Starting phenix.real_space_refine on Thu Sep 18 23:16:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yg1_39233/09_2025/8yg1_39233.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yg1_39233/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yg1_39233/09_2025/8yg1_39233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yg1_39233/09_2025/8yg1_39233.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yg1_39233/09_2025/8yg1_39233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yg1_39233/09_2025/8yg1_39233.map" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.40, per 1000 atoms: 0.21 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: 1.57 Conformation dependent library (CDL) restraints added in 856.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.69 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: 3.25 Time building geometry restraints manager: 2.13 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.740 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.190 ------------------------------------------------------------------------------- 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 : 8.89 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (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 ARG 0.009 0.001 ARG B 747 TYR 0.030 0.002 TYR C 56 PHE 0.043 0.002 PHE B 240 TRP 0.095 0.003 TRP D 143 HIS 0.005 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00346 (21520) covalent geometry : angle 0.69079 (29026) hydrogen bonds : bond 0.17694 ( 981) hydrogen bonds : angle 6.01081 ( 2832) *********************** 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 : 0.744 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: 0.7166 (m-10) REVERT: A 540 LYS cc_start: 0.8510 (tptm) cc_final: 0.8167 (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: 0.8004 (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: 0.1517 time to fit residues: 114.6647 Evaluate side-chains 496 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 485 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 0.1980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.156968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122472 restraints weight = 33225.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126607 restraints weight = 17589.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129437 restraints weight = 11530.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.131052 restraints weight = 8662.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.132372 restraints weight = 7250.930| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21520 Z= 0.151 Angle : 0.587 11.001 29026 Z= 0.313 Chirality : 0.041 0.178 3082 Planarity : 0.004 0.094 3712 Dihedral : 5.393 57.893 2824 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.62 % Favored : 94.15 % Rotamer: Outliers : 3.33 % Allowed : 23.38 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.17), residues: 2528 helix: 0.75 (0.14), residues: 1458 sheet: -1.06 (0.58), residues: 65 loop : -1.49 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 247 TYR 0.021 0.002 TYR A 552 PHE 0.037 0.002 PHE A 933 TRP 0.055 0.002 TRP D 143 HIS 0.007 0.001 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00328 (21520) covalent geometry : angle 0.58666 (29026) hydrogen bonds : bond 0.04813 ( 981) hydrogen bonds : angle 4.73107 ( 2832) *********************** 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 : 0.573 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: 0.7974 (mttt) cc_final: 0.7644 (mttm) REVERT: A 131 THR cc_start: 0.8423 (m) cc_final: 0.8148 (t) REVERT: A 280 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6606 (m-80) REVERT: A 286 TYR cc_start: 0.7423 (m-80) cc_final: 0.7212 (m-10) REVERT: A 391 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7749 (t0) REVERT: A 393 VAL cc_start: 0.6790 (OUTLIER) cc_final: 0.6413 (p) REVERT: A 448 TRP cc_start: 0.7817 (m-10) cc_final: 0.7433 (m-10) REVERT: A 516 GLU cc_start: 0.7936 (tp30) cc_final: 0.7535 (tp30) REVERT: A 823 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7952 (mp) REVERT: A 829 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: A 882 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: A 916 PHE cc_start: 0.8316 (m-80) cc_final: 0.7983 (m-80) REVERT: A 933 PHE cc_start: 0.7896 (m-80) cc_final: 0.7634 (m-10) REVERT: A 969 LYS cc_start: 0.8495 (tptm) cc_final: 0.8208 (tptm) REVERT: A 974 LYS cc_start: 0.9087 (ttpt) cc_final: 0.8745 (tmmt) REVERT: A 984 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8194 (tt) REVERT: B 181 GLU cc_start: 0.7315 (pt0) cc_final: 0.7071 (mt-10) REVERT: B 291 ASP cc_start: 0.7634 (m-30) cc_final: 0.7397 (m-30) REVERT: B 304 LYS cc_start: 0.8231 (mmtm) cc_final: 0.8009 (mmtm) REVERT: B 335 GLU cc_start: 0.7508 (mp0) cc_final: 0.7300 (mp0) REVERT: B 569 MET cc_start: 0.2416 (mtp) cc_final: 0.1935 (mtp) REVERT: B 595 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7381 (mt) REVERT: B 669 ARG cc_start: 0.7211 (tpp80) cc_final: 0.6690 (tpp80) REVERT: B 818 LYS cc_start: 0.8467 (tppt) cc_final: 0.7841 (mmmt) REVERT: C 224 ASN cc_start: 0.7978 (t0) cc_final: 0.7729 (t0) REVERT: D 71 TYR cc_start: 0.6375 (m-80) cc_final: 0.5966 (m-80) REVERT: D 83 GLU cc_start: 0.6072 (mm-30) cc_final: 0.4813 (mt-10) REVERT: D 120 LYS cc_start: 0.8288 (pttt) cc_final: 0.7274 (pmtt) REVERT: D 155 GLU cc_start: 0.6291 (mm-30) cc_final: 0.5939 (mm-30) REVERT: D 197 TYR cc_start: 0.7592 (m-80) cc_final: 0.7137 (m-80) REVERT: D 208 ILE cc_start: 0.8701 (mt) cc_final: 0.8441 (tt) outliers start: 77 outliers final: 28 residues processed: 548 average time/residue: 0.1493 time to fit residues: 124.0426 Evaluate side-chains 522 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 486 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN 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 A residue 984 LEU 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 248 THR Chi-restraints excluded: chain D residue 55 ASP 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 148 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.156331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122020 restraints weight = 32987.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.126086 restraints weight = 17305.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128895 restraints weight = 11328.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130567 restraints weight = 8537.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.131980 restraints weight = 7079.840| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21520 Z= 0.147 Angle : 0.575 11.461 29026 Z= 0.304 Chirality : 0.041 0.174 3082 Planarity : 0.004 0.084 3712 Dihedral : 4.903 53.345 2805 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.34 % Favored : 94.46 % Rotamer: Outliers : 3.63 % Allowed : 23.85 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.17), residues: 2528 helix: 0.82 (0.14), residues: 1465 sheet: -1.22 (0.59), residues: 65 loop : -1.46 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 247 TYR 0.018 0.001 TYR A 649 PHE 0.020 0.001 PHE A 933 TRP 0.066 0.002 TRP D 143 HIS 0.006 0.001 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00330 (21520) covalent geometry : angle 0.57548 (29026) hydrogen bonds : bond 0.04573 ( 981) hydrogen bonds : angle 4.54754 ( 2832) *********************** 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 584 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 500 time to evaluate : 0.829 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: 0.7891 (mttt) cc_final: 0.7629 (mttm) REVERT: A 42 LEU cc_start: 0.8586 (tp) cc_final: 0.8331 (tt) REVERT: A 131 THR cc_start: 0.8382 (m) cc_final: 0.8113 (t) REVERT: A 280 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6647 (m-80) REVERT: A 286 TYR cc_start: 0.7422 (m-80) cc_final: 0.7189 (m-10) REVERT: A 350 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7937 (mmtt) REVERT: A 391 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7868 (t0) REVERT: A 393 VAL cc_start: 0.6772 (OUTLIER) cc_final: 0.6403 (p) REVERT: A 448 TRP cc_start: 0.7821 (m-10) cc_final: 0.7590 (m-10) REVERT: A 516 GLU cc_start: 0.7986 (tp30) cc_final: 0.7646 (tp30) REVERT: A 540 LYS cc_start: 0.8560 (tptm) cc_final: 0.8263 (tppt) REVERT: A 696 THR cc_start: 0.7620 (m) cc_final: 0.7349 (m) REVERT: A 823 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7902 (mp) REVERT: A 829 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7718 (tp40) REVERT: A 882 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8347 (mt-10) REVERT: A 916 PHE cc_start: 0.8329 (m-80) cc_final: 0.7979 (m-80) REVERT: A 969 LYS cc_start: 0.8630 (tptm) cc_final: 0.8318 (tptm) REVERT: A 974 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8476 (tmmt) REVERT: B 291 ASP cc_start: 0.7636 (m-30) cc_final: 0.7266 (m-30) REVERT: B 304 LYS cc_start: 0.8262 (mmtm) cc_final: 0.7836 (mmtm) REVERT: B 329 ASP cc_start: 0.7423 (t0) cc_final: 0.7122 (t0) REVERT: B 354 PHE cc_start: 0.7861 (t80) cc_final: 0.7555 (t80) REVERT: B 569 MET cc_start: 0.2617 (mtp) cc_final: 0.2170 (mtp) REVERT: B 669 ARG cc_start: 0.7219 (tpp80) cc_final: 0.6719 (tpp80) REVERT: B 818 LYS cc_start: 0.8480 (tppt) cc_final: 0.7862 (mmmt) REVERT: B 986 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7770 (tm-30) REVERT: C 224 ASN cc_start: 0.8063 (t0) cc_final: 0.7667 (t0) REVERT: C 235 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7247 (pp) REVERT: C 249 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6501 (m-30) REVERT: D 67 HIS cc_start: 0.7221 (OUTLIER) cc_final: 0.6931 (t-170) REVERT: D 71 TYR cc_start: 0.6107 (m-80) cc_final: 0.5778 (m-80) REVERT: D 83 GLU cc_start: 0.6068 (mm-30) cc_final: 0.4828 (mt-10) REVERT: D 120 LYS cc_start: 0.8295 (pttt) cc_final: 0.7465 (pmtt) REVERT: D 144 LYS cc_start: 0.8059 (mttt) cc_final: 0.7842 (tptt) REVERT: D 208 ILE cc_start: 0.8683 (mt) cc_final: 0.8436 (tt) REVERT: D 222 ASP cc_start: 0.7366 (t0) cc_final: 0.7043 (t0) REVERT: D 256 GLU cc_start: 0.6415 (mt-10) cc_final: 0.6140 (mt-10) outliers start: 84 outliers final: 42 residues processed: 541 average time/residue: 0.1471 time to fit residues: 121.8180 Evaluate side-chains 544 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 493 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain B residue 94 VAL 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 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 236 GLN 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 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 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 122 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 196 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 211 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 GLN A 939 GLN B 67 HIS B 297 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.156360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121981 restraints weight = 33000.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126065 restraints weight = 17326.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128889 restraints weight = 11341.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130520 restraints weight = 8543.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.131940 restraints weight = 7136.019| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21520 Z= 0.138 Angle : 0.560 10.095 29026 Z= 0.295 Chirality : 0.041 0.182 3082 Planarity : 0.004 0.076 3712 Dihedral : 4.803 52.106 2805 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.42 % Favored : 94.38 % Rotamer: Outliers : 3.63 % Allowed : 24.07 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.17), residues: 2528 helix: 0.93 (0.14), residues: 1467 sheet: -1.41 (0.57), residues: 65 loop : -1.52 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 247 TYR 0.020 0.001 TYR A 649 PHE 0.039 0.001 PHE B 240 TRP 0.070 0.002 TRP D 143 HIS 0.004 0.001 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00315 (21520) covalent geometry : angle 0.56049 (29026) hydrogen bonds : bond 0.04190 ( 981) hydrogen bonds : angle 4.39695 ( 2832) *********************** 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 596 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 512 time to evaluate : 0.526 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 42 LEU cc_start: 0.8650 (tp) cc_final: 0.8401 (tt) REVERT: A 109 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 131 THR cc_start: 0.8378 (m) cc_final: 0.8095 (t) REVERT: A 176 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8388 (mtmm) REVERT: A 286 TYR cc_start: 0.7421 (m-80) cc_final: 0.7155 (m-10) REVERT: A 297 GLN cc_start: 0.8135 (mp10) cc_final: 0.7862 (mp10) REVERT: A 350 LYS cc_start: 0.8269 (mmtt) cc_final: 0.8067 (mmtm) REVERT: A 391 ASN cc_start: 0.8216 (t0) cc_final: 0.7981 (t0) REVERT: A 393 VAL cc_start: 0.6699 (OUTLIER) cc_final: 0.6356 (p) REVERT: A 448 TRP cc_start: 0.7817 (m-10) cc_final: 0.7568 (m-10) REVERT: A 516 GLU cc_start: 0.8028 (tp30) cc_final: 0.7672 (tp30) REVERT: A 540 LYS cc_start: 0.8545 (tptm) cc_final: 0.8290 (tppt) REVERT: A 675 LYS cc_start: 0.8449 (mttt) cc_final: 0.7569 (ttmm) REVERT: A 696 THR cc_start: 0.7630 (m) cc_final: 0.7371 (m) REVERT: A 823 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7883 (mp) REVERT: A 829 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7752 (tp40) REVERT: A 881 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.7911 (m90) REVERT: A 882 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: A 916 PHE cc_start: 0.8351 (m-80) cc_final: 0.7987 (m-80) REVERT: A 969 LYS cc_start: 0.8759 (tptm) cc_final: 0.8414 (tptm) REVERT: B 125 ASN cc_start: 0.8177 (p0) cc_final: 0.7827 (p0) REVERT: B 181 GLU cc_start: 0.7311 (pt0) cc_final: 0.6868 (mt-10) REVERT: B 291 ASP cc_start: 0.7690 (m-30) cc_final: 0.7165 (m-30) REVERT: B 297 GLN cc_start: 0.5456 (OUTLIER) cc_final: 0.4477 (tp40) REVERT: B 304 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7864 (mmtm) REVERT: B 329 ASP cc_start: 0.7506 (t0) cc_final: 0.7115 (t0) REVERT: B 362 GLU cc_start: 0.7547 (tp30) cc_final: 0.7260 (tp30) REVERT: B 541 ILE cc_start: 0.8325 (mm) cc_final: 0.8052 (mm) REVERT: B 569 MET cc_start: 0.3150 (OUTLIER) cc_final: 0.2878 (mtp) REVERT: B 595 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7513 (mt) REVERT: B 622 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6568 (mmmt) REVERT: B 669 ARG cc_start: 0.7171 (tpp80) cc_final: 0.6678 (tpp80) REVERT: B 686 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6818 (mm-30) REVERT: B 818 LYS cc_start: 0.8482 (tppt) cc_final: 0.7902 (mmmt) REVERT: B 986 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7775 (tm-30) REVERT: C 117 ILE cc_start: 0.8337 (mp) cc_final: 0.7785 (tt) REVERT: C 224 ASN cc_start: 0.8128 (t0) cc_final: 0.7708 (t0) REVERT: C 235 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7192 (pp) REVERT: C 249 ASP cc_start: 0.6884 (OUTLIER) cc_final: 0.6414 (m-30) REVERT: D 67 HIS cc_start: 0.7226 (OUTLIER) cc_final: 0.6965 (t-170) REVERT: D 83 GLU cc_start: 0.6047 (mm-30) cc_final: 0.4856 (mt-10) REVERT: D 120 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7273 (pmtt) REVERT: D 144 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7870 (tptt) REVERT: D 208 ILE cc_start: 0.8668 (mt) cc_final: 0.8445 (tt) REVERT: D 222 ASP cc_start: 0.7446 (t0) cc_final: 0.7087 (t0) outliers start: 84 outliers final: 43 residues processed: 556 average time/residue: 0.1450 time to fit residues: 122.0371 Evaluate side-chains 556 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 499 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 284 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 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 153 SER 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 297 GLN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 665 LYS Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 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 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 235 LEU Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain D residue 67 HIS Chi-restraints excluded: chain D residue 120 LYS 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 144 LYS 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 251 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 223 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 72 optimal weight: 0.0370 chunk 30 optimal weight: 0.5980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 HIS ** 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 = 0.3987 r_free = 0.3987 target = 0.156190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121890 restraints weight = 32658.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126020 restraints weight = 17163.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128736 restraints weight = 11212.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130355 restraints weight = 8476.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.131766 restraints weight = 7093.977| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21520 Z= 0.133 Angle : 0.551 9.809 29026 Z= 0.290 Chirality : 0.041 0.180 3082 Planarity : 0.003 0.071 3712 Dihedral : 4.601 39.423 2801 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.42 % Favored : 94.38 % Rotamer: Outliers : 3.76 % Allowed : 24.16 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.17), residues: 2528 helix: 1.01 (0.14), residues: 1468 sheet: -1.48 (0.57), residues: 65 loop : -1.50 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 247 TYR 0.016 0.001 TYR A 649 PHE 0.052 0.001 PHE B 240 TRP 0.073 0.002 TRP D 143 HIS 0.006 0.001 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00303 (21520) covalent geometry : angle 0.55060 (29026) hydrogen bonds : bond 0.04010 ( 981) hydrogen bonds : angle 4.32965 ( 2832) *********************** 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 587 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 500 time to evaluate : 0.652 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: 0.7472 (tm-30) cc_final: 0.7033 (tm-30) REVERT: A 42 LEU cc_start: 0.8674 (tp) cc_final: 0.8427 (tt) REVERT: A 45 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.6453 (m-80) REVERT: A 109 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7613 (tm-30) REVERT: A 131 THR cc_start: 0.8384 (m) cc_final: 0.8056 (t) REVERT: A 176 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8359 (mtmm) REVERT: A 286 TYR cc_start: 0.7418 (m-80) cc_final: 0.7162 (m-10) REVERT: A 297 GLN cc_start: 0.8154 (mp10) cc_final: 0.7927 (mp10) REVERT: A 310 ASP cc_start: 0.7094 (m-30) cc_final: 0.6764 (t0) REVERT: A 391 ASN cc_start: 0.8269 (t0) cc_final: 0.8003 (t0) REVERT: A 393 VAL cc_start: 0.6704 (OUTLIER) cc_final: 0.6362 (p) REVERT: A 448 TRP cc_start: 0.7791 (m-10) cc_final: 0.7547 (m-10) REVERT: A 516 GLU cc_start: 0.8041 (tp30) cc_final: 0.7603 (tp30) REVERT: A 540 LYS cc_start: 0.8508 (tptm) cc_final: 0.8260 (tppt) REVERT: A 675 LYS cc_start: 0.8448 (mttt) cc_final: 0.7558 (ttmm) REVERT: A 696 THR cc_start: 0.7684 (m) cc_final: 0.7425 (m) REVERT: A 823 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7866 (mp) REVERT: A 829 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7757 (tp40) REVERT: A 878 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7529 (p) REVERT: A 882 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8353 (mt-10) REVERT: A 916 PHE cc_start: 0.8332 (m-80) cc_final: 0.7937 (m-80) REVERT: A 969 LYS cc_start: 0.8821 (tptm) cc_final: 0.8485 (tptm) REVERT: B 125 ASN cc_start: 0.8250 (p0) cc_final: 0.7837 (p0) REVERT: B 181 GLU cc_start: 0.7317 (pt0) cc_final: 0.6871 (mt-10) REVERT: B 291 ASP cc_start: 0.7707 (m-30) cc_final: 0.7151 (m-30) REVERT: B 304 LYS cc_start: 0.8247 (mmtm) cc_final: 0.7966 (mmtm) REVERT: B 324 TYR cc_start: 0.8095 (t80) cc_final: 0.7673 (t80) REVERT: B 329 ASP cc_start: 0.7459 (t0) cc_final: 0.6947 (t0) REVERT: B 338 TYR cc_start: 0.8073 (m-80) cc_final: 0.7859 (m-80) REVERT: B 357 MET cc_start: 0.6999 (tmm) cc_final: 0.6187 (tmm) REVERT: B 538 LYS cc_start: 0.8516 (mttm) cc_final: 0.8144 (mtmt) REVERT: B 541 ILE cc_start: 0.8347 (mm) cc_final: 0.7923 (mm) REVERT: B 595 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7543 (mt) REVERT: B 622 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6647 (tptp) REVERT: B 686 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6795 (mm-30) REVERT: B 724 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7283 (pttm) REVERT: B 818 LYS cc_start: 0.8469 (tppt) cc_final: 0.7896 (mmmt) REVERT: B 986 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7748 (tm-30) REVERT: C 117 ILE cc_start: 0.8332 (mp) cc_final: 0.7796 (tt) REVERT: C 224 ASN cc_start: 0.8193 (t0) cc_final: 0.7804 (t160) REVERT: C 235 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7166 (pp) REVERT: C 249 ASP cc_start: 0.6896 (OUTLIER) cc_final: 0.6369 (m-30) REVERT: C 254 GLU cc_start: 0.5778 (OUTLIER) cc_final: 0.5347 (tp30) REVERT: D 83 GLU cc_start: 0.5984 (mm-30) cc_final: 0.4853 (mt-10) REVERT: D 120 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7826 (pmtt) REVERT: D 222 ASP cc_start: 0.7441 (t0) cc_final: 0.7105 (t0) outliers start: 87 outliers final: 52 residues processed: 548 average time/residue: 0.1465 time to fit residues: 121.7268 Evaluate side-chains 556 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 491 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 50 VAL 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 619 LEU Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 978 HIS Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 170 VAL 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 346 VAL Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 558 LEU 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 724 LYS Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 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 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 235 LEU Chi-restraints excluded: chain C residue 236 GLN Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 204 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 0.0470 chunk 241 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN ** 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 = 0.3988 r_free = 0.3988 target = 0.156233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121809 restraints weight = 32808.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125906 restraints weight = 17288.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128636 restraints weight = 11303.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130641 restraints weight = 8476.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.131636 restraints weight = 7001.283| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2063 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= 0.126 Angle : 0.553 10.457 29026 Z= 0.291 Chirality : 0.041 0.187 3082 Planarity : 0.003 0.070 3712 Dihedral : 4.511 40.354 2801 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.34 % Favored : 94.46 % Rotamer: Outliers : 3.54 % Allowed : 24.59 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.17), residues: 2528 helix: 1.09 (0.14), residues: 1470 sheet: -1.76 (0.53), residues: 75 loop : -1.47 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 247 TYR 0.017 0.001 TYR D 71 PHE 0.041 0.001 PHE B 240 TRP 0.074 0.002 TRP D 143 HIS 0.006 0.001 HIS A 881 Details of bonding type rmsd covalent geometry : bond 0.00284 (21520) covalent geometry : angle 0.55323 (29026) hydrogen bonds : bond 0.03854 ( 981) hydrogen bonds : angle 4.23219 ( 2832) *********************** 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 580 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 498 time to evaluate : 0.698 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: 0.7472 (tm-30) cc_final: 0.7056 (tm-30) REVERT: A 42 LEU cc_start: 0.8684 (tp) cc_final: 0.8440 (tt) REVERT: A 45 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.6507 (m-80) REVERT: A 109 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7605 (tp-100) REVERT: A 131 THR cc_start: 0.8362 (m) cc_final: 0.8040 (t) REVERT: A 176 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8352 (mtmm) REVERT: A 280 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: A 286 TYR cc_start: 0.7451 (m-80) cc_final: 0.7177 (m-10) REVERT: A 294 ILE cc_start: 0.8438 (tp) cc_final: 0.8217 (tt) REVERT: A 297 GLN cc_start: 0.8166 (mp10) cc_final: 0.7964 (mp10) REVERT: A 350 LYS cc_start: 0.8342 (mmtt) cc_final: 0.8054 (mmtm) REVERT: A 376 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8225 (ttpp) REVERT: A 391 ASN cc_start: 0.8275 (t0) cc_final: 0.8021 (t0) REVERT: A 393 VAL cc_start: 0.6657 (OUTLIER) cc_final: 0.6323 (p) REVERT: A 448 TRP cc_start: 0.7776 (m-10) cc_final: 0.7519 (m-10) REVERT: A 516 GLU cc_start: 0.7993 (tp30) cc_final: 0.7591 (tp30) REVERT: A 563 ASN cc_start: 0.7971 (m-40) cc_final: 0.7315 (t0) REVERT: A 696 THR cc_start: 0.7705 (m) cc_final: 0.7437 (m) REVERT: A 823 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7849 (mp) REVERT: A 829 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7760 (tp40) REVERT: A 882 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: A 916 PHE cc_start: 0.8319 (m-80) cc_final: 0.7853 (m-80) REVERT: A 958 TRP cc_start: 0.7769 (m-10) cc_final: 0.7562 (m-10) REVERT: A 969 LYS cc_start: 0.8861 (tptm) cc_final: 0.8615 (tptm) REVERT: B 125 ASN cc_start: 0.8293 (p0) cc_final: 0.7850 (p0) REVERT: B 181 GLU cc_start: 0.7281 (pt0) cc_final: 0.6902 (mt-10) REVERT: B 203 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8232 (tt) REVERT: B 291 ASP cc_start: 0.7733 (m-30) cc_final: 0.7179 (m-30) REVERT: B 304 LYS cc_start: 0.8247 (mmtm) cc_final: 0.7980 (mmtm) REVERT: B 329 ASP cc_start: 0.7435 (t0) cc_final: 0.6916 (t70) REVERT: B 357 MET cc_start: 0.7005 (tmm) cc_final: 0.6140 (tmm) REVERT: B 408 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6572 (tm-30) REVERT: B 426 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: B 538 LYS cc_start: 0.8432 (mttm) cc_final: 0.8098 (mtmt) REVERT: B 541 ILE cc_start: 0.8349 (mm) cc_final: 0.7809 (mm) REVERT: B 547 ASP cc_start: 0.7423 (t0) cc_final: 0.7175 (t0) REVERT: B 554 ASP cc_start: 0.6932 (t0) cc_final: 0.6355 (t0) REVERT: B 595 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7541 (mt) REVERT: B 686 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6775 (mm-30) REVERT: B 818 LYS cc_start: 0.8474 (tppt) cc_final: 0.7876 (mmmt) REVERT: B 986 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7710 (tm-30) REVERT: C 117 ILE cc_start: 0.8326 (mp) cc_final: 0.7845 (tt) REVERT: C 120 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7511 (ttmt) REVERT: C 224 ASN cc_start: 0.8264 (t0) cc_final: 0.8050 (t0) REVERT: C 235 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7172 (pp) REVERT: C 249 ASP cc_start: 0.6863 (OUTLIER) cc_final: 0.6288 (m-30) REVERT: C 254 GLU cc_start: 0.5720 (OUTLIER) cc_final: 0.5277 (tp30) REVERT: C 290 MET cc_start: 0.7714 (mmm) cc_final: 0.7383 (mmm) REVERT: D 66 TYR cc_start: 0.7683 (m-80) cc_final: 0.6424 (m-80) REVERT: D 83 GLU cc_start: 0.5978 (mm-30) cc_final: 0.4938 (mt-10) REVERT: D 120 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7260 (pmtt) REVERT: D 144 LYS cc_start: 0.8090 (tptt) cc_final: 0.7827 (tptt) REVERT: D 222 ASP cc_start: 0.7452 (t0) cc_final: 0.7085 (t0) outliers start: 82 outliers final: 49 residues processed: 546 average time/residue: 0.1490 time to fit residues: 123.7765 Evaluate side-chains 556 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 493 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 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 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 866 MET Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 100 PHE 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 153 SER 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 D residue 120 LYS Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 241 HIS Chi-restraints excluded: chain D residue 251 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 111 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 210 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 235 optimal weight: 0.1980 chunk 118 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 217 optimal weight: 0.7980 chunk 221 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121058 restraints weight = 32900.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125012 restraints weight = 17303.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127899 restraints weight = 11382.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129601 restraints weight = 8555.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130531 restraints weight = 7122.393| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21520 Z= 0.142 Angle : 0.568 10.234 29026 Z= 0.298 Chirality : 0.041 0.184 3082 Planarity : 0.004 0.066 3712 Dihedral : 4.503 40.223 2801 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.54 % Favored : 94.22 % Rotamer: Outliers : 3.46 % Allowed : 25.19 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.17), residues: 2528 helix: 1.08 (0.14), residues: 1475 sheet: -1.50 (0.58), residues: 65 loop : -1.48 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 233 TYR 0.021 0.001 TYR D 260 PHE 0.038 0.001 PHE B 240 TRP 0.071 0.002 TRP D 143 HIS 0.004 0.001 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00329 (21520) covalent geometry : angle 0.56846 (29026) hydrogen bonds : bond 0.03982 ( 981) hydrogen bonds : angle 4.21910 ( 2832) *********************** 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 574 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 494 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7099 (tm-30) REVERT: A 42 LEU cc_start: 0.8695 (tp) cc_final: 0.8451 (tt) REVERT: A 45 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.6601 (m-80) REVERT: A 109 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7547 (tm-30) REVERT: A 131 THR cc_start: 0.8372 (m) cc_final: 0.8039 (t) REVERT: A 176 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8354 (mtmm) REVERT: A 280 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: A 294 ILE cc_start: 0.8328 (tp) cc_final: 0.8115 (tt) REVERT: A 310 ASP cc_start: 0.7436 (t0) cc_final: 0.6963 (t0) REVERT: A 376 LYS cc_start: 0.8543 (ttpt) cc_final: 0.8250 (ttpp) REVERT: A 391 ASN cc_start: 0.8316 (t0) cc_final: 0.8025 (t0) REVERT: A 393 VAL cc_start: 0.6647 (OUTLIER) cc_final: 0.6342 (p) REVERT: A 448 TRP cc_start: 0.7756 (m-10) cc_final: 0.7519 (m-10) REVERT: A 516 GLU cc_start: 0.8050 (tp30) cc_final: 0.7623 (tp30) REVERT: A 531 MET cc_start: 0.7394 (mmm) cc_final: 0.7177 (mmm) REVERT: A 540 LYS cc_start: 0.8522 (tptm) cc_final: 0.8284 (tppt) REVERT: A 616 MET cc_start: 0.8252 (mmm) cc_final: 0.7432 (mmm) REVERT: A 675 LYS cc_start: 0.8462 (mttt) cc_final: 0.7493 (ttmm) REVERT: A 823 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7829 (mp) REVERT: A 829 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7809 (tp40) REVERT: A 882 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: A 916 PHE cc_start: 0.8351 (m-80) cc_final: 0.7948 (m-80) REVERT: A 958 TRP cc_start: 0.7805 (m-10) cc_final: 0.7583 (m-10) REVERT: A 969 LYS cc_start: 0.8883 (tptm) cc_final: 0.8521 (tptm) REVERT: A 985 LYS cc_start: 0.8470 (mtmm) cc_final: 0.8226 (mttm) REVERT: B 125 ASN cc_start: 0.8284 (p0) cc_final: 0.7998 (p0) REVERT: B 181 GLU cc_start: 0.7300 (pt0) cc_final: 0.6884 (mt-10) REVERT: B 203 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8238 (tt) REVERT: B 291 ASP cc_start: 0.7760 (m-30) cc_final: 0.7200 (m-30) REVERT: B 304 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7951 (mmtm) REVERT: B 329 ASP cc_start: 0.7425 (t0) cc_final: 0.6819 (t0) REVERT: B 335 GLU cc_start: 0.7675 (mp0) cc_final: 0.7467 (mp0) REVERT: B 357 MET cc_start: 0.6948 (tmm) cc_final: 0.6051 (tmm) REVERT: B 408 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6584 (tm-30) REVERT: B 426 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: B 538 LYS cc_start: 0.8501 (mttm) cc_final: 0.8173 (mttt) REVERT: B 541 ILE cc_start: 0.8363 (mm) cc_final: 0.7800 (mm) REVERT: B 547 ASP cc_start: 0.7441 (t0) cc_final: 0.7207 (t0) REVERT: B 554 ASP cc_start: 0.6956 (t0) cc_final: 0.6409 (t0) REVERT: B 564 LYS cc_start: 0.5313 (OUTLIER) cc_final: 0.4824 (mmtt) REVERT: B 595 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7567 (mt) REVERT: B 686 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6787 (mm-30) REVERT: B 818 LYS cc_start: 0.8482 (tppt) cc_final: 0.7876 (mmmt) REVERT: B 986 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7695 (tm-30) REVERT: C 117 ILE cc_start: 0.8346 (mp) cc_final: 0.7882 (tt) REVERT: C 120 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7576 (ttmt) REVERT: C 224 ASN cc_start: 0.8341 (t0) cc_final: 0.8098 (t0) REVERT: C 235 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7236 (pp) REVERT: C 249 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6439 (m-30) REVERT: C 254 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.5284 (tp30) REVERT: C 290 MET cc_start: 0.7678 (mmm) cc_final: 0.7266 (mmm) REVERT: D 66 TYR cc_start: 0.7713 (m-80) cc_final: 0.6483 (m-80) REVERT: D 83 GLU cc_start: 0.6131 (mm-30) cc_final: 0.5019 (mt-10) REVERT: D 120 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7863 (pmtt) REVERT: D 144 LYS cc_start: 0.8065 (tptt) cc_final: 0.7785 (tptt) REVERT: D 222 ASP cc_start: 0.7478 (t0) cc_final: 0.7123 (t0) REVERT: D 283 LEU cc_start: 0.8643 (tp) cc_final: 0.8423 (tp) REVERT: D 285 ARG cc_start: 0.7319 (mtp180) cc_final: 0.7114 (mtp180) outliers start: 80 outliers final: 48 residues processed: 542 average time/residue: 0.1519 time to fit residues: 125.7319 Evaluate side-chains 549 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 486 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 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 184 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 663 ASP 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 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 100 PHE 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 153 SER Chi-restraints excluded: chain C residue 190 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 D residue 120 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 166 optimal weight: 0.5980 chunk 222 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 178 optimal weight: 0.0570 chunk 240 optimal weight: 0.2980 chunk 26 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 132 optimal weight: 0.0980 chunk 248 optimal weight: 1.9990 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 867 ASN ** 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 = 0.4007 r_free = 0.4007 target = 0.157512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123161 restraints weight = 32755.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.127253 restraints weight = 17323.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130129 restraints weight = 11367.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.131789 restraints weight = 8508.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133174 restraints weight = 7095.721| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 21520 Z= 0.109 Angle : 0.557 8.813 29026 Z= 0.292 Chirality : 0.040 0.172 3082 Planarity : 0.003 0.064 3712 Dihedral : 4.380 42.281 2801 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.02 % Favored : 94.74 % Rotamer: Outliers : 2.77 % Allowed : 26.02 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2528 helix: 1.21 (0.14), residues: 1467 sheet: -2.11 (0.49), residues: 59 loop : -1.42 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 233 TYR 0.022 0.001 TYR A 56 PHE 0.029 0.001 PHE B 240 TRP 0.073 0.002 TRP D 143 HIS 0.006 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00243 (21520) covalent geometry : angle 0.55678 (29026) hydrogen bonds : bond 0.03377 ( 981) hydrogen bonds : angle 4.11327 ( 2832) *********************** 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 565 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 501 time to evaluate : 0.767 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: 0.7472 (tm-30) cc_final: 0.7066 (tm-30) REVERT: A 42 LEU cc_start: 0.8655 (tp) cc_final: 0.8399 (tt) REVERT: A 45 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.6607 (m-80) REVERT: A 109 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7591 (tp-100) REVERT: A 131 THR cc_start: 0.8320 (m) cc_final: 0.8017 (t) REVERT: A 135 ASP cc_start: 0.7892 (t0) cc_final: 0.7081 (t0) REVERT: A 176 LYS cc_start: 0.8653 (mtmm) cc_final: 0.8299 (mtmm) REVERT: A 229 LEU cc_start: 0.8201 (tp) cc_final: 0.7971 (tt) REVERT: A 280 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.6933 (m-80) REVERT: A 286 TYR cc_start: 0.7388 (m-80) cc_final: 0.7107 (m-10) REVERT: A 310 ASP cc_start: 0.7407 (t0) cc_final: 0.6946 (t0) REVERT: A 350 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8117 (mmtm) REVERT: A 376 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8227 (ttpp) REVERT: A 391 ASN cc_start: 0.8241 (t0) cc_final: 0.7990 (t0) REVERT: A 448 TRP cc_start: 0.7703 (m-10) cc_final: 0.7450 (m-10) REVERT: A 516 GLU cc_start: 0.8002 (tp30) cc_final: 0.7609 (tp30) REVERT: A 540 LYS cc_start: 0.8502 (tptm) cc_final: 0.8254 (tppt) REVERT: A 560 GLU cc_start: 0.7874 (tt0) cc_final: 0.7266 (tp30) REVERT: A 616 MET cc_start: 0.8162 (mmm) cc_final: 0.7182 (mmm) REVERT: A 675 LYS cc_start: 0.8468 (mttt) cc_final: 0.7424 (ttmm) REVERT: A 681 GLN cc_start: 0.6749 (mt0) cc_final: 0.6224 (mm-40) REVERT: A 823 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7816 (mp) REVERT: A 877 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6805 (t80) REVERT: A 882 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: A 916 PHE cc_start: 0.8306 (m-80) cc_final: 0.7826 (m-80) REVERT: A 969 LYS cc_start: 0.8890 (tptm) cc_final: 0.8490 (tptm) REVERT: A 985 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8205 (mttm) REVERT: B 125 ASN cc_start: 0.8351 (p0) cc_final: 0.8084 (p0) REVERT: B 203 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8230 (tt) REVERT: B 291 ASP cc_start: 0.7726 (m-30) cc_final: 0.7209 (m-30) REVERT: B 304 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7950 (mmtm) REVERT: B 329 ASP cc_start: 0.7398 (t0) cc_final: 0.7066 (t0) REVERT: B 357 MET cc_start: 0.6907 (tmm) cc_final: 0.5746 (tmm) REVERT: B 408 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6501 (tm-30) REVERT: B 472 TYR cc_start: 0.7784 (t80) cc_final: 0.7541 (t80) REVERT: B 538 LYS cc_start: 0.8347 (mttm) cc_final: 0.8057 (mttt) REVERT: B 541 ILE cc_start: 0.8391 (mm) cc_final: 0.8133 (mt) REVERT: B 554 ASP cc_start: 0.6910 (t0) cc_final: 0.6344 (t0) REVERT: B 564 LYS cc_start: 0.5174 (OUTLIER) cc_final: 0.4682 (mmtt) REVERT: B 818 LYS cc_start: 0.8464 (tppt) cc_final: 0.7934 (mmmt) REVERT: C 28 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7064 (tp30) REVERT: C 117 ILE cc_start: 0.8252 (mp) cc_final: 0.7755 (tt) REVERT: C 120 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7549 (ttmt) REVERT: C 224 ASN cc_start: 0.8307 (t0) cc_final: 0.8046 (t0) REVERT: C 225 ILE cc_start: 0.7882 (mm) cc_final: 0.7569 (mm) REVERT: C 235 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7067 (pp) REVERT: C 249 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6317 (m-30) REVERT: C 254 GLU cc_start: 0.5684 (OUTLIER) cc_final: 0.5209 (tp30) REVERT: C 290 MET cc_start: 0.7668 (mmm) cc_final: 0.7154 (mmm) REVERT: D 83 GLU cc_start: 0.6007 (mm-30) cc_final: 0.4970 (mt-10) REVERT: D 120 LYS cc_start: 0.8313 (pttt) cc_final: 0.7783 (pmtt) REVERT: D 144 LYS cc_start: 0.8030 (tptt) cc_final: 0.7768 (tptt) REVERT: D 222 ASP cc_start: 0.7433 (t0) cc_final: 0.7083 (t0) REVERT: D 264 LYS cc_start: 0.8007 (tppt) cc_final: 0.7634 (ttmt) REVERT: D 283 LEU cc_start: 0.8555 (tp) cc_final: 0.8351 (tp) outliers start: 64 outliers final: 43 residues processed: 535 average time/residue: 0.1430 time to fit residues: 116.9901 Evaluate side-chains 551 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 496 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 155 GLU Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 PHE 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 678 PHE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 673 ILE 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 28 GLU 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 100 PHE 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 129 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 153 SER 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 D residue 134 TYR 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 241 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 66 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 225 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 chunk 232 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A 829 GLN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 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 = 0.3979 r_free = 0.3979 target = 0.155472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121101 restraints weight = 32642.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125141 restraints weight = 17303.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127877 restraints weight = 11359.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129751 restraints weight = 8592.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.130559 restraints weight = 7084.151| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21520 Z= 0.151 Angle : 0.585 9.423 29026 Z= 0.308 Chirality : 0.042 0.194 3082 Planarity : 0.004 0.062 3712 Dihedral : 4.422 40.840 2801 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.85 % Favored : 93.91 % Rotamer: Outliers : 2.94 % Allowed : 26.49 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2528 helix: 1.23 (0.14), residues: 1460 sheet: -1.59 (0.56), residues: 65 loop : -1.47 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 233 TYR 0.021 0.002 TYR A 649 PHE 0.041 0.001 PHE B 240 TRP 0.072 0.003 TRP D 143 HIS 0.005 0.001 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00350 (21520) covalent geometry : angle 0.58520 (29026) hydrogen bonds : bond 0.04041 ( 981) hydrogen bonds : angle 4.17557 ( 2832) *********************** 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 562 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 494 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7102 (tm-30) REVERT: A 42 LEU cc_start: 0.8681 (tp) cc_final: 0.8421 (tt) REVERT: A 45 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.6676 (m-80) REVERT: A 109 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 131 THR cc_start: 0.8369 (m) cc_final: 0.8056 (t) REVERT: A 176 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8353 (mtmm) REVERT: A 229 LEU cc_start: 0.8241 (tp) cc_final: 0.8015 (tt) REVERT: A 280 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: A 286 TYR cc_start: 0.7445 (m-80) cc_final: 0.7163 (m-10) REVERT: A 310 ASP cc_start: 0.7464 (t0) cc_final: 0.6986 (t0) REVERT: A 350 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8106 (mmtm) REVERT: A 376 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8237 (ttpp) REVERT: A 448 TRP cc_start: 0.7702 (m-10) cc_final: 0.7479 (m-10) REVERT: A 516 GLU cc_start: 0.8042 (tp30) cc_final: 0.7631 (tp30) REVERT: A 540 LYS cc_start: 0.8508 (tptm) cc_final: 0.8270 (tppt) REVERT: A 560 GLU cc_start: 0.7886 (tt0) cc_final: 0.7256 (tp30) REVERT: A 675 LYS cc_start: 0.8454 (mttt) cc_final: 0.7429 (ttmm) REVERT: A 681 GLN cc_start: 0.6974 (mt0) cc_final: 0.6425 (mm-40) REVERT: A 823 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7817 (mp) REVERT: A 877 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6777 (t80) REVERT: A 882 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: A 916 PHE cc_start: 0.8319 (m-80) cc_final: 0.7878 (m-80) REVERT: A 958 TRP cc_start: 0.8294 (m-10) cc_final: 0.7374 (m100) REVERT: A 965 LYS cc_start: 0.8553 (mmtm) cc_final: 0.8342 (tppt) REVERT: A 969 LYS cc_start: 0.8895 (tptm) cc_final: 0.8393 (tptp) REVERT: A 985 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8219 (mttm) REVERT: B 181 GLU cc_start: 0.7288 (pt0) cc_final: 0.7050 (mt-10) REVERT: B 203 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8251 (tt) REVERT: B 231 TRP cc_start: 0.7562 (t60) cc_final: 0.7081 (t60) REVERT: B 291 ASP cc_start: 0.7774 (m-30) cc_final: 0.7223 (m-30) REVERT: B 304 LYS cc_start: 0.8263 (mmtm) cc_final: 0.7966 (mmtm) REVERT: B 335 GLU cc_start: 0.7641 (mp0) cc_final: 0.7318 (mp0) REVERT: B 357 MET cc_start: 0.6915 (tmm) cc_final: 0.5812 (tmm) REVERT: B 408 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6618 (tm-30) REVERT: B 426 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: B 538 LYS cc_start: 0.8515 (mttm) cc_final: 0.8185 (mttt) REVERT: B 554 ASP cc_start: 0.6934 (t0) cc_final: 0.6376 (t0) REVERT: B 564 LYS cc_start: 0.5331 (OUTLIER) cc_final: 0.4789 (mmtt) REVERT: B 595 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7575 (mt) REVERT: B 818 LYS cc_start: 0.8477 (tppt) cc_final: 0.7840 (mmmt) REVERT: C 117 ILE cc_start: 0.8249 (mp) cc_final: 0.7777 (tt) REVERT: C 120 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7621 (ttmt) REVERT: C 224 ASN cc_start: 0.8345 (t0) cc_final: 0.8088 (t0) REVERT: C 233 ARG cc_start: 0.7737 (mmm-85) cc_final: 0.7515 (mmm160) REVERT: C 235 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7279 (pp) REVERT: C 249 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6477 (m-30) REVERT: C 254 GLU cc_start: 0.5728 (OUTLIER) cc_final: 0.5275 (tp30) REVERT: C 290 MET cc_start: 0.7644 (mmm) cc_final: 0.7120 (mmm) REVERT: D 83 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5106 (mt-10) REVERT: D 120 LYS cc_start: 0.8375 (pttt) cc_final: 0.7248 (pmtt) REVERT: D 144 LYS cc_start: 0.8049 (tptt) cc_final: 0.7778 (tptt) REVERT: D 222 ASP cc_start: 0.7513 (t0) cc_final: 0.7168 (t0) REVERT: D 227 MET cc_start: 0.5834 (OUTLIER) cc_final: 0.5500 (ppp) REVERT: D 264 LYS cc_start: 0.7945 (tppt) cc_final: 0.7583 (ttmt) outliers start: 68 outliers final: 47 residues processed: 531 average time/residue: 0.1506 time to fit residues: 121.9251 Evaluate side-chains 546 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 485 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 155 GLU Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 595 LEU 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 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 100 PHE 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 129 VAL Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 190 TYR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 254 GLU 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 182 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 112 optimal weight: 0.0070 chunk 72 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3979 r_free = 0.3979 target = 0.155701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120975 restraints weight = 32903.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125102 restraints weight = 17718.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127814 restraints weight = 11554.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129503 restraints weight = 8723.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.130864 restraints weight = 7290.850| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21520 Z= 0.146 Angle : 0.595 10.425 29026 Z= 0.311 Chirality : 0.041 0.181 3082 Planarity : 0.004 0.062 3712 Dihedral : 4.448 40.652 2801 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.74 % Favored : 94.07 % Rotamer: Outliers : 2.64 % Allowed : 27.05 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.17), residues: 2528 helix: 1.21 (0.14), residues: 1461 sheet: -1.65 (0.55), residues: 65 loop : -1.45 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 747 TYR 0.021 0.001 TYR B 472 PHE 0.036 0.001 PHE B 240 TRP 0.073 0.003 TRP D 143 HIS 0.005 0.001 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00339 (21520) covalent geometry : angle 0.59472 (29026) hydrogen bonds : bond 0.03921 ( 981) hydrogen bonds : angle 4.15304 ( 2832) ********************** 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 553 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 492 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7112 (tm-30) REVERT: A 42 LEU cc_start: 0.8689 (tp) cc_final: 0.8428 (tt) REVERT: A 45 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.6647 (m-80) REVERT: A 67 HIS cc_start: 0.8049 (t-90) cc_final: 0.7480 (t-170) REVERT: A 75 LYS cc_start: 0.8396 (tppt) cc_final: 0.7606 (ttmm) REVERT: A 109 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7622 (tp-100) REVERT: A 131 THR cc_start: 0.8340 (m) cc_final: 0.8023 (t) REVERT: A 176 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8343 (mtmm) REVERT: A 229 LEU cc_start: 0.8235 (tp) cc_final: 0.8002 (tt) REVERT: A 280 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6956 (m-80) REVERT: A 286 TYR cc_start: 0.7425 (m-80) cc_final: 0.7133 (m-10) REVERT: A 310 ASP cc_start: 0.7476 (t0) cc_final: 0.7039 (t0) REVERT: A 350 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8149 (mmtm) REVERT: A 376 LYS cc_start: 0.8526 (ttpt) cc_final: 0.8276 (ttpp) REVERT: A 448 TRP cc_start: 0.7697 (m-10) cc_final: 0.7470 (m-10) REVERT: A 516 GLU cc_start: 0.8039 (tp30) cc_final: 0.7613 (tp30) REVERT: A 540 LYS cc_start: 0.8512 (tptm) cc_final: 0.8271 (tppt) REVERT: A 560 GLU cc_start: 0.7890 (tt0) cc_final: 0.7257 (tp30) REVERT: A 675 LYS cc_start: 0.8450 (mttt) cc_final: 0.7432 (ttmm) REVERT: A 681 GLN cc_start: 0.6927 (mt0) cc_final: 0.6372 (mm-40) REVERT: A 823 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7821 (mp) REVERT: A 877 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6813 (t80) REVERT: A 882 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: A 916 PHE cc_start: 0.8324 (m-80) cc_final: 0.7889 (m-80) REVERT: A 958 TRP cc_start: 0.8340 (m-10) cc_final: 0.7452 (m100) REVERT: A 965 LYS cc_start: 0.8550 (mmtm) cc_final: 0.8343 (tppt) REVERT: A 969 LYS cc_start: 0.8920 (tptm) cc_final: 0.8576 (tptm) REVERT: A 985 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8202 (mttm) REVERT: B 181 GLU cc_start: 0.7287 (pt0) cc_final: 0.7046 (mt-10) REVERT: B 203 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8224 (tt) REVERT: B 231 TRP cc_start: 0.7483 (t60) cc_final: 0.7052 (t60) REVERT: B 291 ASP cc_start: 0.7762 (m-30) cc_final: 0.7147 (m-30) REVERT: B 304 LYS cc_start: 0.8252 (mmtm) cc_final: 0.7946 (mmtm) REVERT: B 335 GLU cc_start: 0.7659 (mp0) cc_final: 0.7290 (mp0) REVERT: B 357 MET cc_start: 0.6916 (tmm) cc_final: 0.5807 (tmm) REVERT: B 408 GLU cc_start: 0.6870 (tm-30) cc_final: 0.6626 (tm-30) REVERT: B 426 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: B 538 LYS cc_start: 0.8483 (mttm) cc_final: 0.8186 (mttt) REVERT: B 541 ILE cc_start: 0.8517 (mm) cc_final: 0.8217 (mt) REVERT: B 554 ASP cc_start: 0.6965 (t0) cc_final: 0.6408 (t0) REVERT: B 564 LYS cc_start: 0.5336 (OUTLIER) cc_final: 0.4766 (mmtt) REVERT: B 595 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7603 (mt) REVERT: B 646 PHE cc_start: 0.6048 (m-80) cc_final: 0.5653 (m-10) REVERT: B 818 LYS cc_start: 0.8471 (tppt) cc_final: 0.7841 (mmmt) REVERT: C 120 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7626 (ttmt) REVERT: C 224 ASN cc_start: 0.8367 (t0) cc_final: 0.8093 (t0) REVERT: C 233 ARG cc_start: 0.7695 (mmm-85) cc_final: 0.7495 (mmm160) REVERT: C 235 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7283 (pp) REVERT: C 248 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7676 (p) REVERT: C 249 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6489 (m-30) REVERT: C 254 GLU cc_start: 0.5729 (OUTLIER) cc_final: 0.5276 (tp30) REVERT: C 290 MET cc_start: 0.7645 (mmm) cc_final: 0.7080 (mmm) REVERT: D 66 TYR cc_start: 0.7726 (m-80) cc_final: 0.6522 (m-80) REVERT: D 83 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5084 (mt-10) REVERT: D 120 LYS cc_start: 0.8302 (pttt) cc_final: 0.7712 (pmtt) REVERT: D 144 LYS cc_start: 0.8028 (tptt) cc_final: 0.7761 (tptt) REVERT: D 150 SER cc_start: 0.8172 (m) cc_final: 0.7893 (m) REVERT: D 222 ASP cc_start: 0.7540 (t0) cc_final: 0.7176 (t0) REVERT: D 264 LYS cc_start: 0.7963 (tppt) cc_final: 0.7595 (ttmt) outliers start: 61 outliers final: 43 residues processed: 524 average time/residue: 0.1486 time to fit residues: 118.6732 Evaluate side-chains 542 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 485 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 155 GLU 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 432 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 823 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 974 LYS Chi-restraints excluded: chain A residue 987 ARG Chi-restraints excluded: chain B residue 134 TYR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 564 LYS Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 665 LYS Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain C residue 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 100 PHE 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 153 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 134 TYR Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 218 TYR Chi-restraints excluded: chain D residue 241 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 65 optimal weight: 0.4980 chunk 202 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 chunk 251 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 122 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3982 r_free = 0.3982 target = 0.155967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.121381 restraints weight = 32911.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125523 restraints weight = 17461.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.128239 restraints weight = 11441.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129944 restraints weight = 8672.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.130732 restraints weight = 7239.552| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21520 Z= 0.138 Angle : 0.592 10.140 29026 Z= 0.310 Chirality : 0.041 0.196 3082 Planarity : 0.003 0.060 3712 Dihedral : 4.415 40.467 2801 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.54 % Favored : 94.26 % Rotamer: Outliers : 2.77 % Allowed : 27.05 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.17), residues: 2528 helix: 1.25 (0.14), residues: 1458 sheet: -1.62 (0.55), residues: 65 loop : -1.41 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 747 TYR 0.020 0.001 TYR B 472 PHE 0.038 0.001 PHE A 778 TRP 0.070 0.003 TRP D 143 HIS 0.004 0.001 HIS D 67 Details of bonding type rmsd covalent geometry : bond 0.00320 (21520) covalent geometry : angle 0.59168 (29026) hydrogen bonds : bond 0.03820 ( 981) hydrogen bonds : angle 4.12603 ( 2832) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3698.31 seconds wall clock time: 64 minutes 36.26 seconds (3876.26 seconds total)