 Angle : 0.596 13.217 29026 Z= 0.312 Chirality : 0.042 0.180 3082 Planarity : 0.004 0.063 3712 Dihedral : 4.575 38.201 2801 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.89 % Favored : 93.87 % Rotamer: Outliers : 3.15 % Allowed : 26.97 % Favored : 69.88 % 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: 0.03 (0.17), residues: 2528 helix: 1.05 (0.14), residues: 1468 sheet: -1.43 (0.53), residues: 75 loop : -1.44 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP D 143 HIS 0.007 0.001 HIS D 67 PHE 0.026 0.001 PHE B 240 TYR 0.020 0.002 TYR A 649 ARG 0.013 0.000 ARG D 233 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 981) hydrogen bonds : angle 4.23019 ( 2832) covalent geometry : bond 0.00379 (21520) covalent geometry : angle 0.59567 (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 579 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 506 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7182 (tm-30) REVERT: A 42 LEU cc_start: 0.8678 (tp) cc_final: 0.8358 (tt) REVERT: A 45 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.6801 (m-80) REVERT: A 109 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7626 (tm-30) REVERT: A 131 THR cc_start: 0.8391 (m) cc_final: 0.8060 (t) REVERT: A 135 ASP cc_start: 0.7417 (t0) cc_final: 0.7003 (t0) REVERT: A 176 LYS cc_start: 0.8712 (mtmm) cc_final: 0.8372 (mtmm) REVERT: A 229 LEU cc_start: 0.8198 (tp) cc_final: 0.7974 (tt) REVERT: A 235 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7448 (mp) REVERT: A 280 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.7089 (m-80) REVERT: A 294 ILE cc_start: 0.8404 (tp) cc_final: 0.8157 (tt) REVERT: A 310 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7147 (t0) REVERT: A 329 ASP cc_start: 0.7345 (t0) cc_final: 0.7075 (t0) REVERT: A 350 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8136 (mmtm) REVERT: A 364 LYS cc_start: 0.7584 (ttmm) cc_final: 0.7230 (tttt) REVERT: A 376 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8221 (ttpp) REVERT: A 393 VAL cc_start: 0.6672 (OUTLIER) cc_final: 0.6400 (p) REVERT: A 408 GLU cc_start: 0.7129 (tp30) cc_final: 0.6884 (tp30) REVERT: A 448 TRP cc_start: 0.7693 (m-10) cc_final: 0.7471 (m-10) REVERT: A 516 GLU cc_start: 0.8068 (tp30) cc_final: 0.7619 (tp30) REVERT: A 540 LYS cc_start: 0.8499 (tptm) cc_final: 0.8244 (tppt) REVERT: A 560 GLU cc_start: 0.7951 (tt0) cc_final: 0.7315 (tp30) REVERT: A 675 LYS cc_start: 0.8444 (mttt) cc_final: 0.7413 (ttmm) REVERT: A 681 GLN cc_start: 0.7018 (mt0) cc_final: 0.6448 (mm-40) REVERT: A 823 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7887 (mp) REVERT: A 829 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7884 (tp-100) REVERT: A 877 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.6910 (t80) REVERT: A 882 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: A 916 PHE cc_start: 0.8328 (m-80) cc_final: 0.7875 (m-80) REVERT: A 958 TRP cc_start: 0.8386 (m-10) cc_final: 0.7643 (m-10) REVERT: A 969 LYS cc_start: 0.8940 (tptm) cc_final: 0.8422 (tptp) REVERT: A 974 LYS cc_start: 0.8936 (tmmt) cc_final: 0.8705 (tmmt) REVERT: B 93 ASN cc_start: 0.8389 (t0) cc_final: 0.8140 (t0) REVERT: B 291 ASP cc_start: 0.7774 (m-30) cc_final: 0.7151 (m-30) REVERT: B 304 LYS cc_start: 0.8197 (mmtm) cc_final: 0.7785 (mmtm) REVERT: B 324 TYR cc_start: 0.8024 (t80) cc_final: 0.7753 (t80) REVERT: B 357 MET cc_start: 0.7059 (mmm) cc_final: 0.6218 (tmm) REVERT: B 408 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6732 (tm-30) REVERT: B 426 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: B 538 LYS cc_start: 0.8530 (mttm) cc_final: 0.8222 (mttt) REVERT: B 569 MET cc_start: 0.1089 (mtp) cc_final: 0.0499 (mtp) REVERT: B 595 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7651 (mt) REVERT: B 646 PHE cc_start: 0.6203 (m-80) cc_final: 0.5817 (m-10) REVERT: B 684 ILE cc_start: 0.7312 (mm) cc_final: 0.7054 (mm) REVERT: B 686 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6855 (mm-30) REVERT: B 818 LYS cc_start: 0.8468 (tppt) cc_final: 0.7943 (mmmt) REVERT: C 75 LYS cc_start: 0.5283 (OUTLIER) cc_final: 0.3842 (pptt) REVERT: C 120 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7583 (ttmt) REVERT: C 193 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7594 (t80) REVERT: C 203 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7498 (mt) REVERT: C 248 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.7853 (p) REVERT: C 249 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6647 (m-30) REVERT: C 254 GLU cc_start: 0.5819 (OUTLIER) cc_final: 0.5371 (tp30) REVERT: C 261 TYR cc_start: 0.8145 (m-10) cc_final: 0.7894 (m-10) REVERT: D 66 TYR cc_start: 0.7768 (m-80) cc_final: 0.6524 (m-80) REVERT: D 83 GLU cc_start: 0.6246 (mm-30) cc_final: 0.5159 (mt-10) REVERT: D 112 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7465 (tptp) REVERT: D 120 LYS cc_start: 0.8157 (pttt) cc_final: 0.7667 (pmtt) REVERT: D 144 LYS cc_start: 0.8039 (tptt) cc_final: 0.7744 (tptt) REVERT: D 150 SER cc_start: 0.8252 (m) cc_final: 0.8018 (m) REVERT: D 222 ASP cc_start: 0.7624 (t0) cc_final: 0.7234 (t0) outliers start: 73 outliers final: 52 residues processed: 549 average time/residue: 0.3397 time to fit residues: 282.9042 Evaluate side-chains 572 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 501 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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 155 GLU Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 310 ASP 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 B residue 134 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 248 THR 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 586 LEU Chi-restraints excluded: chain B residue 595 LEU 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 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 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 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 134 TYR Chi-restraints excluded: chain D residue 136 ASN 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 195 GLN Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 3 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 135 optimal weight: 0.0570 chunk 149 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 231 optimal weight: 0.0370 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 698 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.154936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120668 restraints weight = 32874.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124712 restraints weight = 17321.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127367 restraints weight = 11339.213| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2820 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= 0.134 Angle : 0.584 12.776 29026 Z= 0.307 Chirality : 0.041 0.165 3082 Planarity : 0.004 0.062 3712 Dihedral : 4.504 39.667 2800 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.50 % Favored : 94.26 % Rotamer: Outliers : 3.15 % Allowed : 27.31 % 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: 0.12 (0.17), residues: 2528 helix: 1.14 (0.14), residues: 1470 sheet: -1.41 (0.53), residues: 75 loop : -1.43 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP D 143 HIS 0.006 0.001 HIS D 67 PHE 0.026 0.001 PHE B 240 TYR 0.014 0.001 TYR A 962 ARG 0.009 0.000 ARG B 747 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 981) hydrogen bonds : angle 4.14785 ( 2832) covalent geometry : bond 0.00307 (21520) covalent geometry : angle 0.58443 (29026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7724.06 seconds wall clock time: 134 minutes 8.68 seconds (8048.68 seconds total)