Starting phenix.real_space_refine on Wed Jan 22 18:43:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yl5_39382/01_2025/8yl5_39382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yl5_39382/01_2025/8yl5_39382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yl5_39382/01_2025/8yl5_39382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yl5_39382/01_2025/8yl5_39382.map" model { file = "/net/cci-nas-00/data/ceres_data/8yl5_39382/01_2025/8yl5_39382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yl5_39382/01_2025/8yl5_39382.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 134 5.16 5 C 22662 2.51 5 N 5658 2.21 5 O 6562 1.98 5 H 34366 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 69382 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 16370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 16370 Classifications: {'peptide': 992} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 972} Chain: "B" Number of atoms: 16459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 16459 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 977} Chain: "C" Number of atoms: 16370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 16370 Classifications: {'peptide': 992} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 972} Chain: "D" Number of atoms: 16459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 16459 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 977} Chain: "E" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1862 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "F" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1862 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Time building chain proxies: 23.14, per 1000 atoms: 0.33 Number of scatterers: 69382 At special positions: 0 Unit cell: (105.6, 135.36, 277.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 134 16.00 O 6562 8.00 N 5658 7.00 C 22662 6.00 H 34366 1.00 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: 13.17 Conformation dependent library (CDL) restraints added in 3.9 seconds 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8016 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 14 sheets defined 68.3% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.675A pdb=" N LEU A 22 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 39 removed outlier: 3.532A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 removed outlier: 4.196A pdb=" N SER A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 71 removed outlier: 3.828A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.967A pdb=" N TYR A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.601A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.748A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 209 Processing helix chain 'A' and resid 222 through 235 Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 290 removed outlier: 3.695A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 removed outlier: 4.304A pdb=" N ASN A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 318 through 321 removed outlier: 3.767A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.716A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 366 through 373 removed outlier: 3.606A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 392 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.796A pdb=" N HIS A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 447 through 462 Processing helix chain 'A' and resid 468 through 500 removed outlier: 3.647A pdb=" N GLY A 494 " --> pdb=" O THR A 490 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU A 497 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 547 removed outlier: 4.055A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 547 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 551 through 572 removed outlier: 3.520A pdb=" N ASN A 563 " --> pdb=" O PHE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 597 removed outlier: 3.657A pdb=" N LEU A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 599 No H-bonds generated for 'chain 'A' and resid 598 through 599' Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.766A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.647A pdb=" N HIS A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 634 removed outlier: 4.247A pdb=" N ASP A 632 " --> pdb=" O THR A 628 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 658 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 701 removed outlier: 4.514A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 4.301A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (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 743 Processing helix chain 'A' and resid 750 through 761 Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.749A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 831 through 840 removed outlier: 3.551A pdb=" N ILE A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 846 through 857 Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 878 through 903 Processing helix chain 'A' and resid 911 through 922 Processing helix chain 'A' and resid 927 through 934 removed outlier: 3.705A pdb=" N MET A 930 " --> pdb=" O ASN A 927 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 950 through 954 removed outlier: 3.651A pdb=" N LYS A 953 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 956 No H-bonds generated for 'chain 'A' and resid 955 through 956' Processing helix chain 'A' and resid 957 through 962 removed outlier: 4.044A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR A 962 " --> pdb=" O TRP A 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 962' Processing helix chain 'A' and resid 963 through 973 removed outlier: 3.504A pdb=" N GLY A 972 " --> pdb=" O GLY A 968 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 991 Processing helix chain 'A' and resid 994 through 1003 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 23 through 39 removed outlier: 3.858A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 removed outlier: 4.132A pdb=" N SER B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.958A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.743A pdb=" N TYR B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.670A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.601A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.742A pdb=" N VAL B 183 " --> pdb=" O GLY B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.510A pdb=" N TYR B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.910A pdb=" N ASN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 3.755A pdb=" N LYS B 264 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.515A pdb=" N ILE B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 275' Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.539A pdb=" N ARG B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 317 through 322 removed outlier: 3.739A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 334 removed outlier: 3.501A pdb=" N LEU B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 332 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 373 removed outlier: 3.708A pdb=" N ARG B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 466 removed outlier: 3.801A pdb=" N SER B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 500 removed outlier: 6.038A pdb=" N LEU B 497 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.795A pdb=" N LEU B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.146A pdb=" N ASP B 526 " --> pdb=" O ASN B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.370A pdb=" N PHE B 544 " --> pdb=" O ILE B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 removed outlier: 3.771A pdb=" N THR B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 563 removed outlier: 3.660A pdb=" N ASN B 563 " --> pdb=" O GLU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 569 removed outlier: 4.285A pdb=" N GLU B 568 " --> pdb=" O LYS B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 598 removed outlier: 3.564A pdb=" N VAL B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.998A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 604 " --> pdb=" O TRP B 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 600 through 604' Processing helix chain 'B' and resid 605 through 634 removed outlier: 3.529A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 669 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.744A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 711 Processing helix chain 'B' and resid 712 through 723 Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 762 removed outlier: 3.665A pdb=" N LEU B 761 " --> pdb=" O TRP B 757 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 762 " --> pdb=" O LEU B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 removed outlier: 3.502A pdb=" N ILE B 772 " --> pdb=" O PRO B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.615A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 812 " --> pdb=" O ILE B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 Processing helix chain 'B' and resid 831 through 840 removed outlier: 3.816A pdb=" N LYS B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 846 through 855 Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 878 through 903 Processing helix chain 'B' and resid 911 through 922 removed outlier: 3.758A pdb=" N THR B 915 " --> pdb=" O ASP B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 932 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.575A pdb=" N LYS B 953 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 961 Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 976 through 992 removed outlier: 3.828A pdb=" N VAL B 980 " --> pdb=" O MET B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.686A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 23 through 40 Processing helix chain 'C' and resid 48 through 54 removed outlier: 4.133A pdb=" N SER C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.784A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 96 Proline residue: C 88 - end of helix removed outlier: 3.533A pdb=" N GLY C 96 " --> pdb=" O TYR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.702A 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 186 through 192 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 222 through 236 removed outlier: 3.752A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 288 removed outlier: 4.482A pdb=" N ARG C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 297 Processing helix chain 'C' and resid 304 through 317 Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 355 through 366 removed outlier: 3.976A pdb=" N ARG C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 373 removed outlier: 3.834A pdb=" N ARG C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 392 removed outlier: 4.180A pdb=" N GLU C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.960A pdb=" N HIS C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 411 through 416' Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 447 through 461 removed outlier: 3.674A pdb=" N ASP C 453 " --> pdb=" O GLU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 494 Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 508 through 519 Processing helix chain 'C' and resid 527 through 531 Processing helix chain 'C' and resid 532 through 538 Processing helix chain 'C' and resid 539 through 545 removed outlier: 3.687A pdb=" N GLU C 543 " --> pdb=" O LYS C 540 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE C 544 " --> pdb=" O ILE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 550 removed outlier: 4.053A pdb=" N PHE C 550 " --> pdb=" O ASP C 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 547 through 550' Processing helix chain 'C' and resid 551 through 572 removed outlier: 3.690A pdb=" N THR C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C 560 " --> pdb=" O VAL C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 598 removed outlier: 3.567A pdb=" N LEU C 585 " --> pdb=" O ASP C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 604 removed outlier: 3.646A pdb=" N VAL C 603 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 637 removed outlier: 3.629A pdb=" N HIS C 609 " --> pdb=" O PHE C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 658 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 680 through 701 removed outlier: 4.038A pdb=" N ALA C 701 " --> pdb=" O LYS C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 723 removed outlier: 4.034A pdb=" N GLN C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER C 714 " --> pdb=" O THR C 710 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU C 715 " --> pdb=" O GLN C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 729 through 743 Processing helix chain 'C' and resid 750 through 762 Processing helix chain 'C' and resid 768 through 786 Processing helix chain 'C' and resid 800 through 812 removed outlier: 4.080A pdb=" N TYR C 804 " --> pdb=" O TYR C 800 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 805 " --> pdb=" O SER C 801 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 826 Processing helix chain 'C' and resid 831 through 841 removed outlier: 3.621A pdb=" N ILE C 835 " --> pdb=" O LYS C 831 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 841 " --> pdb=" O PHE C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 845 Processing helix chain 'C' and resid 846 through 857 Processing helix chain 'C' and resid 861 through 871 Processing helix chain 'C' and resid 878 through 903 Processing helix chain 'C' and resid 911 through 922 Processing helix chain 'C' and resid 927 through 933 Processing helix chain 'C' and resid 937 through 945 Processing helix chain 'C' and resid 950 through 955 removed outlier: 6.113A pdb=" N ILE C 955 " --> pdb=" O LYS C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 962 removed outlier: 4.156A pdb=" N LYS C 960 " --> pdb=" O PRO C 956 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 971 Processing helix chain 'C' and resid 976 through 991 Processing helix chain 'C' and resid 993 through 1003 removed outlier: 4.288A pdb=" N LEU C 997 " --> pdb=" O ASP C 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.832A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.683A pdb=" N PHE D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.570A 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 155 through 159 removed outlier: 3.505A pdb=" N VAL D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 192 removed outlier: 3.505A pdb=" N TYR D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 197 through 210 Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.867A pdb=" N ASN D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 265 Processing helix chain 'D' and resid 281 through 298 Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'D' and resid 318 through 322 removed outlier: 3.601A pdb=" N ALA D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 334 removed outlier: 3.796A pdb=" N HIS D 332 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 366 Processing helix chain 'D' and resid 366 through 373 removed outlier: 3.591A pdb=" N ARG D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 392 Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.820A pdb=" N HIS D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 427 Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 447 through 466 removed outlier: 3.684A pdb=" N ILE D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP D 464 " --> pdb=" O LEU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 500 removed outlier: 3.514A pdb=" N ARG D 478 " --> pdb=" O SER D 474 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU D 497 " --> pdb=" O ASN D 493 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU D 498 " --> pdb=" O GLY D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 519 removed outlier: 3.786A pdb=" N LEU D 512 " --> pdb=" O THR D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 529 removed outlier: 3.898A pdb=" N ASP D 526 " --> pdb=" O ASN D 523 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE D 528 " --> pdb=" O ASP D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 539 Processing helix chain 'D' and resid 540 through 546 removed outlier: 4.507A pdb=" N PHE D 544 " --> pdb=" O ILE D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 557 Processing helix chain 'D' and resid 558 through 563 Processing helix chain 'D' and resid 564 through 569 Processing helix chain 'D' and resid 579 through 598 removed outlier: 3.615A pdb=" N ASN D 598 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 removed outlier: 3.618A pdb=" N HIS D 609 " --> pdb=" O PHE D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 659 removed outlier: 3.607A pdb=" N PHE D 659 " --> pdb=" O ILE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 660 through 671 Processing helix chain 'D' and resid 672 through 676 Processing helix chain 'D' and resid 680 through 701 Processing helix chain 'D' and resid 705 through 723 removed outlier: 4.149A pdb=" N SER D 714 " --> pdb=" O THR D 710 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU D 715 " --> pdb=" O GLN D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 729 through 744 removed outlier: 3.862A pdb=" N PHE D 744 " --> pdb=" O LEU D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 763 Processing helix chain 'D' and resid 768 through 786 Processing helix chain 'D' and resid 800 through 812 removed outlier: 3.750A pdb=" N TYR D 804 " --> pdb=" O TYR D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 826 Processing helix chain 'D' and resid 831 through 841 Processing helix chain 'D' and resid 842 through 845 Processing helix chain 'D' and resid 846 through 855 Processing helix chain 'D' and resid 861 through 871 Processing helix chain 'D' and resid 878 through 903 Processing helix chain 'D' and resid 911 through 922 removed outlier: 3.508A pdb=" N THR D 915 " --> pdb=" O ASP D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 928 through 932 Processing helix chain 'D' and resid 937 through 945 Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 955 through 960 removed outlier: 4.314A pdb=" N LEU D 959 " --> pdb=" O ILE D 955 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS D 960 " --> pdb=" O PRO D 956 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 955 through 960' Processing helix chain 'D' and resid 963 through 973 Processing helix chain 'D' and resid 973 through 991 removed outlier: 4.391A pdb=" N HIS D 978 " --> pdb=" O LYS D 974 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N HIS D 979 " --> pdb=" O HIS D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1003 removed outlier: 3.540A pdb=" N LEU D 997 " --> pdb=" O ASP D 993 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 13 removed outlier: 4.154A pdb=" N ASP E 13 " --> pdb=" O ALA E 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 10 through 13' Processing helix chain 'E' and resid 93 through 106 removed outlier: 4.133A pdb=" N GLU E 97 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 13 removed outlier: 3.563A pdb=" N HIS F 12 " --> pdb=" O GLY F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 106 removed outlier: 4.140A pdb=" N ILE F 98 " --> pdb=" O ASP F 94 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.201A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 removed outlier: 6.438A pdb=" N PHE E 23 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.373A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU B 42 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE B 213 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE B 246 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N PHE B 215 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 6.436A 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: 6.353A pdb=" N SER C 150 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LYS C 169 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 152 " --> pdb=" O LYS C 169 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 129 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE C 44 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 338 through 340 removed outlier: 3.563A pdb=" N VAL C 346 " --> pdb=" O CYS C 395 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 573 through 575 removed outlier: 6.717A pdb=" N PHE F 23 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.328A 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: 6.431A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU D 42 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE D 130 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL D 43 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE D 216 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE D 45 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE D 213 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE D 246 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE D 215 " --> pdb=" O ILE D 246 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AB2, first strand: chain 'E' and resid 71 through 72 removed outlier: 5.302A pdb=" N GLU E 38 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU E 33 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ASN E 40 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE E 31 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE E 44 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N VAL E 27 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS E 85 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL E 32 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE E 83 " --> pdb=" O VAL E 32 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 71 through 72 removed outlier: 4.103A pdb=" N GLU E 115 " --> pdb=" O PHE E 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 71 through 73 removed outlier: 4.703A pdb=" N ILE F 66 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLU F 38 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU F 33 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ASN F 40 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE F 31 " --> pdb=" O ASN F 40 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE F 44 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N VAL F 27 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL F 32 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE F 83 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 71 through 73 removed outlier: 4.703A pdb=" N ILE F 66 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU F 115 " --> pdb=" O PHE F 44 " (cutoff:3.500A) 1862 hydrogen bonds defined for protein. 5328 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: 24.09 Time building geometry restraints manager: 16.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 34320 1.03 - 1.23: 433 1.23 - 1.43: 15338 1.43 - 1.63: 19885 1.63 - 1.82: 222 Bond restraints: 70198 Sorted by residual: bond pdb=" N ILE C 130 " pdb=" CA ILE C 130 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.82e+00 bond pdb=" N GLY D 679 " pdb=" CA GLY D 679 " ideal model delta sigma weight residual 1.444 1.474 -0.030 9.60e-03 1.09e+04 9.66e+00 bond pdb=" N ILE B 312 " pdb=" CA ILE B 312 " ideal model delta sigma weight residual 1.461 1.497 -0.037 1.19e-02 7.06e+03 9.48e+00 bond pdb=" N VAL B 346 " pdb=" CA VAL B 346 " ideal model delta sigma weight residual 1.455 1.496 -0.040 1.32e-02 5.74e+03 9.29e+00 bond pdb=" N LEU B 322 " pdb=" CA LEU B 322 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.21e-02 6.83e+03 9.24e+00 ... (remaining 70193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 125718 2.46 - 4.91: 720 4.91 - 7.37: 39 7.37 - 9.82: 13 9.82 - 12.28: 12 Bond angle restraints: 126502 Sorted by residual: angle pdb=" CA LYS D 831 " pdb=" C LYS D 831 " pdb=" O LYS D 831 " ideal model delta sigma weight residual 122.63 116.15 6.48 1.29e+00 6.01e-01 2.52e+01 angle pdb=" CA ASP C 135 " pdb=" C ASP C 135 " pdb=" O ASP C 135 " ideal model delta sigma weight residual 121.88 116.92 4.96 1.13e+00 7.83e-01 1.92e+01 angle pdb=" N TYR D 912 " pdb=" CA TYR D 912 " pdb=" C TYR D 912 " ideal model delta sigma weight residual 111.82 106.83 4.99 1.16e+00 7.43e-01 1.85e+01 angle pdb=" N LEU C 841 " pdb=" CA LEU C 841 " pdb=" C LEU C 841 " ideal model delta sigma weight residual 112.59 107.42 5.17 1.22e+00 6.72e-01 1.80e+01 angle pdb=" N LEU A 445 " pdb=" CA LEU A 445 " pdb=" C LEU A 445 " ideal model delta sigma weight residual 114.04 108.90 5.14 1.24e+00 6.50e-01 1.72e+01 ... (remaining 126497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 29038 17.92 - 35.84: 2994 35.84 - 53.76: 765 53.76 - 71.67: 172 71.67 - 89.59: 29 Dihedral angle restraints: 32998 sinusoidal: 17416 harmonic: 15582 Sorted by residual: dihedral pdb=" CA LEU A 53 " pdb=" C LEU A 53 " pdb=" N SER A 54 " pdb=" CA SER A 54 " ideal model delta harmonic sigma weight residual 180.00 159.08 20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LYS A 234 " pdb=" C LYS A 234 " pdb=" N LEU A 235 " pdb=" CA LEU A 235 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA LEU C 53 " pdb=" C LEU C 53 " pdb=" N SER C 54 " pdb=" CA SER C 54 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 32995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4189 0.048 - 0.096: 706 0.096 - 0.144: 204 0.144 - 0.192: 25 0.192 - 0.240: 2 Chirality restraints: 5126 Sorted by residual: chirality pdb=" CA ILE C 130 " pdb=" N ILE C 130 " pdb=" C ILE C 130 " pdb=" CB ILE C 130 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE B 325 " pdb=" N ILE B 325 " pdb=" C ILE B 325 " pdb=" CB ILE B 325 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA VAL D 470 " pdb=" N VAL D 470 " pdb=" C VAL D 470 " pdb=" CB VAL D 470 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 5123 not shown) Planarity restraints: 10282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 669 " -0.371 9.50e-02 1.11e+02 3.21e-01 1.99e+03 pdb=" NE ARG B 669 " -0.204 2.00e-02 2.50e+03 pdb=" CZ ARG B 669 " -0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG B 669 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 669 " 0.048 2.00e-02 2.50e+03 pdb="HH11 ARG B 669 " 0.631 2.00e-02 2.50e+03 pdb="HH12 ARG B 669 " -0.576 2.00e-02 2.50e+03 pdb="HH21 ARG B 669 " 0.107 2.00e-02 2.50e+03 pdb="HH22 ARG B 669 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 175 " -0.143 9.50e-02 1.11e+02 2.10e-01 9.40e+02 pdb=" NE ARG A 175 " -0.125 2.00e-02 2.50e+03 pdb=" CZ ARG A 175 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG A 175 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG A 175 " 0.049 2.00e-02 2.50e+03 pdb="HH11 ARG A 175 " 0.395 2.00e-02 2.50e+03 pdb="HH12 ARG A 175 " -0.409 2.00e-02 2.50e+03 pdb="HH21 ARG A 175 " -0.025 2.00e-02 2.50e+03 pdb="HH22 ARG A 175 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 145 " 0.130 9.50e-02 1.11e+02 1.89e-01 7.60e+02 pdb=" NE ARG C 145 " 0.046 2.00e-02 2.50e+03 pdb=" CZ ARG C 145 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 145 " 0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG C 145 " -0.047 2.00e-02 2.50e+03 pdb="HH11 ARG C 145 " -0.289 2.00e-02 2.50e+03 pdb="HH12 ARG C 145 " 0.356 2.00e-02 2.50e+03 pdb="HH21 ARG C 145 " 0.140 2.00e-02 2.50e+03 pdb="HH22 ARG C 145 " -0.259 2.00e-02 2.50e+03 ... (remaining 10279 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 4072 2.20 - 2.80: 141484 2.80 - 3.40: 188961 3.40 - 4.00: 240457 4.00 - 4.60: 373904 Nonbonded interactions: 948878 Sorted by model distance: nonbonded pdb=" OE1 GLU A 449 " pdb=" H GLU A 449 " model vdw 1.599 2.450 nonbonded pdb=" OD1 ASN C 523 " pdb=" H ASP C 526 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLU B 731 " pdb=" H GLU B 731 " model vdw 1.614 2.450 nonbonded pdb=" OE1 GLU A 947 " pdb=" H GLU A 947 " model vdw 1.623 2.450 nonbonded pdb=" OE1 GLU A 731 " pdb=" H GLU A 731 " model vdw 1.637 2.450 ... (remaining 948873 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 1005) selection = chain 'C' selection = (chain 'D' and resid 14 through 1005) } ncs_group { reference = chain 'E' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.870 Extract box with map and model: 2.110 Check model and map are aligned: 0.500 Set scattering table: 0.690 Process input model: 105.530 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.004 0.049 35832 Z= 0.235 Angle : 0.629 11.150 48274 Z= 0.377 Chirality : 0.041 0.240 5126 Planarity : 0.003 0.048 6162 Dihedral : 16.541 89.593 13340 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.41 % Allowed : 18.43 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.13), residues: 4196 helix: 1.31 (0.11), residues: 2500 sheet: -2.06 (0.31), residues: 232 loop : -0.72 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 143 HIS 0.014 0.001 HIS B 852 PHE 0.018 0.001 PHE A 440 TYR 0.018 0.001 TYR B 888 ARG 0.005 0.000 ARG C 760 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 436 time to evaluate : 4.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 396 MET cc_start: 0.7517 (mmm) cc_final: 0.7181 (mmm) REVERT: C 101 ASP cc_start: 0.7546 (t0) cc_final: 0.7266 (t0) REVERT: C 407 ILE cc_start: 0.7295 (tp) cc_final: 0.7056 (tp) REVERT: D 304 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7501 (mmtt) REVERT: D 616 MET cc_start: 0.9040 (mmt) cc_final: 0.8769 (mmt) outliers start: 16 outliers final: 10 residues processed: 446 average time/residue: 0.9572 time to fit residues: 667.0057 Evaluate side-chains 429 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 419 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 913 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 352 optimal weight: 1.9990 chunk 316 optimal weight: 0.3980 chunk 175 optimal weight: 1.9990 chunk 108 optimal weight: 0.0770 chunk 213 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 327 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 379 optimal weight: 20.0000 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 ASN C 202 ASN C 598 ASN D 867 ASN F 88 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.188470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.124433 restraints weight = 155432.095| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.60 r_work: 0.3346 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35832 Z= 0.175 Angle : 0.489 6.741 48274 Z= 0.267 Chirality : 0.037 0.155 5126 Planarity : 0.003 0.050 6162 Dihedral : 4.481 58.632 4653 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.14 % Allowed : 17.32 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.13), residues: 4196 helix: 1.46 (0.11), residues: 2526 sheet: -2.07 (0.31), residues: 230 loop : -0.74 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 143 HIS 0.005 0.001 HIS E 88 PHE 0.012 0.001 PHE C 942 TYR 0.016 0.001 TYR D 472 ARG 0.005 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 439 time to evaluate : 4.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 TYR cc_start: 0.7465 (m-80) cc_final: 0.7170 (m-80) REVERT: A 680 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6386 (mp0) REVERT: A 921 PHE cc_start: 0.8669 (t80) cc_final: 0.8433 (t80) REVERT: B 396 MET cc_start: 0.7183 (mmm) cc_final: 0.6592 (mmm) REVERT: B 624 GLU cc_start: 0.8253 (tm-30) cc_final: 0.8007 (tm-30) REVERT: C 35 GLU cc_start: 0.8525 (tp30) cc_final: 0.8180 (tp30) REVERT: C 291 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.6044 (m-30) REVERT: C 866 MET cc_start: 0.7680 (mmp) cc_final: 0.7437 (mmp) REVERT: D 343 ASN cc_start: 0.8407 (p0) cc_final: 0.8102 (p0) REVERT: D 616 MET cc_start: 0.9218 (mmt) cc_final: 0.8820 (mmt) REVERT: D 913 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.4861 (pmm) REVERT: D 940 TYR cc_start: 0.6267 (t80) cc_final: 0.6059 (t80) REVERT: E 94 ASP cc_start: 0.5069 (OUTLIER) cc_final: 0.4768 (t0) REVERT: E 97 GLU cc_start: 0.7468 (pp20) cc_final: 0.6926 (pp20) REVERT: F 25 TRP cc_start: 0.8108 (t60) cc_final: 0.7723 (t60) REVERT: F 44 PHE cc_start: 0.2785 (OUTLIER) cc_final: 0.2277 (m-10) outliers start: 44 outliers final: 30 residues processed: 472 average time/residue: 0.9640 time to fit residues: 723.0741 Evaluate side-chains 453 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 419 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 1001 MET Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 883 GLU Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 913 MET Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 116 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 145 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 224 optimal weight: 0.0770 chunk 84 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 381 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 308 optimal weight: 0.9980 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 428 GLN D 782 GLN D 867 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.187525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126037 restraints weight = 155827.746| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.13 r_work: 0.3284 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 35832 Z= 0.206 Angle : 0.474 6.728 48274 Z= 0.259 Chirality : 0.037 0.145 5126 Planarity : 0.003 0.053 6162 Dihedral : 4.413 58.650 4650 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.06 % Allowed : 17.63 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.13), residues: 4196 helix: 1.47 (0.11), residues: 2538 sheet: -2.17 (0.30), residues: 234 loop : -0.83 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 143 HIS 0.005 0.001 HIS E 88 PHE 0.015 0.001 PHE C 712 TYR 0.017 0.001 TYR A 471 ARG 0.005 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 433 time to evaluate : 4.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 396 MET cc_start: 0.7234 (mmm) cc_final: 0.6904 (mmm) REVERT: B 624 GLU cc_start: 0.8267 (tm-30) cc_final: 0.8018 (tm-30) REVERT: C 35 GLU cc_start: 0.8491 (tp30) cc_final: 0.8194 (tp30) REVERT: C 291 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.5792 (m-30) REVERT: C 866 MET cc_start: 0.7565 (mmp) cc_final: 0.7258 (mmp) REVERT: D 913 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.4931 (pmm) REVERT: E 97 GLU cc_start: 0.7361 (pp20) cc_final: 0.7082 (pp20) REVERT: F 44 PHE cc_start: 0.2901 (OUTLIER) cc_final: 0.2390 (m-10) REVERT: F 65 ASP cc_start: 0.8123 (t0) cc_final: 0.7906 (t0) REVERT: F 119 LEU cc_start: 0.7336 (tp) cc_final: 0.7118 (tp) outliers start: 41 outliers final: 33 residues processed: 468 average time/residue: 0.9554 time to fit residues: 711.8282 Evaluate side-chains 450 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 414 time to evaluate : 4.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 782 GLN Chi-restraints excluded: chain D residue 883 GLU Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 913 MET Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 116 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 239 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 333 optimal weight: 6.9990 chunk 392 optimal weight: 9.9990 chunk 398 optimal weight: 8.9990 chunk 405 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 327 optimal weight: 0.6980 chunk 395 optimal weight: 2.9990 chunk 345 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 852 HIS ** C 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 867 ASN F 88 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.184729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123341 restraints weight = 155526.261| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.81 r_work: 0.3278 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 35832 Z= 0.343 Angle : 0.527 7.662 48274 Z= 0.292 Chirality : 0.039 0.168 5126 Planarity : 0.003 0.055 6162 Dihedral : 4.524 56.722 4646 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.58 % Allowed : 18.30 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.13), residues: 4196 helix: 1.19 (0.10), residues: 2554 sheet: -2.28 (0.30), residues: 234 loop : -1.03 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 60 HIS 0.007 0.001 HIS B 852 PHE 0.022 0.002 PHE C 100 TYR 0.023 0.002 TYR A 471 ARG 0.004 0.000 ARG F 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 430 time to evaluate : 4.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 680 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6504 (mp0) REVERT: B 396 MET cc_start: 0.7386 (mmm) cc_final: 0.7063 (mmm) REVERT: B 624 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8278 (tm-30) REVERT: C 35 GLU cc_start: 0.8616 (tp30) cc_final: 0.8308 (tp30) REVERT: C 290 MET cc_start: 0.8337 (mpp) cc_final: 0.8049 (mpp) REVERT: C 291 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.6741 (t0) REVERT: C 866 MET cc_start: 0.7682 (mmp) cc_final: 0.7297 (mmp) REVERT: D 306 ASP cc_start: 0.5458 (p0) cc_final: 0.5213 (p0) REVERT: D 335 GLU cc_start: 0.8000 (mp0) cc_final: 0.7674 (mp0) REVERT: D 343 ASN cc_start: 0.8553 (p0) cc_final: 0.8059 (p0) REVERT: E 94 ASP cc_start: 0.5302 (OUTLIER) cc_final: 0.5007 (t0) REVERT: E 97 GLU cc_start: 0.7478 (pp20) cc_final: 0.6858 (pp20) REVERT: F 44 PHE cc_start: 0.2916 (OUTLIER) cc_final: 0.2391 (m-10) REVERT: F 48 PHE cc_start: 0.6954 (t80) cc_final: 0.6659 (t80) REVERT: F 65 ASP cc_start: 0.8068 (t0) cc_final: 0.7726 (t0) REVERT: F 119 LEU cc_start: 0.7444 (tp) cc_final: 0.7235 (tp) outliers start: 61 outliers final: 42 residues processed: 478 average time/residue: 0.9846 time to fit residues: 754.3856 Evaluate side-chains 457 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 412 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 883 GLU Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 913 MET Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 116 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 387 optimal weight: 10.0000 chunk 263 optimal weight: 3.9990 chunk 130 optimal weight: 0.4980 chunk 332 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 348 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 386 optimal weight: 9.9990 chunk 357 optimal weight: 1.9990 chunk 279 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 852 HIS ** C 979 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.185887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123872 restraints weight = 155718.643| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.76 r_work: 0.3295 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35832 Z= 0.216 Angle : 0.483 7.365 48274 Z= 0.265 Chirality : 0.037 0.149 5126 Planarity : 0.003 0.054 6162 Dihedral : 4.389 55.679 4643 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.58 % Allowed : 18.59 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.13), residues: 4196 helix: 1.34 (0.10), residues: 2564 sheet: -2.23 (0.30), residues: 234 loop : -0.97 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 60 HIS 0.004 0.001 HIS E 88 PHE 0.020 0.001 PHE A 921 TYR 0.016 0.001 TYR A 471 ARG 0.005 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 423 time to evaluate : 4.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 396 MET cc_start: 0.7391 (mmm) cc_final: 0.7110 (mmm) REVERT: B 624 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8086 (tm-30) REVERT: C 35 GLU cc_start: 0.8480 (tp30) cc_final: 0.8175 (tp30) REVERT: C 291 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.6388 (t0) REVERT: C 866 MET cc_start: 0.7676 (mmp) cc_final: 0.7288 (mmp) REVERT: D 335 GLU cc_start: 0.7860 (mp0) cc_final: 0.7542 (mp0) REVERT: D 343 ASN cc_start: 0.8350 (p0) cc_final: 0.8027 (p0) REVERT: E 33 LEU cc_start: 0.8693 (tp) cc_final: 0.8486 (tp) REVERT: E 120 ASP cc_start: 0.7785 (t0) cc_final: 0.7515 (t0) REVERT: F 44 PHE cc_start: 0.2736 (OUTLIER) cc_final: 0.2271 (m-10) REVERT: F 65 ASP cc_start: 0.8131 (t0) cc_final: 0.7776 (t0) REVERT: F 119 LEU cc_start: 0.7310 (tp) cc_final: 0.7099 (tp) outliers start: 61 outliers final: 46 residues processed: 472 average time/residue: 0.9372 time to fit residues: 702.9014 Evaluate side-chains 451 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 403 time to evaluate : 4.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 521 ASN Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain C residue 711 GLN Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 883 GLU Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 913 MET Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 194 optimal weight: 5.9990 chunk 402 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 281 optimal weight: 9.9990 chunk 269 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 563 ASN ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.184277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122198 restraints weight = 155306.448| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.74 r_work: 0.3249 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35832 Z= 0.321 Angle : 0.519 8.127 48274 Z= 0.285 Chirality : 0.038 0.152 5126 Planarity : 0.003 0.054 6162 Dihedral : 4.475 55.552 4643 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.04 % Allowed : 18.33 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.13), residues: 4196 helix: 1.20 (0.10), residues: 2556 sheet: -2.31 (0.30), residues: 234 loop : -1.08 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 60 HIS 0.009 0.001 HIS B 852 PHE 0.021 0.001 PHE C 100 TYR 0.022 0.002 TYR A 471 ARG 0.006 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 414 time to evaluate : 4.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 962 TYR cc_start: 0.7915 (m-10) cc_final: 0.7606 (m-10) REVERT: B 396 MET cc_start: 0.7445 (mmm) cc_final: 0.7133 (mmm) REVERT: B 624 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8254 (tm-30) REVERT: C 35 GLU cc_start: 0.8617 (tp30) cc_final: 0.8313 (tp30) REVERT: C 289 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8019 (m) REVERT: C 291 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.6157 (m-30) REVERT: C 866 MET cc_start: 0.7762 (mmp) cc_final: 0.7366 (mmp) REVERT: D 143 TRP cc_start: 0.7556 (t-100) cc_final: 0.7294 (t60) REVERT: D 335 GLU cc_start: 0.8024 (mp0) cc_final: 0.7654 (mp0) REVERT: D 343 ASN cc_start: 0.8473 (p0) cc_final: 0.8146 (p0) REVERT: E 33 LEU cc_start: 0.8843 (tp) cc_final: 0.8633 (tp) REVERT: E 120 ASP cc_start: 0.8105 (t0) cc_final: 0.7699 (t0) REVERT: F 44 PHE cc_start: 0.2834 (OUTLIER) cc_final: 0.2325 (m-10) REVERT: F 65 ASP cc_start: 0.8028 (t0) cc_final: 0.7681 (t0) REVERT: F 119 LEU cc_start: 0.7403 (tp) cc_final: 0.7192 (tp) outliers start: 79 outliers final: 56 residues processed: 479 average time/residue: 0.9328 time to fit residues: 712.5416 Evaluate side-chains 466 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 407 time to evaluate : 4.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 669 ARG Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 526 ASP Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 883 GLU Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 913 MET Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 116 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 140 optimal weight: 0.6980 chunk 301 optimal weight: 0.6980 chunk 253 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 313 optimal weight: 0.6980 chunk 241 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 ASN B 786 HIS B 852 HIS ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.186233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123737 restraints weight = 154785.902| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.74 r_work: 0.3312 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35832 Z= 0.173 Angle : 0.469 8.457 48274 Z= 0.254 Chirality : 0.036 0.145 5126 Planarity : 0.003 0.053 6162 Dihedral : 4.300 55.741 4641 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.42 % Allowed : 18.85 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.13), residues: 4196 helix: 1.49 (0.11), residues: 2562 sheet: -2.23 (0.30), residues: 234 loop : -0.96 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 25 HIS 0.004 0.001 HIS B 786 PHE 0.015 0.001 PHE A 921 TYR 0.015 0.001 TYR C 912 ARG 0.006 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 422 time to evaluate : 4.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 962 TYR cc_start: 0.7996 (m-10) cc_final: 0.7693 (m-10) REVERT: B 396 MET cc_start: 0.7390 (mmm) cc_final: 0.6862 (mmm) REVERT: B 624 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8167 (tm-30) REVERT: C 35 GLU cc_start: 0.8590 (tp30) cc_final: 0.8320 (tp30) REVERT: C 291 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.6575 (t0) REVERT: C 294 ILE cc_start: 0.7716 (mt) cc_final: 0.7513 (mt) REVERT: C 866 MET cc_start: 0.7730 (mmp) cc_final: 0.7358 (mmp) REVERT: D 335 GLU cc_start: 0.7997 (mp0) cc_final: 0.7593 (mp0) REVERT: D 343 ASN cc_start: 0.8433 (p0) cc_final: 0.8048 (p0) REVERT: E 33 LEU cc_start: 0.8623 (tp) cc_final: 0.8398 (tp) REVERT: E 120 ASP cc_start: 0.8113 (t0) cc_final: 0.7710 (t0) REVERT: F 44 PHE cc_start: 0.3152 (OUTLIER) cc_final: 0.2593 (m-10) REVERT: F 65 ASP cc_start: 0.8139 (t0) cc_final: 0.7804 (t0) REVERT: F 119 LEU cc_start: 0.7315 (tp) cc_final: 0.7102 (tp) outliers start: 55 outliers final: 51 residues processed: 464 average time/residue: 0.9207 time to fit residues: 684.2975 Evaluate side-chains 462 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 409 time to evaluate : 4.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 810 HIS Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 852 HIS Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 883 GLU Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 913 MET Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 151 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 388 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 402 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 chunk 387 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 852 HIS ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.184719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124252 restraints weight = 155068.076| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.63 r_work: 0.3258 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35832 Z= 0.262 Angle : 0.497 8.497 48274 Z= 0.271 Chirality : 0.037 0.191 5126 Planarity : 0.003 0.052 6162 Dihedral : 4.334 55.707 4641 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.71 % Allowed : 18.80 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.13), residues: 4196 helix: 1.44 (0.11), residues: 2548 sheet: -2.26 (0.30), residues: 234 loop : -1.01 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 143 HIS 0.011 0.001 HIS B 852 PHE 0.017 0.001 PHE C 100 TYR 0.019 0.001 TYR A 471 ARG 0.005 0.000 ARG B 747 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 422 time to evaluate : 4.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8212 (mmm) cc_final: 0.8005 (mmm) REVERT: A 449 GLU cc_start: 0.7531 (mp0) cc_final: 0.7250 (mp0) REVERT: A 507 PHE cc_start: 0.7664 (m-80) cc_final: 0.7392 (m-80) REVERT: A 962 TYR cc_start: 0.7914 (m-10) cc_final: 0.7620 (m-10) REVERT: B 24 ASN cc_start: 0.6756 (t0) cc_final: 0.6434 (t0) REVERT: B 396 MET cc_start: 0.7517 (mmm) cc_final: 0.7215 (mmm) REVERT: B 624 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8075 (tm-30) REVERT: C 35 GLU cc_start: 0.8504 (tp30) cc_final: 0.8211 (tp30) REVERT: C 289 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7834 (m) REVERT: C 291 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.5785 (m-30) REVERT: C 866 MET cc_start: 0.7789 (mmp) cc_final: 0.7422 (mmp) REVERT: D 335 GLU cc_start: 0.7964 (mp0) cc_final: 0.7577 (mp0) REVERT: D 343 ASN cc_start: 0.8467 (p0) cc_final: 0.8058 (p0) REVERT: D 976 MET cc_start: 0.7603 (mtt) cc_final: 0.6963 (mtt) REVERT: E 33 LEU cc_start: 0.8662 (tp) cc_final: 0.8436 (tp) REVERT: E 97 GLU cc_start: 0.7788 (pp20) cc_final: 0.7503 (pp20) REVERT: E 120 ASP cc_start: 0.8108 (t0) cc_final: 0.7696 (t0) REVERT: F 44 PHE cc_start: 0.2958 (OUTLIER) cc_final: 0.2513 (m-10) REVERT: F 65 ASP cc_start: 0.8043 (t0) cc_final: 0.7710 (t0) REVERT: F 119 LEU cc_start: 0.7450 (tp) cc_final: 0.7244 (tp) outliers start: 66 outliers final: 56 residues processed: 471 average time/residue: 0.9782 time to fit residues: 737.5106 Evaluate side-chains 469 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 410 time to evaluate : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 810 HIS Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 883 GLU Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 913 MET Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 116 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 113 optimal weight: 1.9990 chunk 397 optimal weight: 0.9980 chunk 305 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 317 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 345 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 283 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.185009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122125 restraints weight = 155356.248| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.87 r_work: 0.3264 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35832 Z= 0.236 Angle : 0.490 9.125 48274 Z= 0.266 Chirality : 0.037 0.154 5126 Planarity : 0.003 0.052 6162 Dihedral : 4.319 55.729 4641 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.58 % Allowed : 18.98 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 4196 helix: 1.47 (0.11), residues: 2548 sheet: -2.28 (0.30), residues: 234 loop : -1.02 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 143 HIS 0.009 0.001 HIS B 852 PHE 0.016 0.001 PHE C 100 TYR 0.027 0.001 TYR D 888 ARG 0.005 0.000 ARG F 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 417 time to evaluate : 4.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8251 (mmm) cc_final: 0.8006 (mmm) REVERT: A 449 GLU cc_start: 0.7557 (mp0) cc_final: 0.7251 (mp0) REVERT: A 507 PHE cc_start: 0.7677 (m-80) cc_final: 0.7405 (m-80) REVERT: A 962 TYR cc_start: 0.7970 (m-10) cc_final: 0.7685 (m-10) REVERT: B 24 ASN cc_start: 0.6695 (t0) cc_final: 0.6384 (t0) REVERT: B 396 MET cc_start: 0.7452 (mmm) cc_final: 0.6921 (mmm) REVERT: B 624 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8044 (tm-30) REVERT: C 35 GLU cc_start: 0.8501 (tp30) cc_final: 0.8207 (tp30) REVERT: C 289 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7774 (m) REVERT: C 291 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.6625 (t0) REVERT: C 866 MET cc_start: 0.7788 (mmp) cc_final: 0.7419 (mmp) REVERT: D 335 GLU cc_start: 0.7970 (mp0) cc_final: 0.7580 (mp0) REVERT: D 343 ASN cc_start: 0.8491 (p0) cc_final: 0.8091 (p0) REVERT: D 976 MET cc_start: 0.7674 (mtt) cc_final: 0.7013 (mtt) REVERT: E 33 LEU cc_start: 0.8645 (tp) cc_final: 0.8412 (tp) REVERT: E 97 GLU cc_start: 0.7703 (pp20) cc_final: 0.7399 (pp20) REVERT: E 120 ASP cc_start: 0.8158 (t0) cc_final: 0.7923 (t0) REVERT: F 44 PHE cc_start: 0.3038 (OUTLIER) cc_final: 0.2516 (m-10) REVERT: F 65 ASP cc_start: 0.8118 (t0) cc_final: 0.7811 (t0) REVERT: F 119 LEU cc_start: 0.7429 (tp) cc_final: 0.7222 (tp) outliers start: 61 outliers final: 56 residues processed: 464 average time/residue: 0.9285 time to fit residues: 685.9258 Evaluate side-chains 467 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 408 time to evaluate : 4.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 810 HIS Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 669 ARG Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 671 CYS Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 883 GLU Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 913 MET Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 156 optimal weight: 0.9980 chunk 400 optimal weight: 2.9990 chunk 162 optimal weight: 0.3980 chunk 306 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 334 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 273 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 786 HIS ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.185683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123680 restraints weight = 154927.153| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.72 r_work: 0.3301 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35832 Z= 0.174 Angle : 0.478 9.414 48274 Z= 0.256 Chirality : 0.037 0.154 5126 Planarity : 0.003 0.064 6162 Dihedral : 4.253 55.803 4641 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.53 % Allowed : 19.16 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.13), residues: 4196 helix: 1.63 (0.11), residues: 2530 sheet: -2.23 (0.30), residues: 234 loop : -0.94 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 143 HIS 0.010 0.001 HIS B 852 PHE 0.015 0.001 PHE C 942 TYR 0.030 0.001 TYR D 888 ARG 0.009 0.000 ARG A 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 414 time to evaluate : 4.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 GLU cc_start: 0.7594 (mp0) cc_final: 0.7285 (mp0) REVERT: A 507 PHE cc_start: 0.7696 (m-80) cc_final: 0.7444 (m-80) REVERT: A 962 TYR cc_start: 0.7999 (m-10) cc_final: 0.7647 (m-10) REVERT: B 24 ASN cc_start: 0.6991 (t0) cc_final: 0.6677 (t0) REVERT: B 396 MET cc_start: 0.7469 (mmm) cc_final: 0.6939 (mmm) REVERT: B 624 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8152 (tm-30) REVERT: B 786 HIS cc_start: 0.6711 (OUTLIER) cc_final: 0.6395 (m170) REVERT: C 35 GLU cc_start: 0.8613 (tp30) cc_final: 0.8313 (tp30) REVERT: C 98 MET cc_start: 0.7442 (mmm) cc_final: 0.7209 (mmt) REVERT: C 289 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7909 (m) REVERT: C 291 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.6761 (t0) REVERT: C 866 MET cc_start: 0.7803 (mmp) cc_final: 0.7425 (mmp) REVERT: D 335 GLU cc_start: 0.8017 (mp0) cc_final: 0.7601 (mp0) REVERT: D 343 ASN cc_start: 0.8527 (p0) cc_final: 0.8124 (p0) REVERT: D 976 MET cc_start: 0.7684 (mtt) cc_final: 0.7011 (mtt) REVERT: E 33 LEU cc_start: 0.8667 (tp) cc_final: 0.8427 (tp) REVERT: E 120 ASP cc_start: 0.8358 (t0) cc_final: 0.8130 (t0) REVERT: F 44 PHE cc_start: 0.3156 (OUTLIER) cc_final: 0.2611 (m-10) REVERT: F 65 ASP cc_start: 0.8189 (t0) cc_final: 0.7924 (t0) REVERT: F 119 LEU cc_start: 0.7389 (tp) cc_final: 0.7180 (tp) outliers start: 59 outliers final: 54 residues processed: 459 average time/residue: 0.9345 time to fit residues: 683.8545 Evaluate side-chains 468 residues out of total 3868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 410 time to evaluate : 4.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 134 TYR Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 810 HIS Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 469 CYS Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 711 GLN Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 134 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 290 MET Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 711 GLN Chi-restraints excluded: chain C residue 744 PHE Chi-restraints excluded: chain C residue 842 LEU Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 670 SER Chi-restraints excluded: chain D residue 688 LEU Chi-restraints excluded: chain D residue 883 GLU Chi-restraints excluded: chain D residue 912 TYR Chi-restraints excluded: chain D residue 913 MET Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain F residue 42 CYS Chi-restraints excluded: chain F residue 44 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 360 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 319 optimal weight: 0.6980 chunk 302 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 397 optimal weight: 0.7980 chunk 307 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 786 HIS ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.185619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123549 restraints weight = 155206.833| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.85 r_work: 0.3277 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 35832 Z= 0.198 Angle : 0.602 57.300 48274 Z= 0.369 Chirality : 0.037 0.160 5126 Planarity : 0.003 0.087 6162 Dihedral : 4.266 55.804 4641 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.55 % Allowed : 19.16 % Favored : 79.29 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.13), residues: 4196 helix: 1.58 (0.11), residues: 2548 sheet: -2.23 (0.30), residues: 234 loop : -0.97 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP D 143 HIS 0.124 0.002 HIS B 786 PHE 0.012 0.001 PHE A 712 TYR 0.024 0.001 TYR D 888 ARG 0.007 0.000 ARG A 514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31544.93 seconds wall clock time: 538 minutes 39.31 seconds (32319.31 seconds total)