Starting phenix.real_space_refine on Mon Aug 25 09:17:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2i_17366/08_2025/8p2i_17366.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2i_17366/08_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_17366/08_2025/8p2i_17366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2i_17366/08_2025/8p2i_17366.map" model { file = "/net/cci-nas-00/data/ceres_data/8p2i_17366/08_2025/8p2i_17366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2i_17366/08_2025/8p2i_17366.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.25, per 1000 atoms: 0.23 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: 2.27 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.31 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: 6.93 Time building geometry restraints manager: 3.03 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.390 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.790 ------------------------------------------------------------------------------- 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 : 8.52 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (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 ARG 0.029 0.001 ARG F 25 TYR 0.039 0.001 TYR E 134 PHE 0.029 0.001 PHE A 421 TRP 0.066 0.001 TRP E 175 HIS 0.013 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00273 (27996) covalent geometry : angle 0.62675 (37796) hydrogen bonds : bond 0.18765 ( 1241) hydrogen bonds : angle 7.14876 ( 3459) metal coordination : bond 0.00448 ( 24) metal coordination : angle 5.26854 ( 33) *********************** 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 : 0.919 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: 0.2198 time to fit residues: 69.8721 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 : 1.213 ------------------------------------------------------------------------------- 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 197 optimal weight: 9.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.0770 chunk 298 optimal weight: 9.9990 overall best weight: 4.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 376 GLN ** B 680 ASN ** 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.064074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.043670 restraints weight = 97178.413| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.80 r_work: 0.2530 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 28020 Z= 0.198 Angle : 0.600 16.168 37829 Z= 0.307 Chirality : 0.045 0.195 4195 Planarity : 0.005 0.046 4896 Dihedral : 4.286 30.945 3800 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.71 % Allowed : 14.89 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.15), residues: 3402 helix: 1.48 (0.15), residues: 1294 sheet: -0.17 (0.24), residues: 471 loop : 0.09 (0.16), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 377 TYR 0.038 0.002 TYR E 134 PHE 0.028 0.001 PHE A 421 TRP 0.035 0.001 TRP E 175 HIS 0.009 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00459 (27996) covalent geometry : angle 0.58009 (37796) hydrogen bonds : bond 0.04747 ( 1241) hydrogen bonds : angle 5.51166 ( 3459) metal coordination : bond 0.00735 ( 24) metal coordination : angle 5.26943 ( 33) *********************** 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: 51 poor density : 206 time to evaluate : 1.120 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: A 748 MET cc_start: 0.9197 (mtm) cc_final: 0.8952 (mtm) REVERT: B 550 ASP cc_start: 0.8687 (t0) cc_final: 0.8394 (t0) REVERT: B 906 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9040 (tt) REVERT: C 222 HIS cc_start: 0.8454 (t70) cc_final: 0.7975 (t-90) REVERT: C 227 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8533 (tp) REVERT: E 1 MET cc_start: 0.8614 (tpp) cc_final: 0.8381 (tpp) REVERT: E 88 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.7912 (p90) REVERT: H 47 ASP cc_start: 0.9076 (t0) cc_final: 0.8783 (t0) REVERT: H 59 ASP cc_start: 0.8625 (t0) cc_final: 0.8087 (m-30) REVERT: P 16 LYS cc_start: 0.9251 (ttmm) cc_final: 0.8825 (mmmt) REVERT: G 61 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7219 (mmp80) outliers start: 51 outliers final: 23 residues processed: 244 average time/residue: 0.1980 time to fit residues: 74.5236 Evaluate side-chains 219 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 428 HIS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 975 LYS Chi-restraints excluded: chain C residue 117 MET Chi-restraints excluded: chain C residue 202 ARG 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 H residue 46 SER Chi-restraints excluded: chain G residue 8 VAL 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 162 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 272 optimal weight: 50.0000 chunk 188 optimal weight: 6.9990 chunk 301 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 186 optimal weight: 0.0870 chunk 156 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 78 HIS ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN ** B 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 HIS G 12 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.061081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.041257 restraints weight = 102459.569| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.65 r_work: 0.2523 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28020 Z= 0.179 Angle : 0.562 15.629 37829 Z= 0.286 Chirality : 0.044 0.185 4195 Planarity : 0.004 0.048 4896 Dihedral : 4.195 31.198 3797 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.08 % Allowed : 15.03 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.15), residues: 3402 helix: 1.59 (0.15), residues: 1290 sheet: -0.24 (0.24), residues: 461 loop : 0.06 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 166 TYR 0.028 0.001 TYR E 134 PHE 0.017 0.001 PHE A 421 TRP 0.023 0.001 TRP I 30 HIS 0.009 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00415 (27996) covalent geometry : angle 0.54397 (37796) hydrogen bonds : bond 0.04367 ( 1241) hydrogen bonds : angle 5.17572 ( 3459) metal coordination : bond 0.00666 ( 24) metal coordination : angle 4.80167 ( 33) *********************** 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 275 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8799 (mmp) cc_final: 0.8594 (mmp) REVERT: A 855 ASP cc_start: 0.9203 (OUTLIER) cc_final: 0.8966 (p0) REVERT: B 550 ASP cc_start: 0.8711 (t0) cc_final: 0.8446 (t0) REVERT: B 906 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9103 (tt) REVERT: B 948 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: C 117 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8339 (mtp) REVERT: C 222 HIS cc_start: 0.8656 (t70) cc_final: 0.8205 (t-90) REVERT: C 227 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8534 (tp) REVERT: C 247 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: D 259 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8321 (mp) REVERT: E 1 MET cc_start: 0.8613 (tpp) cc_final: 0.8325 (tpp) REVERT: E 114 MET cc_start: 0.6368 (mtm) cc_final: 0.5831 (mmt) REVERT: E 145 ARG cc_start: 0.7721 (mmm-85) cc_final: 0.7455 (mtt-85) REVERT: E 165 MET cc_start: 0.7165 (tmm) cc_final: 0.6927 (tmm) REVERT: E 167 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8551 (tm-30) REVERT: F 75 ASP cc_start: 0.8409 (p0) cc_final: 0.8048 (p0) REVERT: H 25 GLU cc_start: 0.8995 (mp0) cc_final: 0.7964 (mp0) REVERT: H 47 ASP cc_start: 0.9090 (t0) cc_final: 0.8686 (t0) REVERT: H 56 LYS cc_start: 0.9188 (mmtm) cc_final: 0.8744 (mmtm) REVERT: H 59 ASP cc_start: 0.8704 (t0) cc_final: 0.8159 (m-30) REVERT: P 23 ARG cc_start: 0.7391 (ttp80) cc_final: 0.7038 (ttp80) REVERT: G 4 LYS cc_start: 0.5665 (OUTLIER) cc_final: 0.4848 (mmtm) outliers start: 62 outliers final: 23 residues processed: 264 average time/residue: 0.2089 time to fit residues: 84.2974 Evaluate side-chains 227 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 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 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 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 F residue 13 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain H residue 46 SER 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 I residue 12 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 72 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 176 optimal weight: 10.0000 chunk 327 optimal weight: 0.2980 chunk 163 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 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** F 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.061014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.041222 restraints weight = 102184.193| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.61 r_work: 0.2527 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28020 Z= 0.152 Angle : 0.545 14.306 37829 Z= 0.277 Chirality : 0.044 0.200 4195 Planarity : 0.004 0.050 4896 Dihedral : 4.127 31.069 3797 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.08 % Allowed : 15.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.15), residues: 3402 helix: 1.64 (0.15), residues: 1291 sheet: -0.28 (0.24), residues: 453 loop : 0.05 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 25 TYR 0.031 0.001 TYR E 88 PHE 0.019 0.001 PHE A 421 TRP 0.021 0.001 TRP I 30 HIS 0.005 0.001 HIS E 109 Details of bonding type rmsd covalent geometry : bond 0.00355 (27996) covalent geometry : angle 0.52921 (37796) hydrogen bonds : bond 0.04050 ( 1241) hydrogen bonds : angle 4.96323 ( 3459) metal coordination : bond 0.00576 ( 24) metal coordination : angle 4.44872 ( 33) *********************** 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 270 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 208 time to evaluate : 1.120 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 142 MET cc_start: 0.8935 (mmp) cc_final: 0.8699 (mmp) REVERT: B 78 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.8231 (p90) REVERT: B 550 ASP cc_start: 0.8717 (t0) cc_final: 0.8486 (t0) REVERT: B 906 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9070 (tt) REVERT: B 948 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: B 1030 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.8876 (mp0) REVERT: C 60 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8547 (mt-10) REVERT: C 117 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8189 (mtp) REVERT: C 222 HIS cc_start: 0.8658 (t70) cc_final: 0.8276 (t-90) REVERT: C 227 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8496 (tp) REVERT: C 247 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7944 (tm-30) REVERT: E 1 MET cc_start: 0.8673 (tpp) cc_final: 0.8074 (tpp) REVERT: E 2 TYR cc_start: 0.8536 (m-10) cc_final: 0.8193 (m-10) REVERT: E 3 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8354 (ptpt) REVERT: E 109 HIS cc_start: 0.8172 (t70) cc_final: 0.7856 (t-90) REVERT: E 114 MET cc_start: 0.6993 (mtm) cc_final: 0.6757 (mmt) REVERT: E 134 TYR cc_start: 0.5193 (t80) cc_final: 0.4968 (t80) REVERT: E 149 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7760 (mt) REVERT: F 73 MET cc_start: 0.7066 (tpp) cc_final: 0.6838 (tpp) REVERT: F 75 ASP cc_start: 0.8247 (p0) cc_final: 0.7919 (p0) REVERT: H 25 GLU cc_start: 0.8569 (mp0) cc_final: 0.8358 (mp0) REVERT: H 47 ASP cc_start: 0.9065 (t0) cc_final: 0.8546 (t0) REVERT: H 59 ASP cc_start: 0.8784 (t0) cc_final: 0.8383 (t0) REVERT: P 23 ARG cc_start: 0.7430 (ttp80) cc_final: 0.6918 (ttp80) REVERT: I 11 TYR cc_start: 0.8945 (t80) cc_final: 0.8628 (t80) outliers start: 62 outliers final: 32 residues processed: 258 average time/residue: 0.1824 time to fit residues: 72.7964 Evaluate side-chains 236 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 897 LEU Chi-restraints excluded: chain B residue 78 HIS 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 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 292 SER Chi-restraints excluded: chain C residue 343 THR 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 82 HIS 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 F residue 13 THR Chi-restraints excluded: chain F residue 20 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 N residue 25 VAL 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 58 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 315 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS B 78 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.060849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.040787 restraints weight = 101644.890| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.73 r_work: 0.2487 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1660 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= 0.249 Angle : 0.593 14.649 37829 Z= 0.302 Chirality : 0.045 0.162 4195 Planarity : 0.004 0.052 4896 Dihedral : 4.249 31.940 3797 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.29 % Allowed : 15.80 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.15), residues: 3402 helix: 1.59 (0.15), residues: 1286 sheet: -0.39 (0.24), residues: 449 loop : -0.04 (0.16), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 25 TYR 0.042 0.001 TYR E 88 PHE 0.016 0.001 PHE A 421 TRP 0.020 0.001 TRP I 30 HIS 0.023 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00586 (27996) covalent geometry : angle 0.57863 (37796) hydrogen bonds : bond 0.04341 ( 1241) hydrogen bonds : angle 5.01577 ( 3459) metal coordination : bond 0.00829 ( 24) metal coordination : angle 4.50014 ( 33) *********************** 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 271 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 203 time to evaluate : 1.039 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 142 MET cc_start: 0.8997 (mmp) cc_final: 0.8723 (mmp) REVERT: A 421 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8889 (t80) REVERT: A 464 MET cc_start: 0.9199 (mtm) cc_final: 0.8811 (mtp) REVERT: A 855 ASP cc_start: 0.9236 (OUTLIER) cc_final: 0.8972 (p0) REVERT: B 340 TYR cc_start: 0.9396 (OUTLIER) cc_final: 0.8660 (t80) REVERT: B 948 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8043 (tm-30) REVERT: C 60 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8640 (mt-10) REVERT: C 222 HIS cc_start: 0.8663 (t70) cc_final: 0.8306 (t-90) REVERT: C 227 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8466 (tp) REVERT: C 247 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: E 1 MET cc_start: 0.8768 (tpp) cc_final: 0.8117 (tpp) REVERT: E 3 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8354 (ptpt) REVERT: E 114 MET cc_start: 0.6973 (mtm) cc_final: 0.6594 (mmm) REVERT: E 134 TYR cc_start: 0.5178 (OUTLIER) cc_final: 0.4891 (t80) REVERT: E 149 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7719 (mt) REVERT: F 33 ILE cc_start: 0.8724 (mm) cc_final: 0.8496 (tp) REVERT: F 75 ASP cc_start: 0.8334 (p0) cc_final: 0.7960 (p0) REVERT: H 23 GLU cc_start: 0.8271 (tp30) cc_final: 0.7808 (tp30) REVERT: H 24 GLU cc_start: 0.7746 (pm20) cc_final: 0.7502 (pm20) REVERT: H 47 ASP cc_start: 0.9054 (t0) cc_final: 0.8524 (t0) REVERT: H 59 ASP cc_start: 0.8851 (t0) cc_final: 0.8428 (t0) REVERT: P 23 ARG cc_start: 0.7769 (ttp80) cc_final: 0.6947 (ttp80) REVERT: G 4 LYS cc_start: 0.5711 (OUTLIER) cc_final: 0.4783 (mmtm) REVERT: G 61 ARG cc_start: 0.8275 (tpp80) cc_final: 0.7856 (tpp80) REVERT: I 11 TYR cc_start: 0.9073 (t80) cc_final: 0.8605 (t80) outliers start: 68 outliers final: 37 residues processed: 257 average time/residue: 0.1926 time to fit residues: 77.1809 Evaluate side-chains 241 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 193 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 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 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 82 HIS Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 149 ILE 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 60 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 129 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 228 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 211 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.060805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.040949 restraints weight = 102242.759| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.63 r_work: 0.2511 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28020 Z= 0.162 Angle : 0.548 13.513 37829 Z= 0.278 Chirality : 0.044 0.167 4195 Planarity : 0.004 0.052 4896 Dihedral : 4.179 32.342 3797 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.35 % Allowed : 16.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.15), residues: 3402 helix: 1.68 (0.15), residues: 1290 sheet: -0.41 (0.24), residues: 454 loop : -0.01 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 25 TYR 0.024 0.001 TYR I 56 PHE 0.029 0.001 PHE G 76 TRP 0.015 0.001 TRP I 30 HIS 0.005 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00379 (27996) covalent geometry : angle 0.53358 (37796) hydrogen bonds : bond 0.03960 ( 1241) hydrogen bonds : angle 4.83887 ( 3459) metal coordination : bond 0.00561 ( 24) metal coordination : angle 4.19660 ( 33) *********************** 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 275 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 205 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8996 (mmp) cc_final: 0.8777 (mmp) REVERT: A 421 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.9060 (t80) REVERT: A 855 ASP cc_start: 0.9222 (OUTLIER) cc_final: 0.8960 (p0) REVERT: B 303 MET cc_start: 0.9574 (mmt) cc_final: 0.9352 (mmm) REVERT: B 340 TYR cc_start: 0.9381 (OUTLIER) cc_final: 0.8613 (t80) REVERT: B 906 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9143 (tt) REVERT: B 948 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7984 (tm-30) REVERT: B 1030 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.8853 (mp0) REVERT: C 60 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8632 (mt-10) REVERT: C 117 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8210 (mtp) REVERT: C 222 HIS cc_start: 0.8656 (t70) cc_final: 0.8316 (t-90) REVERT: C 227 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8460 (tp) REVERT: C 247 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: E 1 MET cc_start: 0.8707 (tpp) cc_final: 0.8067 (tpp) REVERT: E 3 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8355 (ptpt) REVERT: E 88 TYR cc_start: 0.8344 (p90) cc_final: 0.8034 (p90) REVERT: E 145 ARG cc_start: 0.8339 (mtp85) cc_final: 0.8020 (mtt-85) REVERT: E 166 ARG cc_start: 0.8939 (ptp90) cc_final: 0.8727 (ptp90) REVERT: E 167 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: F 33 ILE cc_start: 0.8754 (mm) cc_final: 0.8512 (tp) REVERT: F 42 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8260 (ptt-90) REVERT: F 73 MET cc_start: 0.7194 (tpp) cc_final: 0.6531 (tpp) REVERT: F 75 ASP cc_start: 0.8247 (p0) cc_final: 0.7945 (p0) REVERT: F 85 MET cc_start: 0.5076 (tpt) cc_final: 0.4558 (tmm) REVERT: H 47 ASP cc_start: 0.9059 (t0) cc_final: 0.8504 (t0) REVERT: H 59 ASP cc_start: 0.8856 (t0) cc_final: 0.8425 (t0) REVERT: P 23 ARG cc_start: 0.7679 (ttp80) cc_final: 0.6985 (ttp80) REVERT: G 4 LYS cc_start: 0.5625 (OUTLIER) cc_final: 0.4691 (mmtm) REVERT: G 61 ARG cc_start: 0.8196 (tpp80) cc_final: 0.7673 (tpp80) REVERT: I 11 TYR cc_start: 0.9010 (t80) cc_final: 0.8659 (t80) outliers start: 70 outliers final: 34 residues processed: 259 average time/residue: 0.1850 time to fit residues: 75.2137 Evaluate side-chains 243 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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 343 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 7 GLN 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 167 GLN 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 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 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 331 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 288 optimal weight: 50.0000 chunk 273 optimal weight: 6.9990 chunk 316 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 321 optimal weight: 20.0000 chunk 225 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN ** B 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.061209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.040994 restraints weight = 100344.292| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 3.79 r_work: 0.2463 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 28020 Z= 0.303 Angle : 0.731 55.708 37829 Z= 0.333 Chirality : 0.046 0.161 4195 Planarity : 0.005 0.084 4896 Dihedral : 4.386 32.963 3797 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.76 % Allowed : 16.37 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.15), residues: 3402 helix: 1.52 (0.15), residues: 1286 sheet: -0.50 (0.23), residues: 448 loop : -0.12 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 25 TYR 0.025 0.002 TYR I 56 PHE 0.016 0.002 PHE A 421 TRP 0.013 0.002 TRP E 175 HIS 0.008 0.001 HIS N 52 Details of bonding type rmsd covalent geometry : bond 0.00710 (27996) covalent geometry : angle 0.62922 (37796) hydrogen bonds : bond 0.04505 ( 1241) hydrogen bonds : angle 5.03518 ( 3459) metal coordination : bond 0.00956 ( 24) metal coordination : angle 12.64148 ( 33) *********************** 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 277 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 195 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.9152 (t80) REVERT: A 855 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8946 (p0) REVERT: B 340 TYR cc_start: 0.9475 (OUTLIER) cc_final: 0.8695 (t80) REVERT: B 948 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8066 (tm-30) REVERT: C 60 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8697 (mt-10) REVERT: C 222 HIS cc_start: 0.8639 (t70) cc_final: 0.8274 (t-90) REVERT: C 227 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8454 (tp) REVERT: C 234 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8272 (mp) REVERT: C 247 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: E 1 MET cc_start: 0.8834 (tpp) cc_final: 0.8223 (tpp) REVERT: E 3 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8354 (ptpt) REVERT: E 114 MET cc_start: 0.5344 (mmm) cc_final: 0.4478 (mmm) REVERT: F 33 ILE cc_start: 0.8731 (mm) cc_final: 0.8496 (tp) REVERT: F 73 MET cc_start: 0.7116 (tpp) cc_final: 0.6523 (tpp) REVERT: F 75 ASP cc_start: 0.8279 (p0) cc_final: 0.8074 (p0) REVERT: F 85 MET cc_start: 0.5032 (tpt) cc_final: 0.4550 (tmm) REVERT: H 23 GLU cc_start: 0.8736 (tp30) cc_final: 0.8458 (tp30) REVERT: H 47 ASP cc_start: 0.9048 (t0) cc_final: 0.8630 (t0) REVERT: H 59 ASP cc_start: 0.8856 (t0) cc_final: 0.8402 (t0) REVERT: P 23 ARG cc_start: 0.7690 (ttp80) cc_final: 0.7056 (ttp80) REVERT: G 4 LYS cc_start: 0.5864 (OUTLIER) cc_final: 0.4800 (mmtm) REVERT: G 61 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7613 (tpp80) REVERT: G 77 LYS cc_start: 0.9472 (tppt) cc_final: 0.9194 (tppt) REVERT: I 11 TYR cc_start: 0.9074 (t80) cc_final: 0.8818 (t80) outliers start: 82 outliers final: 45 residues processed: 260 average time/residue: 0.2083 time to fit residues: 84.3635 Evaluate side-chains 246 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 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 497 GLU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 524 VAL 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 234 ILE 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 D residue 7 GLN Chi-restraints excluded: chain D residue 59 GLU 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 F residue 54 LEU 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 33 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 20 VAL 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 93 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 322 optimal weight: 9.9990 chunk 289 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 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 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.062698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.042218 restraints weight = 98316.214| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 3.87 r_work: 0.2478 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 28020 Z= 0.243 Angle : 0.701 52.864 37829 Z= 0.317 Chirality : 0.045 0.166 4195 Planarity : 0.004 0.053 4896 Dihedral : 4.366 33.248 3797 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.32 % Allowed : 16.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.15), residues: 3402 helix: 1.49 (0.15), residues: 1293 sheet: -0.43 (0.24), residues: 433 loop : -0.17 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 25 TYR 0.018 0.001 TYR B 340 PHE 0.031 0.002 PHE C 215 TRP 0.013 0.001 TRP E 175 HIS 0.007 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00572 (27996) covalent geometry : angle 0.59780 (37796) hydrogen bonds : bond 0.04308 ( 1241) hydrogen bonds : angle 4.95298 ( 3459) metal coordination : bond 0.00833 ( 24) metal coordination : angle 12.41075 ( 33) *********************** 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 267 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 198 time to evaluate : 1.183 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 855 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8948 (p0) REVERT: B 340 TYR cc_start: 0.9445 (OUTLIER) cc_final: 0.8651 (t80) REVERT: B 948 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: C 60 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8659 (mt-10) REVERT: C 222 HIS cc_start: 0.8578 (t70) cc_final: 0.8226 (t-90) REVERT: C 227 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8440 (tp) REVERT: C 234 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8214 (mp) REVERT: C 247 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8030 (tp30) REVERT: E 1 MET cc_start: 0.8777 (tpp) cc_final: 0.8178 (tpp) REVERT: E 3 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8354 (ptpt) REVERT: E 165 MET cc_start: 0.5514 (tpt) cc_final: 0.5163 (tpt) REVERT: F 33 ILE cc_start: 0.8747 (mm) cc_final: 0.8512 (tp) REVERT: F 75 ASP cc_start: 0.8284 (p0) cc_final: 0.7992 (p0) REVERT: F 85 MET cc_start: 0.5230 (tpt) cc_final: 0.4999 (tmm) REVERT: H 47 ASP cc_start: 0.9039 (t0) cc_final: 0.8610 (t0) REVERT: H 59 ASP cc_start: 0.8834 (t0) cc_final: 0.8416 (t0) REVERT: P 23 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7050 (ttp80) REVERT: G 4 LYS cc_start: 0.5828 (OUTLIER) cc_final: 0.4792 (mmtm) REVERT: G 61 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7432 (tpp80) REVERT: G 77 LYS cc_start: 0.9474 (tppt) cc_final: 0.9199 (tppt) REVERT: I 11 TYR cc_start: 0.9016 (t80) cc_final: 0.8716 (t80) outliers start: 69 outliers final: 47 residues processed: 252 average time/residue: 0.2076 time to fit residues: 81.7337 Evaluate side-chains 248 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 844 ILE 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 497 GLU Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 524 VAL 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 234 ILE 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 D residue 7 GLN Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 259 LEU 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 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 9 CYS Chi-restraints excluded: chain I residue 12 ILE Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 34 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 83 optimal weight: 9.9990 chunk 245 optimal weight: 0.7980 chunk 317 optimal weight: 10.0000 chunk 269 optimal weight: 6.9990 chunk 179 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 194 optimal weight: 0.3980 chunk 292 optimal weight: 9.9990 chunk 170 optimal weight: 0.0050 chunk 250 optimal weight: 8.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- 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** E 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.063064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.042733 restraints weight = 98199.664| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.84 r_work: 0.2519 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28020 Z= 0.109 Angle : 0.657 50.277 37829 Z= 0.291 Chirality : 0.044 0.169 4195 Planarity : 0.004 0.053 4896 Dihedral : 4.132 33.399 3797 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.61 % Allowed : 17.85 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.15), residues: 3402 helix: 1.69 (0.15), residues: 1295 sheet: -0.30 (0.24), residues: 449 loop : -0.03 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 25 TYR 0.019 0.001 TYR E 134 PHE 0.020 0.001 PHE A 421 TRP 0.016 0.001 TRP E 175 HIS 0.005 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00250 (27996) covalent geometry : angle 0.55211 (37796) hydrogen bonds : bond 0.03634 ( 1241) hydrogen bonds : angle 4.70026 ( 3459) metal coordination : bond 0.00446 ( 24) metal coordination : angle 12.08480 ( 33) *********************** 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: 48 poor density : 211 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 855 ASP cc_start: 0.9248 (OUTLIER) cc_final: 0.8961 (p0) REVERT: B 340 TYR cc_start: 0.9377 (OUTLIER) cc_final: 0.8647 (t80) REVERT: B 948 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: C 60 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8575 (mt-10) REVERT: C 117 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8238 (mtp) REVERT: C 222 HIS cc_start: 0.8558 (t70) cc_final: 0.8214 (t-90) REVERT: C 227 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8478 (tp) REVERT: C 247 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7845 (mm-30) REVERT: E 114 MET cc_start: 0.5190 (mmm) cc_final: 0.4656 (mmm) REVERT: F 33 ILE cc_start: 0.8795 (mm) cc_final: 0.8560 (tp) REVERT: F 75 ASP cc_start: 0.8151 (p0) cc_final: 0.7930 (p0) REVERT: F 85 MET cc_start: 0.5011 (tpt) cc_final: 0.4740 (tmm) REVERT: H 47 ASP cc_start: 0.9072 (t0) cc_final: 0.8489 (t0) REVERT: H 59 ASP cc_start: 0.8888 (t0) cc_final: 0.8503 (t0) REVERT: P 23 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7005 (ttp80) REVERT: G 61 ARG cc_start: 0.8163 (tpp80) cc_final: 0.7633 (tpp80) REVERT: G 77 LYS cc_start: 0.9468 (tppt) cc_final: 0.9184 (tppt) REVERT: I 11 TYR cc_start: 0.8986 (t80) cc_final: 0.8679 (t80) outliers start: 48 outliers final: 28 residues processed: 250 average time/residue: 0.2061 time to fit residues: 80.5464 Evaluate side-chains 236 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 844 ILE 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 929 LYS Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 975 LYS 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 C residue 344 VAL Chi-restraints excluded: chain D residue 253 ILE 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 L residue 41 THR Chi-restraints excluded: chain N residue 25 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 183 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 303 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** E 82 HIS ** E 112 GLN ** 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 = 0.3288 r_free = 0.3288 target = 0.061654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.041494 restraints weight = 100398.762| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 3.71 r_work: 0.2508 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28020 Z= 0.161 Angle : 0.668 48.959 37829 Z= 0.299 Chirality : 0.044 0.193 4195 Planarity : 0.004 0.052 4896 Dihedral : 4.139 33.855 3797 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.28 % Allowed : 18.25 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.15), residues: 3402 helix: 1.70 (0.15), residues: 1295 sheet: -0.31 (0.24), residues: 437 loop : -0.03 (0.16), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 25 TYR 0.022 0.001 TYR E 134 PHE 0.034 0.001 PHE G 76 TRP 0.017 0.001 TRP E 175 HIS 0.006 0.001 HIS N 52 Details of bonding type rmsd covalent geometry : bond 0.00383 (27996) covalent geometry : angle 0.56730 (37796) hydrogen bonds : bond 0.03789 ( 1241) hydrogen bonds : angle 4.71707 ( 3459) metal coordination : bond 0.00541 ( 24) metal coordination : angle 11.95200 ( 33) ********************** 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 241 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 855 ASP cc_start: 0.9227 (OUTLIER) cc_final: 0.8956 (p0) REVERT: B 340 TYR cc_start: 0.9370 (OUTLIER) cc_final: 0.8685 (t80) REVERT: B 948 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: C 60 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8652 (mt-10) REVERT: C 117 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8251 (mtp) REVERT: C 222 HIS cc_start: 0.8551 (t70) cc_final: 0.8238 (t-90) REVERT: C 227 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8499 (tp) REVERT: C 247 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7923 (mm-30) REVERT: E 114 MET cc_start: 0.4996 (mmm) cc_final: 0.4694 (mmm) REVERT: E 145 ARG cc_start: 0.8274 (mtp85) cc_final: 0.7901 (mtp85) REVERT: E 166 ARG cc_start: 0.8933 (ptp90) cc_final: 0.8662 (ptp90) REVERT: E 167 GLN cc_start: 0.8743 (mm110) cc_final: 0.7984 (tm-30) REVERT: F 33 ILE cc_start: 0.8835 (mm) cc_final: 0.8597 (tp) REVERT: F 75 ASP cc_start: 0.8206 (p0) cc_final: 0.7973 (p0) REVERT: F 85 MET cc_start: 0.5026 (tpt) cc_final: 0.4753 (tmm) REVERT: H 47 ASP cc_start: 0.9016 (t0) cc_final: 0.8584 (t0) REVERT: H 59 ASP cc_start: 0.8856 (t0) cc_final: 0.8483 (t0) REVERT: P 23 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7127 (ttp80) REVERT: G 61 ARG cc_start: 0.8145 (tpp80) cc_final: 0.7648 (tpp80) REVERT: G 77 LYS cc_start: 0.9463 (tppt) cc_final: 0.9204 (tppt) REVERT: G 84 GLU cc_start: 0.9043 (pm20) cc_final: 0.8700 (mp0) REVERT: I 11 TYR cc_start: 0.8986 (t80) cc_final: 0.8703 (t80) REVERT: I 28 GLU cc_start: 0.8941 (tp30) cc_final: 0.8491 (mm-30) REVERT: I 30 TRP cc_start: 0.8534 (p-90) cc_final: 0.7977 (p90) outliers start: 38 outliers final: 30 residues processed: 234 average time/residue: 0.2089 time to fit residues: 76.6851 Evaluate side-chains 238 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 844 ILE 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 929 LYS Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 975 LYS 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 343 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 253 ILE 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 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 22 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain I residue 12 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 3 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 331 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.061660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.041727 restraints weight = 99538.868| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 3.68 r_work: 0.2512 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28020 Z= 0.138 Angle : 0.651 47.263 37829 Z= 0.291 Chirality : 0.044 0.191 4195 Planarity : 0.004 0.052 4896 Dihedral : 4.077 34.410 3797 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.48 % Allowed : 18.15 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.15), residues: 3402 helix: 1.80 (0.15), residues: 1283 sheet: -0.32 (0.24), residues: 455 loop : 0.03 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 25 TYR 0.021 0.001 TYR E 134 PHE 0.034 0.001 PHE C 215 TRP 0.016 0.001 TRP E 175 HIS 0.006 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00326 (27996) covalent geometry : angle 0.55204 (37796) hydrogen bonds : bond 0.03588 ( 1241) hydrogen bonds : angle 4.63847 ( 3459) metal coordination : bond 0.00470 ( 24) metal coordination : angle 11.68372 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6452.85 seconds wall clock time: 111 minutes 38.36 seconds (6698.36 seconds total)