Starting phenix.real_space_refine on Sun May 25 12:44:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2i_17366/05_2025/8p2i_17366.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2i_17366/05_2025/8p2i_17366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p2i_17366/05_2025/8p2i_17366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2i_17366/05_2025/8p2i_17366.map" model { file = "/net/cci-nas-00/data/ceres_data/8p2i_17366/05_2025/8p2i_17366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2i_17366/05_2025/8p2i_17366.cif" } resolution = 3.4 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= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 Mg 1 5.21 5 S 115 5.16 5 C 17485 2.51 5 N 4779 2.21 5 O 5093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 107 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27479 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 7197 Classifications: {'peptide': 901} Link IDs: {'PCIS': 2, 'PTRANS': 50, 'TRANS': 848} Chain: "B" Number of atoms: 8825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8825 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 61, 'TRANS': 1039} Chain breaks: 1 Chain: "C" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3057 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 16, 'TRANS': 373} Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2086 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain: "E" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1528 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain: "F" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 946 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "H" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 5, 'TRANS': 69} Chain: "K" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 6, 'TRANS': 47} Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 777 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "N" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 543 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "P" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 393 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain: "G" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "I" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 459 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 434 SG CYS A 57 68.517 86.994 65.865 1.00 0.73 S ATOM 456 SG CYS A 60 70.231 83.525 65.883 1.00 30.00 S ATOM 499 SG CYS A 67 68.242 84.698 68.947 1.00 0.77 S ATOM 736 SG CYS A 97 107.135 110.103 85.956 1.00 0.80 S ATOM 762 SG CYS A 100 108.716 107.861 83.400 1.00 0.73 S ATOM 1138 SG CYS A 144 110.445 108.406 86.772 1.00 0.72 S ATOM 1161 SG CYS A 147 110.292 111.211 84.135 1.00 0.78 S ATOM 15554 SG CYS B1059 87.495 80.929 66.465 1.00 0.85 S ATOM 15577 SG CYS B1062 87.870 83.896 68.805 1.00 30.00 S ATOM 15707 SG CYS B1077 85.017 83.846 66.324 1.00 0.84 S ATOM 15727 SG CYS B1080 88.557 84.322 65.088 1.00 0.68 S ATOM 25483 SG CYS N 7 29.948 53.852 119.569 1.00 0.59 S ATOM 25507 SG CYS N 10 28.663 50.235 119.638 1.00 0.59 S ATOM 25787 SG CYS N 44 31.081 51.588 122.397 1.00 0.60 S ATOM 25793 SG CYS N 45 27.427 52.321 122.221 1.00 0.60 S ATOM 26029 SG CYS P 8 19.535 89.631 95.213 1.00 86.83 S ATOM 26055 SG CYS P 11 16.052 89.593 96.329 1.00 84.70 S ATOM 26184 SG CYS P 27 16.964 91.622 93.121 1.00 79.74 S ATOM 26209 SG CYS P 30 18.075 92.829 96.558 1.00 30.00 S ATOM 27042 SG CYS I 6 53.986 141.615 73.381 1.00204.53 S ATOM 27069 SG CYS I 9 56.456 144.632 72.908 1.00190.06 S ATOM 27146 SG CYS I 18 53.347 144.278 75.554 1.00201.96 S ATOM 27166 SG CYS I 21 52.872 145.307 72.291 1.00203.74 S Time building chain proxies: 15.09, per 1000 atoms: 0.55 Number of scatterers: 27479 At special positions: 0 Unit cell: (130.68, 160.688, 168.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 115 16.00 Mg 1 11.99 O 5093 8.00 N 4779 7.00 C 17485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.16 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 70 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 60 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 57 " pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 100 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 97 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 147 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 144 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1062 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1077 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1059 " pdb=" ZN I 101 " pdb="ZN ZN I 101 " - pdb=" SG CYS I 21 " pdb="ZN ZN I 101 " - pdb=" SG CYS I 18 " pdb="ZN ZN I 101 " - pdb=" SG CYS I 6 " pdb="ZN ZN I 101 " - pdb=" SG CYS I 9 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 45 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 10 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 44 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 7 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 8 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 11 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 30 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 27 " Number of angles added : 33 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6370 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 43 sheets defined 43.2% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 106 through 119 removed outlier: 3.724A pdb=" N LEU A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 removed outlier: 3.743A pdb=" N GLU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 179 through 189 removed outlier: 3.729A pdb=" N LYS A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 199 removed outlier: 3.838A pdb=" N ASP A 194 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Proline residue: A 196 - end of helix Processing helix chain 'A' and resid 206 through 209 Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 236 through 258 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.692A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.831A pdb=" N TYR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 482 Processing helix chain 'A' and resid 483 through 488 removed outlier: 4.018A pdb=" N ILE A 488 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 519 through 531 Processing helix chain 'A' and resid 553 through 559 removed outlier: 3.654A pdb=" N LEU A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 590 removed outlier: 3.746A pdb=" N CYS A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.791A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 663 removed outlier: 3.631A pdb=" N GLY A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N GLU A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.027A pdb=" N GLU A 671 " --> pdb=" O ILE A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 701 removed outlier: 3.708A pdb=" N ARG A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 739 removed outlier: 3.545A pdb=" N VAL A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 756 through 765 removed outlier: 3.607A pdb=" N ILE A 760 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 799 Processing helix chain 'A' and resid 811 through 848 removed outlier: 3.787A pdb=" N GLU A 824 " --> pdb=" O MET A 820 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 removed outlier: 3.522A pdb=" N ASP A 873 " --> pdb=" O TYR A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 901 Processing helix chain 'B' and resid 10 through 26 removed outlier: 3.849A pdb=" N SER B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 51 removed outlier: 3.693A pdb=" N SER B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU B 43 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLN B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 138 through 145 removed outlier: 3.533A pdb=" N LYS B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 266 through 279 Processing helix chain 'B' and resid 283 through 299 removed outlier: 4.024A pdb=" N LEU B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 309 through 329 Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 347 through 379 Processing helix chain 'B' and resid 380 through 386 Processing helix chain 'B' and resid 386 through 393 Processing helix chain 'B' and resid 396 through 411 removed outlier: 4.152A pdb=" N LEU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 436 Processing helix chain 'B' and resid 449 through 454 removed outlier: 3.641A pdb=" N ASP B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 460 removed outlier: 3.552A pdb=" N TRP B 460 " --> pdb=" O GLY B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 502 removed outlier: 3.774A pdb=" N ILE B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 546 removed outlier: 3.717A pdb=" N LEU B 535 " --> pdb=" O ASP B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 596 Processing helix chain 'B' and resid 600 through 607 Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.549A pdb=" N GLU B 619 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 630 Processing helix chain 'B' and resid 640 through 645 removed outlier: 3.926A pdb=" N LEU B 645 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 652 removed outlier: 3.573A pdb=" N VAL B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 Processing helix chain 'B' and resid 659 through 670 Processing helix chain 'B' and resid 680 through 684 Processing helix chain 'B' and resid 702 through 708 removed outlier: 4.089A pdb=" N LYS B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 707 " --> pdb=" O ARG B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 713 Processing helix chain 'B' and resid 727 through 731 removed outlier: 4.107A pdb=" N ASN B 730 " --> pdb=" O GLN B 727 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET B 731 " --> pdb=" O GLY B 728 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 727 through 731' Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 762 through 766 removed outlier: 3.578A pdb=" N GLY B 765 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN B 766 " --> pdb=" O LEU B 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 762 through 766' Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 891 through 895 Processing helix chain 'B' and resid 911 through 917 removed outlier: 4.233A pdb=" N SER B 915 " --> pdb=" O HIS B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 935 removed outlier: 3.822A pdb=" N LEU B 922 " --> pdb=" O THR B 918 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 929 " --> pdb=" O ALA B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 958 Processing helix chain 'B' and resid 994 through 998 Processing helix chain 'B' and resid 1027 through 1038 Processing helix chain 'B' and resid 1039 through 1048 Processing helix chain 'B' and resid 1092 through 1105 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 18 through 36 removed outlier: 3.775A pdb=" N GLU C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 57 Processing helix chain 'C' and resid 64 through 75 Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 97 through 108 removed outlier: 3.793A pdb=" N ARG C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 140 Processing helix chain 'C' and resid 144 through 147 No H-bonds generated for 'chain 'C' and resid 144 through 147' Processing helix chain 'C' and resid 165 through 171 removed outlier: 3.676A pdb=" N LEU C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.823A pdb=" N LYS C 208 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 221 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.593A pdb=" N VAL C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 255' Processing helix chain 'C' and resid 269 through 278 removed outlier: 3.656A pdb=" N GLU C 275 " --> pdb=" O HIS C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 297 removed outlier: 3.728A pdb=" N GLN C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 removed outlier: 4.152A pdb=" N ILE C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 333 through 339 removed outlier: 3.502A pdb=" N ARG C 337 " --> pdb=" O SER C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.560A pdb=" N VAL C 379 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 38 Processing helix chain 'D' and resid 57 through 68 removed outlier: 3.531A pdb=" N HIS D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 169 through 181 removed outlier: 3.968A pdb=" N LEU D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 233 through 258 Processing helix chain 'E' and resid 14 through 18 Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.540A pdb=" N ALA E 25 " --> pdb=" O ASP E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 173 through 189 Processing helix chain 'F' and resid 13 through 31 removed outlier: 3.844A pdb=" N GLU F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 51 removed outlier: 4.162A pdb=" N PHE F 51 " --> pdb=" O HIS F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 70 Processing helix chain 'F' and resid 74 through 85 Processing helix chain 'F' and resid 88 through 98 removed outlier: 3.832A pdb=" N LEU F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS F 98 " --> pdb=" O VAL F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 116 removed outlier: 3.509A pdb=" N ASP F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 12 Processing helix chain 'H' and resid 22 through 33 Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.749A pdb=" N LEU H 40 " --> pdb=" O LEU H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 54 Processing helix chain 'K' and resid 5 through 23 Processing helix chain 'K' and resid 35 through 46 Processing helix chain 'L' and resid 21 through 33 removed outlier: 4.005A pdb=" N LEU L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 94 removed outlier: 3.505A pdb=" N ALA L 88 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS L 94 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 28 Processing helix chain 'N' and resid 30 through 39 Processing helix chain 'N' and resid 42 through 52 removed outlier: 3.586A pdb=" N ARG N 46 " --> pdb=" O ARG N 42 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET N 48 " --> pdb=" O CYS N 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 30 removed outlier: 4.416A pdb=" N ARG G 27 " --> pdb=" O TYR G 23 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR G 28 " --> pdb=" O SER G 24 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR G 29 " --> pdb=" O LYS G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 61 removed outlier: 3.879A pdb=" N VAL G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 78 Processing helix chain 'G' and resid 79 through 84 Processing helix chain 'I' and resid 42 through 49 removed outlier: 3.594A pdb=" N LYS I 46 " --> pdb=" O SER I 42 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 1110 through 1114 removed outlier: 5.853A pdb=" N SER B1114 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE A 5 " --> pdb=" O SER B1114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 81 removed outlier: 6.788A pdb=" N THR A 213 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 10.377A pdb=" N ARG A 78 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N VAL A 211 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 154 through 157 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 320 Processing sheet with id=AA6, first strand: chain 'B' and resid 1000 through 1002 removed outlier: 3.820A pdb=" N THR A 327 " --> pdb=" O MET A 464 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL A 340 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET A 440 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL A 342 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.732A pdb=" N ARG A 411 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR A 380 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS A 412 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA A 378 " --> pdb=" O HIS A 412 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 517 through 518 Processing sheet with id=AA9, first strand: chain 'A' and resid 567 through 570 removed outlier: 6.540A pdb=" N TYR A 608 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 768 through 769 Processing sheet with id=AB2, first strand: chain 'A' and resid 771 through 772 Processing sheet with id=AB3, first strand: chain 'A' and resid 851 through 852 removed outlier: 4.117A pdb=" N LYS A 851 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 859 " --> pdb=" O LYS A 851 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 858 " --> pdb=" O VAL A 866 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 60 through 69 removed outlier: 5.712A pdb=" N GLU B 103 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE B 67 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TYR B 101 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL B 69 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 60 through 69 removed outlier: 5.712A pdb=" N GLU B 103 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE B 67 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TYR B 101 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL B 69 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ALA B 98 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU B 122 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU B 100 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AB7, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB8, first strand: chain 'B' and resid 343 through 346 removed outlier: 6.337A pdb=" N SER B 167 " --> pdb=" O THR B 440 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 177 through 181 Processing sheet with id=AC1, first strand: chain 'B' and resid 485 through 486 Processing sheet with id=AC2, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AC3, first strand: chain 'B' and resid 505 through 506 removed outlier: 3.549A pdb=" N VAL B 505 " --> pdb=" O THR B 528 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU B 521 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY B 527 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 688 through 692 removed outlier: 3.712A pdb=" N LYS B 847 " --> pdb=" O THR B 863 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG B 865 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL B 845 " --> pdb=" O ARG B 865 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU B 867 " --> pdb=" O GLY B 843 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLY B 843 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 843 " --> pdb=" O VAL B 801 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 688 through 692 removed outlier: 3.712A pdb=" N LYS B 847 " --> pdb=" O THR B 863 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG B 865 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N VAL B 845 " --> pdb=" O ARG B 865 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU B 867 " --> pdb=" O GLY B 843 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLY B 843 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA P 4 " --> pdb=" O LEU P 17 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AC7, first strand: chain 'B' and resid 965 through 966 removed outlier: 7.264A pdb=" N ILE B 735 " --> pdb=" O GLY B 887 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 889 " --> pdb=" O ILE B 735 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 737 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 982 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 769 through 770 Processing sheet with id=AC9, first strand: chain 'B' and resid 806 through 808 removed outlier: 6.810A pdb=" N VAL B 835 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 897 through 898 Processing sheet with id=AD2, first strand: chain 'B' and resid 1054 through 1059 Processing sheet with id=AD3, first strand: chain 'B' and resid 1067 through 1069 Processing sheet with id=AD4, first strand: chain 'C' and resid 233 through 238 removed outlier: 3.565A pdb=" N MET C 117 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 142 through 143 removed outlier: 4.463A pdb=" N LYS C 225 " --> pdb=" O THR C 142 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 148 through 154 Processing sheet with id=AD7, first strand: chain 'E' and resid 37 through 39 removed outlier: 4.127A pdb=" N THR E 37 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N SER E 47 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N TRP E 77 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU E 49 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N LEU E 75 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL E 51 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASP E 73 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU E 69 " --> pdb=" O LYS E 55 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY E 57 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TYR E 67 " --> pdb=" O GLY E 57 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 37 through 39 removed outlier: 4.127A pdb=" N THR E 37 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY E 57 " --> pdb=" O MET C 383 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU C 381 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS C 380 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 5 through 11 removed outlier: 3.724A pdb=" N GLU D 5 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS D 17 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LYS D 11 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N SER D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR D 158 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ASN D 220 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 10.728A pdb=" N LYS D 156 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 9.605A pdb=" N TYR D 222 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 10.277A pdb=" N TYR D 154 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N PHE D 224 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N PHE D 152 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 107 through 108 removed outlier: 7.012A pdb=" N ARG D 130 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN D 52 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL D 132 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 46 " --> pdb=" O TYR D 136 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS D 138 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL D 44 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY D 140 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N PHE D 42 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 99 through 102 removed outlier: 3.890A pdb=" N VAL D 123 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 171 through 172 removed outlier: 3.889A pdb=" N ARG E 143 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY E 162 " --> pdb=" O ILE E 147 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE E 161 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N HIS E 109 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ARG E 100 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL E 89 " --> pdb=" O ARG E 100 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.835A pdb=" N GLU H 17 " --> pdb=" O LYS H 64 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 2 through 8 removed outlier: 7.023A pdb=" N GLU L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS L 8 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU L 12 " --> pdb=" O LYS L 8 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 66 through 69 removed outlier: 3.669A pdb=" N GLY G 68 " --> pdb=" O ARG G 9 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA G 35 " --> pdb=" O GLU G 49 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 4 through 5 1268 hydrogen bonds defined for protein. 3459 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: 12.46 Time building geometry restraints manager: 8.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9166 1.34 - 1.46: 5468 1.46 - 1.58: 13162 1.58 - 1.70: 0 1.70 - 1.82: 200 Bond restraints: 27996 Sorted by residual: bond pdb=" C ALA B 660 " pdb=" N PRO B 661 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.34e+00 bond pdb=" CA LEU F 7 " pdb=" C LEU F 7 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.08e-02 8.57e+03 1.68e+00 bond pdb=" CA MET F 85 " pdb=" C MET F 85 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.26e-02 6.30e+03 1.37e+00 bond pdb=" CB ILE F 95 " pdb=" CG2 ILE F 95 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.23e+00 bond pdb=" CA VAL D 218 " pdb=" CB VAL D 218 " ideal model delta sigma weight residual 1.537 1.523 0.014 1.29e-02 6.01e+03 1.20e+00 ... (remaining 27991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 37401 2.51 - 5.02: 354 5.02 - 7.53: 32 7.53 - 10.03: 6 10.03 - 12.54: 3 Bond angle restraints: 37796 Sorted by residual: angle pdb=" CA MET E 93 " pdb=" CB MET E 93 " pdb=" CG MET E 93 " ideal model delta sigma weight residual 114.10 124.16 -10.06 2.00e+00 2.50e-01 2.53e+01 angle pdb=" CA ARG F 25 " pdb=" CB ARG F 25 " pdb=" CG ARG F 25 " ideal model delta sigma weight residual 114.10 124.02 -9.92 2.00e+00 2.50e-01 2.46e+01 angle pdb=" CB ARG F 25 " pdb=" CG ARG F 25 " pdb=" CD ARG F 25 " ideal model delta sigma weight residual 111.30 120.92 -9.62 2.30e+00 1.89e-01 1.75e+01 angle pdb=" CB MET E 165 " pdb=" CG MET E 165 " pdb=" SD MET E 165 " ideal model delta sigma weight residual 112.70 125.24 -12.54 3.00e+00 1.11e-01 1.75e+01 angle pdb=" N VAL B 305 " pdb=" CA VAL B 305 " pdb=" C VAL B 305 " ideal model delta sigma weight residual 113.20 109.55 3.65 9.60e-01 1.09e+00 1.44e+01 ... (remaining 37791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15174 17.98 - 35.95: 1569 35.95 - 53.93: 379 53.93 - 71.90: 81 71.90 - 89.88: 40 Dihedral angle restraints: 17243 sinusoidal: 7328 harmonic: 9915 Sorted by residual: dihedral pdb=" CA MET E 93 " pdb=" C MET E 93 " pdb=" N PRO E 94 " pdb=" CA PRO E 94 " ideal model delta harmonic sigma weight residual -180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA TYR E 134 " pdb=" C TYR E 134 " pdb=" N LEU E 135 " pdb=" CA LEU E 135 " ideal model delta harmonic sigma weight residual -180.00 -155.95 -24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA LYS E 133 " pdb=" C LYS E 133 " pdb=" N TYR E 134 " pdb=" CA TYR E 134 " ideal model delta harmonic sigma weight residual -180.00 -156.11 -23.89 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 17240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2749 0.034 - 0.068: 933 0.068 - 0.102: 353 0.102 - 0.136: 152 0.136 - 0.171: 8 Chirality restraints: 4195 Sorted by residual: chirality pdb=" CA PRO E 94 " pdb=" N PRO E 94 " pdb=" C PRO E 94 " pdb=" CB PRO E 94 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA TYR E 134 " pdb=" N TYR E 134 " pdb=" C TYR E 134 " pdb=" CB TYR E 134 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA ILE B 772 " pdb=" N ILE B 772 " pdb=" C ILE B 772 " pdb=" CB ILE B 772 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 4192 not shown) Planarity restraints: 4896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 175 " 0.027 2.00e-02 2.50e+03 2.46e-02 1.51e+01 pdb=" CG TRP E 175 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP E 175 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP E 175 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 175 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 175 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 175 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 175 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 175 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP E 175 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 134 " 0.021 2.00e-02 2.50e+03 1.64e-02 5.36e+00 pdb=" CG TYR E 134 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR E 134 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR E 134 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 134 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 134 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR E 134 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 134 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 165 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C MET E 165 " -0.035 2.00e-02 2.50e+03 pdb=" O MET E 165 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG E 166 " 0.012 2.00e-02 2.50e+03 ... (remaining 4893 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 237 2.58 - 3.16: 22831 3.16 - 3.74: 43344 3.74 - 4.32: 59387 4.32 - 4.90: 100132 Nonbonded interactions: 225931 Sorted by model distance: nonbonded pdb=" OD1 ASP A 458 " pdb="MG MG A1002 " model vdw 2.002 2.170 nonbonded pdb=" OD1 ASP A 462 " pdb="MG MG A1002 " model vdw 2.058 2.170 nonbonded pdb=" OD1 ASP A 620 " pdb=" N LYS A 621 " model vdw 2.134 3.120 nonbonded pdb=" OD1 ASP A 460 " pdb="MG MG A1002 " model vdw 2.140 2.170 nonbonded pdb=" OD1 ASP B 296 " pdb=" NH2 ARG B 310 " model vdw 2.166 3.120 ... (remaining 225926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 70.230 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28020 Z= 0.134 Angle : 0.646 13.845 37829 Z= 0.352 Chirality : 0.043 0.171 4195 Planarity : 0.004 0.042 4896 Dihedral : 15.883 89.875 10873 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.20 % Allowed : 16.30 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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 (0.15), residues: 3402 helix: 1.40 (0.15), residues: 1262 sheet: -0.13 (0.24), residues: 470 loop : 0.17 (0.16), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP E 175 HIS 0.013 0.001 HIS A 428 PHE 0.029 0.001 PHE A 421 TYR 0.039 0.001 TYR E 134 ARG 0.029 0.001 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.18765 ( 1241) hydrogen bonds : angle 7.14876 ( 3459) metal coordination : bond 0.00448 ( 24) metal coordination : angle 5.26854 ( 33) covalent geometry : bond 0.00273 (27996) covalent geometry : angle 0.62675 (37796) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 200 time to evaluate : 3.497 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 outliers start: 6 outliers final: 2 residues processed: 205 average time/residue: 0.4339 time to fit residues: 138.2123 Evaluate side-chains 192 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain G residue 52 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 8.9990 chunk 255 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 264 optimal weight: 1.9990 chunk 102 optimal weight: 0.0770 chunk 160 optimal weight: 0.0870 chunk 196 optimal weight: 20.0000 chunk 306 optimal weight: 9.9990 overall best weight: 2.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 376 GLN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 ASN C 325 HIS E 109 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN F 47 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.063057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.042931 restraints weight = 99790.529| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.75 r_work: 0.2571 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28020 Z= 0.132 Angle : 0.565 14.609 37829 Z= 0.289 Chirality : 0.044 0.195 4195 Planarity : 0.004 0.042 4896 Dihedral : 4.164 31.041 3800 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.55 % Allowed : 14.82 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.91 (0.15), residues: 3402 helix: 1.52 (0.15), residues: 1296 sheet: -0.04 (0.23), residues: 479 loop : 0.16 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 175 HIS 0.007 0.001 HIS A 428 PHE 0.028 0.001 PHE G 76 TYR 0.036 0.001 TYR E 134 ARG 0.007 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 1241) hydrogen bonds : angle 5.44473 ( 3459) metal coordination : bond 0.00568 ( 24) metal coordination : angle 5.05108 ( 33) covalent geometry : bond 0.00298 (27996) covalent geometry : angle 0.54532 (37796) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 3.355 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: C 117 MET cc_start: 0.8407 (mtp) cc_final: 0.8178 (mtp) REVERT: C 222 HIS cc_start: 0.8474 (t70) cc_final: 0.8020 (t-90) REVERT: C 227 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8523 (tp) REVERT: E 1 MET cc_start: 0.8561 (tpp) cc_final: 0.8338 (tpp) REVERT: E 88 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.8023 (p90) REVERT: H 47 ASP cc_start: 0.9083 (t0) cc_final: 0.8761 (t0) REVERT: H 59 ASP cc_start: 0.8565 (t0) cc_final: 0.8003 (m-30) REVERT: G 61 ARG cc_start: 0.8245 (tpp80) cc_final: 0.7225 (mmp80) outliers start: 46 outliers final: 17 residues processed: 246 average time/residue: 0.4387 time to fit residues: 166.2203 Evaluate side-chains 214 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 975 LYS Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain I residue 12 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 14 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 310 optimal weight: 8.9990 chunk 286 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN B 680 ASN G 12 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.061036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.041124 restraints weight = 102142.565| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.63 r_work: 0.2517 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 28020 Z= 0.206 Angle : 0.580 15.192 37829 Z= 0.295 Chirality : 0.045 0.154 4195 Planarity : 0.004 0.044 4896 Dihedral : 4.207 31.248 3797 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.85 % Allowed : 15.39 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.84 (0.15), residues: 3402 helix: 1.59 (0.15), residues: 1290 sheet: -0.23 (0.24), residues: 464 loop : 0.07 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 30 HIS 0.007 0.001 HIS A 428 PHE 0.019 0.001 PHE A 421 TYR 0.030 0.001 TYR E 134 ARG 0.009 0.000 ARG E 166 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 1241) hydrogen bonds : angle 5.17911 ( 3459) metal coordination : bond 0.00739 ( 24) metal coordination : angle 4.76471 ( 33) covalent geometry : bond 0.00484 (27996) covalent geometry : angle 0.56279 (37796) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 3.215 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: B 906 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9097 (tt) REVERT: B 948 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: C 222 HIS cc_start: 0.8641 (t70) cc_final: 0.8238 (t-90) REVERT: C 227 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8488 (tp) REVERT: C 247 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: D 259 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8305 (mp) REVERT: E 1 MET cc_start: 0.8673 (tpp) cc_final: 0.8413 (tpp) REVERT: E 114 MET cc_start: 0.5958 (mtt) cc_final: 0.5249 (mmt) REVERT: E 145 ARG cc_start: 0.8382 (mtp85) cc_final: 0.8012 (mtt-85) REVERT: E 165 MET cc_start: 0.7164 (tmm) cc_final: 0.6938 (tmm) REVERT: E 167 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8615 (tm-30) REVERT: F 75 ASP cc_start: 0.8322 (p0) cc_final: 0.7993 (p0) REVERT: H 47 ASP cc_start: 0.9061 (t0) cc_final: 0.8643 (t0) REVERT: H 56 LYS cc_start: 0.9179 (mmtm) cc_final: 0.8722 (mmtm) REVERT: H 59 ASP cc_start: 0.8722 (t0) cc_final: 0.8132 (m-30) REVERT: P 16 LYS cc_start: 0.9557 (mttp) cc_final: 0.9235 (mmmt) REVERT: P 23 ARG cc_start: 0.8330 (mtp-110) cc_final: 0.7824 (ttp80) REVERT: G 61 ARG cc_start: 0.8220 (tpp80) cc_final: 0.7935 (tpp80) outliers start: 55 outliers final: 27 residues processed: 253 average time/residue: 0.4546 time to fit residues: 176.0184 Evaluate side-chains 228 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 975 LYS Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1037 HIS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 59 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 0.0060 chunk 38 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 HIS ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN F 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.041465 restraints weight = 102582.473| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.63 r_work: 0.2536 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28020 Z= 0.139 Angle : 0.534 13.788 37829 Z= 0.272 Chirality : 0.044 0.194 4195 Planarity : 0.004 0.050 4896 Dihedral : 4.097 31.246 3797 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.82 % Allowed : 15.43 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.92 (0.15), residues: 3402 helix: 1.67 (0.15), residues: 1292 sheet: -0.10 (0.24), residues: 459 loop : 0.06 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 30 HIS 0.005 0.001 HIS E 109 PHE 0.018 0.001 PHE A 421 TYR 0.030 0.001 TYR E 88 ARG 0.009 0.000 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 1241) hydrogen bonds : angle 4.92548 ( 3459) metal coordination : bond 0.00524 ( 24) metal coordination : angle 4.37435 ( 33) covalent geometry : bond 0.00321 (27996) covalent geometry : angle 0.51857 (37796) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 MET cc_start: 0.9312 (mtm) cc_final: 0.9107 (mtp) REVERT: A 855 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8975 (p0) REVERT: B 290 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8598 (ttp80) REVERT: B 906 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9056 (tt) REVERT: B 1030 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.8823 (mp0) REVERT: C 60 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8541 (mt-10) REVERT: C 117 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8283 (mtp) REVERT: C 222 HIS cc_start: 0.8656 (t70) cc_final: 0.8261 (t-90) REVERT: C 227 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8499 (tp) REVERT: C 247 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7927 (tm-30) REVERT: E 1 MET cc_start: 0.8665 (tpp) cc_final: 0.8373 (tpp) REVERT: E 109 HIS cc_start: 0.8202 (t70) cc_final: 0.7828 (t-90) REVERT: E 114 MET cc_start: 0.6180 (mtt) cc_final: 0.5069 (mmt) REVERT: E 134 TYR cc_start: 0.5409 (t80) cc_final: 0.5097 (t80) REVERT: E 145 ARG cc_start: 0.8405 (mtp85) cc_final: 0.7889 (mtt180) REVERT: E 149 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7754 (mt) REVERT: F 21 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8809 (tp) REVERT: F 42 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8395 (ptt-90) REVERT: F 75 ASP cc_start: 0.8243 (p0) cc_final: 0.7903 (p0) REVERT: H 47 ASP cc_start: 0.9052 (t0) cc_final: 0.8605 (t0) REVERT: H 51 LYS cc_start: 0.9385 (mmtm) cc_final: 0.9166 (mttp) REVERT: H 56 LYS cc_start: 0.9195 (mmtm) cc_final: 0.8750 (mmtm) REVERT: H 59 ASP cc_start: 0.8774 (t0) cc_final: 0.8208 (m-30) REVERT: G 4 LYS cc_start: 0.5635 (OUTLIER) cc_final: 0.4825 (mmtm) REVERT: G 61 ARG cc_start: 0.8236 (tpp80) cc_final: 0.7784 (tpp80) REVERT: I 11 TYR cc_start: 0.8949 (t80) cc_final: 0.8650 (t80) outliers start: 54 outliers final: 23 residues processed: 250 average time/residue: 0.4376 time to fit residues: 169.1186 Evaluate side-chains 228 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 975 LYS Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1037 HIS Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 167 GLN Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 167 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 212 optimal weight: 0.4980 chunk 216 optimal weight: 20.0000 chunk 186 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 283 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 chunk 335 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.060859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.040880 restraints weight = 102051.924| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 3.70 r_work: 0.2501 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28020 Z= 0.209 Angle : 0.573 13.632 37829 Z= 0.290 Chirality : 0.045 0.211 4195 Planarity : 0.004 0.051 4896 Dihedral : 4.178 32.365 3797 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.18 % Allowed : 15.93 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.83 (0.15), residues: 3402 helix: 1.65 (0.15), residues: 1288 sheet: -0.26 (0.24), residues: 449 loop : 0.01 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 30 HIS 0.005 0.001 HIS N 52 PHE 0.017 0.001 PHE A 421 TYR 0.047 0.001 TYR E 88 ARG 0.009 0.000 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 1241) hydrogen bonds : angle 4.92098 ( 3459) metal coordination : bond 0.00706 ( 24) metal coordination : angle 4.27737 ( 33) covalent geometry : bond 0.00491 (27996) covalent geometry : angle 0.55870 (37796) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 202 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8879 (t80) REVERT: A 464 MET cc_start: 0.9187 (mtm) cc_final: 0.8820 (mtp) REVERT: A 855 ASP cc_start: 0.9235 (OUTLIER) cc_final: 0.8971 (p0) REVERT: B 303 MET cc_start: 0.9589 (mmt) cc_final: 0.9320 (mmm) REVERT: B 906 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9079 (tt) REVERT: B 948 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: C 60 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8573 (mt-10) REVERT: C 117 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8256 (mtp) REVERT: C 222 HIS cc_start: 0.8657 (t70) cc_final: 0.8280 (t-90) REVERT: C 227 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8458 (tp) REVERT: C 247 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7978 (tm-30) REVERT: E 1 MET cc_start: 0.8711 (tpp) cc_final: 0.8072 (tpp) REVERT: E 3 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8343 (ptpt) REVERT: E 114 MET cc_start: 0.6025 (mtt) cc_final: 0.5669 (mmm) REVERT: E 145 ARG cc_start: 0.8386 (mtp85) cc_final: 0.7769 (mtt-85) REVERT: E 167 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8500 (tm-30) REVERT: F 33 ILE cc_start: 0.8732 (mm) cc_final: 0.8510 (tp) REVERT: F 42 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8275 (ptt-90) REVERT: F 75 ASP cc_start: 0.8251 (p0) cc_final: 0.7885 (p0) REVERT: H 23 GLU cc_start: 0.8375 (tp30) cc_final: 0.7998 (tp30) REVERT: H 47 ASP cc_start: 0.9077 (t0) cc_final: 0.8550 (t0) REVERT: H 59 ASP cc_start: 0.8840 (t0) cc_final: 0.8436 (t0) REVERT: P 23 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.7759 (ttp80) REVERT: G 4 LYS cc_start: 0.5713 (OUTLIER) cc_final: 0.4850 (mmtm) REVERT: G 61 ARG cc_start: 0.8263 (tpp80) cc_final: 0.7765 (tpp80) REVERT: I 11 TYR cc_start: 0.9058 (t80) cc_final: 0.8610 (t80) outliers start: 65 outliers final: 32 residues processed: 253 average time/residue: 0.4256 time to fit residues: 166.5983 Evaluate side-chains 237 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 975 LYS Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1037 HIS Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 171 optimal weight: 20.0000 chunk 284 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 318 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 303 optimal weight: 20.0000 chunk 242 optimal weight: 2.9990 chunk 319 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 305 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 HIS ** B 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN ** G 65 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 = 0.3271 r_free = 0.3271 target = 0.061144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.040886 restraints weight = 101110.135| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 3.77 r_work: 0.2481 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 28020 Z= 0.242 Angle : 0.594 14.387 37829 Z= 0.302 Chirality : 0.045 0.186 4195 Planarity : 0.004 0.052 4896 Dihedral : 4.288 33.242 3797 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.29 % Allowed : 16.37 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.74 (0.15), residues: 3402 helix: 1.62 (0.15), residues: 1285 sheet: -0.36 (0.24), residues: 445 loop : -0.07 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 30 HIS 0.006 0.001 HIS N 52 PHE 0.017 0.002 PHE A 421 TYR 0.039 0.002 TYR E 88 ARG 0.013 0.000 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 1241) hydrogen bonds : angle 4.93174 ( 3459) metal coordination : bond 0.00821 ( 24) metal coordination : angle 4.42692 ( 33) covalent geometry : bond 0.00569 (27996) covalent geometry : angle 0.57985 (37796) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 200 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.9068 (t80) REVERT: A 855 ASP cc_start: 0.9228 (OUTLIER) cc_final: 0.8959 (p0) REVERT: B 340 TYR cc_start: 0.9440 (OUTLIER) cc_final: 0.8643 (t80) REVERT: B 948 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8028 (tm-30) REVERT: C 60 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8643 (mt-10) REVERT: C 222 HIS cc_start: 0.8686 (t70) cc_final: 0.8319 (t-90) REVERT: C 227 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8465 (tp) REVERT: C 247 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: E 1 MET cc_start: 0.8764 (tpp) cc_final: 0.8111 (tpp) REVERT: E 3 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8349 (ptpt) REVERT: E 114 MET cc_start: 0.6554 (mtt) cc_final: 0.6211 (mmm) REVERT: E 134 TYR cc_start: 0.5237 (t80) cc_final: 0.5009 (t80) REVERT: E 145 ARG cc_start: 0.8363 (mtp85) cc_final: 0.8140 (mtt-85) REVERT: F 33 ILE cc_start: 0.8760 (mm) cc_final: 0.8536 (tp) REVERT: F 73 MET cc_start: 0.7091 (tpp) cc_final: 0.6617 (tpp) REVERT: F 75 ASP cc_start: 0.8214 (p0) cc_final: 0.7927 (p0) REVERT: H 47 ASP cc_start: 0.9072 (t0) cc_final: 0.8543 (t0) REVERT: H 59 ASP cc_start: 0.8864 (t0) cc_final: 0.8435 (t0) REVERT: G 4 LYS cc_start: 0.5753 (OUTLIER) cc_final: 0.4782 (mmtm) REVERT: G 61 ARG cc_start: 0.8277 (tpp80) cc_final: 0.7847 (tpp80) REVERT: I 11 TYR cc_start: 0.9062 (t80) cc_final: 0.8778 (t80) outliers start: 68 outliers final: 36 residues processed: 253 average time/residue: 0.4181 time to fit residues: 165.8730 Evaluate side-chains 236 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 975 LYS Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1037 HIS Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 12 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 272 optimal weight: 50.0000 chunk 279 optimal weight: 30.0000 chunk 151 optimal weight: 5.9990 chunk 316 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 chunk 318 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 253 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.061370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.041178 restraints weight = 101037.685| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 3.77 r_work: 0.2494 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28020 Z= 0.189 Angle : 0.665 53.631 37829 Z= 0.295 Chirality : 0.044 0.219 4195 Planarity : 0.004 0.053 4896 Dihedral : 4.215 33.566 3797 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.42 % Allowed : 16.81 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.81 (0.15), residues: 3402 helix: 1.69 (0.15), residues: 1287 sheet: -0.33 (0.24), residues: 435 loop : -0.06 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 30 HIS 0.005 0.001 HIS N 52 PHE 0.016 0.001 PHE A 421 TYR 0.039 0.001 TYR E 88 ARG 0.014 0.000 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 1241) hydrogen bonds : angle 4.82940 ( 3459) metal coordination : bond 0.00647 ( 24) metal coordination : angle 12.39256 ( 33) covalent geometry : bond 0.00444 (27996) covalent geometry : angle 0.55511 (37796) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 202 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.9072 (t80) REVERT: A 855 ASP cc_start: 0.9228 (OUTLIER) cc_final: 0.8957 (p0) REVERT: B 340 TYR cc_start: 0.9413 (OUTLIER) cc_final: 0.8687 (t80) REVERT: B 906 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9158 (tt) REVERT: B 948 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: B 1030 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.8856 (mp0) REVERT: C 60 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8647 (mt-10) REVERT: C 222 HIS cc_start: 0.8646 (t70) cc_final: 0.8303 (t-90) REVERT: C 227 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8449 (tp) REVERT: C 234 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8206 (mp) REVERT: C 247 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7982 (mm-30) REVERT: E 1 MET cc_start: 0.8741 (tpp) cc_final: 0.8112 (tpp) REVERT: E 3 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8342 (ptpt) REVERT: E 114 MET cc_start: 0.6477 (mtt) cc_final: 0.5510 (mmt) REVERT: E 134 TYR cc_start: 0.5148 (OUTLIER) cc_final: 0.4867 (t80) REVERT: E 145 ARG cc_start: 0.8381 (mtp85) cc_final: 0.8166 (mtt-85) REVERT: F 33 ILE cc_start: 0.8745 (mm) cc_final: 0.8521 (tp) REVERT: F 42 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8447 (ptt-90) REVERT: F 75 ASP cc_start: 0.8244 (p0) cc_final: 0.7976 (p0) REVERT: H 23 GLU cc_start: 0.8503 (tp30) cc_final: 0.8207 (tp30) REVERT: H 47 ASP cc_start: 0.9066 (t0) cc_final: 0.8518 (t0) REVERT: H 59 ASP cc_start: 0.8865 (t0) cc_final: 0.8496 (t0) REVERT: G 4 LYS cc_start: 0.5712 (OUTLIER) cc_final: 0.4702 (mmtm) REVERT: G 61 ARG cc_start: 0.8297 (tpp80) cc_final: 0.7877 (tpp80) REVERT: G 77 LYS cc_start: 0.9459 (tppt) cc_final: 0.9171 (tppt) REVERT: I 11 TYR cc_start: 0.9062 (t80) cc_final: 0.8735 (t80) outliers start: 72 outliers final: 42 residues processed: 256 average time/residue: 0.4507 time to fit residues: 180.0727 Evaluate side-chains 253 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 975 LYS Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1037 HIS Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 281 optimal weight: 50.0000 chunk 318 optimal weight: 7.9990 chunk 302 optimal weight: 0.0970 chunk 75 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 277 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 287 optimal weight: 6.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 HIS ** B 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.061256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.041361 restraints weight = 101668.507| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.66 r_work: 0.2515 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28020 Z= 0.146 Angle : 0.654 51.592 37829 Z= 0.288 Chirality : 0.044 0.190 4195 Planarity : 0.004 0.059 4896 Dihedral : 4.138 34.021 3797 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.15 % Allowed : 17.24 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.89 (0.15), residues: 3402 helix: 1.75 (0.15), residues: 1289 sheet: -0.26 (0.24), residues: 435 loop : -0.01 (0.16), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 30 HIS 0.004 0.001 HIS N 52 PHE 0.030 0.001 PHE G 76 TYR 0.031 0.001 TYR E 88 ARG 0.015 0.000 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 1241) hydrogen bonds : angle 4.71246 ( 3459) metal coordination : bond 0.00541 ( 24) metal coordination : angle 12.16612 ( 33) covalent geometry : bond 0.00345 (27996) covalent geometry : angle 0.54687 (37796) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 208 time to evaluate : 3.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.9073 (t80) REVERT: A 428 HIS cc_start: 0.9072 (OUTLIER) cc_final: 0.8598 (p90) REVERT: A 855 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8954 (p0) REVERT: B 78 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.8190 (p90) REVERT: B 303 MET cc_start: 0.9591 (mmt) cc_final: 0.9346 (mmm) REVERT: B 340 TYR cc_start: 0.9393 (OUTLIER) cc_final: 0.8647 (t80) REVERT: B 906 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9147 (tt) REVERT: B 948 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7961 (tm-30) REVERT: B 1030 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.8808 (mp0) REVERT: C 60 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8624 (mt-10) REVERT: C 117 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8225 (mtp) REVERT: C 222 HIS cc_start: 0.8646 (t70) cc_final: 0.8301 (t-90) REVERT: C 227 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8463 (tp) REVERT: C 234 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8182 (mp) REVERT: C 247 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: E 1 MET cc_start: 0.8674 (tpp) cc_final: 0.8293 (tpp) REVERT: E 3 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.8630 (ptpt) REVERT: E 114 MET cc_start: 0.5690 (mtt) cc_final: 0.4678 (mmt) REVERT: E 134 TYR cc_start: 0.5086 (OUTLIER) cc_final: 0.4725 (t80) REVERT: E 145 ARG cc_start: 0.8369 (mtp85) cc_final: 0.7813 (mtt180) REVERT: F 33 ILE cc_start: 0.8775 (mm) cc_final: 0.8548 (tp) REVERT: F 75 ASP cc_start: 0.8126 (p0) cc_final: 0.7910 (p0) REVERT: F 85 MET cc_start: 0.4564 (tpt) cc_final: 0.3663 (tmm) REVERT: H 47 ASP cc_start: 0.9045 (t0) cc_final: 0.8482 (t0) REVERT: H 59 ASP cc_start: 0.8847 (t0) cc_final: 0.8461 (t0) REVERT: N 55 LEU cc_start: 0.9452 (mt) cc_final: 0.9230 (mp) REVERT: P 23 ARG cc_start: 0.8305 (mtp-110) cc_final: 0.7867 (ttp80) REVERT: G 4 LYS cc_start: 0.5765 (OUTLIER) cc_final: 0.4789 (mmtm) REVERT: G 61 ARG cc_start: 0.8288 (tpp80) cc_final: 0.7878 (tpp80) REVERT: G 77 LYS cc_start: 0.9444 (tppt) cc_final: 0.9154 (tppt) REVERT: I 11 TYR cc_start: 0.9022 (t80) cc_final: 0.8716 (t80) outliers start: 64 outliers final: 38 residues processed: 257 average time/residue: 0.4062 time to fit residues: 163.4058 Evaluate side-chains 253 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 199 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain B residue 78 HIS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 975 LYS Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1037 HIS Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 9 CYS Chi-restraints excluded: chain I residue 12 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 91 optimal weight: 5.9990 chunk 287 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 318 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 335 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 189 optimal weight: 0.2980 chunk 176 optimal weight: 9.9990 chunk 319 optimal weight: 0.7980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.041725 restraints weight = 101313.493| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.63 r_work: 0.2547 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28020 Z= 0.140 Angle : 0.657 49.639 37829 Z= 0.290 Chirality : 0.044 0.215 4195 Planarity : 0.004 0.052 4896 Dihedral : 4.122 34.390 3797 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.98 % Allowed : 17.31 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.91 (0.15), residues: 3402 helix: 1.76 (0.15), residues: 1294 sheet: -0.24 (0.24), residues: 448 loop : 0.01 (0.16), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 175 HIS 0.008 0.001 HIS B 78 PHE 0.015 0.001 PHE A 421 TYR 0.030 0.001 TYR E 88 ARG 0.016 0.000 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 1241) hydrogen bonds : angle 4.66284 ( 3459) metal coordination : bond 0.00487 ( 24) metal coordination : angle 11.99864 ( 33) covalent geometry : bond 0.00328 (27996) covalent geometry : angle 0.55359 (37796) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 200 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 HIS cc_start: 0.8873 (OUTLIER) cc_final: 0.8560 (p90) REVERT: A 855 ASP cc_start: 0.9199 (OUTLIER) cc_final: 0.8924 (p0) REVERT: B 340 TYR cc_start: 0.9343 (OUTLIER) cc_final: 0.8543 (t80) REVERT: B 906 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9177 (tt) REVERT: B 948 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: B 1030 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8774 (mp0) REVERT: C 60 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8654 (mt-10) REVERT: C 117 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8332 (mtp) REVERT: C 222 HIS cc_start: 0.8607 (t70) cc_final: 0.8271 (t-90) REVERT: C 227 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8519 (tp) REVERT: C 234 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8279 (mp) REVERT: C 247 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7927 (tm-30) REVERT: E 1 MET cc_start: 0.8654 (tpp) cc_final: 0.8041 (tpp) REVERT: E 3 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8393 (ptpt) REVERT: E 145 ARG cc_start: 0.8438 (mtp85) cc_final: 0.7906 (mtt180) REVERT: F 33 ILE cc_start: 0.8827 (mm) cc_final: 0.8600 (tp) REVERT: F 75 ASP cc_start: 0.8187 (p0) cc_final: 0.7935 (p0) REVERT: H 47 ASP cc_start: 0.9072 (t0) cc_final: 0.8557 (t0) REVERT: H 59 ASP cc_start: 0.8856 (t0) cc_final: 0.8496 (t0) REVERT: N 55 LEU cc_start: 0.9453 (mt) cc_final: 0.9241 (mp) REVERT: P 23 ARG cc_start: 0.8252 (mtp-110) cc_final: 0.7754 (ttp80) REVERT: G 4 LYS cc_start: 0.5897 (OUTLIER) cc_final: 0.4921 (mmtm) REVERT: I 11 TYR cc_start: 0.9045 (t80) cc_final: 0.8718 (t80) REVERT: I 30 TRP cc_start: 0.8631 (p-90) cc_final: 0.7879 (p90) outliers start: 59 outliers final: 38 residues processed: 244 average time/residue: 0.4123 time to fit residues: 158.5201 Evaluate side-chains 248 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 197 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 975 LYS Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1037 HIS Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 9 CYS Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 193 optimal weight: 3.9990 chunk 316 optimal weight: 8.9990 chunk 307 optimal weight: 0.4980 chunk 99 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 324 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 333 optimal weight: 20.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.061766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.041746 restraints weight = 100784.285| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.70 r_work: 0.2524 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28020 Z= 0.148 Angle : 0.653 47.963 37829 Z= 0.291 Chirality : 0.044 0.192 4195 Planarity : 0.004 0.051 4896 Dihedral : 4.113 34.769 3797 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.82 % Allowed : 17.55 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.99 (0.15), residues: 3402 helix: 1.82 (0.15), residues: 1288 sheet: -0.21 (0.24), residues: 448 loop : 0.07 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 175 HIS 0.004 0.001 HIS N 52 PHE 0.034 0.001 PHE G 76 TYR 0.030 0.001 TYR E 134 ARG 0.017 0.000 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 1241) hydrogen bonds : angle 4.63342 ( 3459) metal coordination : bond 0.00504 ( 24) metal coordination : angle 11.72210 ( 33) covalent geometry : bond 0.00349 (27996) covalent geometry : angle 0.55433 (37796) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 3.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 HIS cc_start: 0.8932 (OUTLIER) cc_final: 0.8676 (p90) REVERT: A 855 ASP cc_start: 0.9222 (OUTLIER) cc_final: 0.8955 (p0) REVERT: B 340 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8543 (t80) REVERT: B 906 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9181 (tt) REVERT: B 948 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: B 1030 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.8823 (mp0) REVERT: C 60 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8650 (mt-10) REVERT: C 117 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8271 (mtp) REVERT: C 222 HIS cc_start: 0.8619 (t70) cc_final: 0.8321 (t-90) REVERT: C 227 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8501 (tp) REVERT: C 234 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8247 (mp) REVERT: C 247 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: E 1 MET cc_start: 0.8648 (tpp) cc_final: 0.8042 (tpp) REVERT: E 3 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8401 (ptpt) REVERT: E 145 ARG cc_start: 0.8459 (mtp85) cc_final: 0.7991 (mtt180) REVERT: F 33 ILE cc_start: 0.8838 (mm) cc_final: 0.8605 (tp) REVERT: F 75 ASP cc_start: 0.8238 (p0) cc_final: 0.7887 (p0) REVERT: F 85 MET cc_start: 0.5034 (tpt) cc_final: 0.4467 (tmm) REVERT: H 47 ASP cc_start: 0.9045 (t0) cc_final: 0.8499 (t0) REVERT: H 59 ASP cc_start: 0.8887 (t0) cc_final: 0.8543 (t0) REVERT: N 55 LEU cc_start: 0.9457 (mt) cc_final: 0.9245 (mp) REVERT: P 23 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.7750 (ttp80) REVERT: G 4 LYS cc_start: 0.5900 (OUTLIER) cc_final: 0.4914 (mmtm) REVERT: G 77 LYS cc_start: 0.9442 (tppt) cc_final: 0.9152 (tppt) REVERT: I 11 TYR cc_start: 0.9005 (t80) cc_final: 0.8655 (t80) REVERT: I 28 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8894 (mm-30) REVERT: I 30 TRP cc_start: 0.8640 (p-90) cc_final: 0.7999 (p90) outliers start: 54 outliers final: 38 residues processed: 246 average time/residue: 0.4265 time to fit residues: 165.8523 Evaluate side-chains 251 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 929 LYS Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 975 LYS Chi-restraints excluded: chain B residue 1030 GLU Chi-restraints excluded: chain B residue 1037 HIS Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain I residue 9 CYS Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 92 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 210 optimal weight: 0.1980 chunk 309 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 166 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 157 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN F 110 GLN H 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.062734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.042660 restraints weight = 99913.750| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 3.81 r_work: 0.2547 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28020 Z= 0.101 Angle : 0.639 45.252 37829 Z= 0.286 Chirality : 0.043 0.188 4195 Planarity : 0.004 0.051 4896 Dihedral : 3.999 35.042 3797 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.41 % Allowed : 18.02 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 1.08 (0.15), residues: 3402 helix: 1.92 (0.15), residues: 1283 sheet: -0.20 (0.24), residues: 470 loop : 0.13 (0.16), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 175 HIS 0.004 0.001 HIS A 428 PHE 0.038 0.001 PHE A 421 TYR 0.034 0.001 TYR E 134 ARG 0.015 0.000 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 1241) hydrogen bonds : angle 4.48638 ( 3459) metal coordination : bond 0.00470 ( 24) metal coordination : angle 11.08713 ( 33) covalent geometry : bond 0.00229 (27996) covalent geometry : angle 0.54865 (37796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12950.11 seconds wall clock time: 224 minutes 50.58 seconds (13490.58 seconds total)