Starting phenix.real_space_refine on Mon Aug 25 06:55:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rbo_19033/08_2025/8rbo_19033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rbo_19033/08_2025/8rbo_19033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rbo_19033/08_2025/8rbo_19033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rbo_19033/08_2025/8rbo_19033.map" model { file = "/net/cci-nas-00/data/ceres_data/8rbo_19033/08_2025/8rbo_19033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rbo_19033/08_2025/8rbo_19033.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 5 6.06 5 Mg 1 5.21 5 S 112 5.16 5 C 16774 2.51 5 N 4583 2.21 5 O 4893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s 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: 26368 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 7197 Classifications: {'peptide': 901} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 848} Chain: "B" Number of atoms: 8803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8803 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} 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: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 432 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 6, 'TRANS': 49} 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 434 SG CYS A 57 95.712 90.655 55.603 1.00 0.73 S ATOM 456 SG CYS A 60 93.380 92.863 57.552 1.00 30.00 S ATOM 499 SG CYS A 67 92.745 89.071 57.394 1.00 0.77 S ATOM 736 SG CYS A 97 61.285 86.157 20.467 1.00 0.80 S ATOM 762 SG CYS A 100 61.364 89.892 20.165 1.00 0.73 S ATOM 1138 SG CYS A 144 58.017 88.094 19.818 1.00 0.72 S ATOM 1161 SG CYS A 147 60.602 87.732 17.091 1.00 0.78 S ATOM 15532 SG CYS B1059 79.702 101.951 50.261 1.00 0.85 S ATOM 15555 SG CYS B1062 78.844 100.778 46.785 1.00 30.00 S ATOM 15685 SG CYS B1077 82.339 100.209 48.605 1.00 0.84 S ATOM 15705 SG CYS B1080 80.976 103.304 46.494 1.00 0.68 S ATOM 25480 SG CYS N 7 74.542 47.527 113.120 1.00 0.59 S ATOM 25504 SG CYS N 10 74.130 48.598 116.785 1.00 0.59 S ATOM 25784 SG CYS N 44 71.065 47.459 114.609 1.00 0.60 S ATOM 25790 SG CYS N 45 73.576 45.187 116.170 1.00 0.60 S ATOM 26026 SG CYS P 8 107.456 40.766 84.122 1.00 86.83 S ATOM 26052 SG CYS P 11 108.976 37.965 85.953 1.00 84.70 S ATOM 26181 SG CYS P 27 110.951 39.773 83.090 1.00 79.74 S ATOM 26206 SG CYS P 30 108.039 37.481 82.285 1.00 30.00 S Time building chain proxies: 4.61, per 1000 atoms: 0.17 Number of scatterers: 26368 At special positions: 0 Unit cell: (133.584, 168.432, 154.88, 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 5 29.99 S 112 16.00 Mg 1 11.99 O 4893 8.00 N 4583 7.00 C 16774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 829.8 milliseconds Enol-peptide restraints added in 476.8 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 57 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 60 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 67 " pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 97 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 100 " 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 B1059 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " 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 : 27 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6108 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 41 sheets defined 43.0% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 106 through 119 Processing helix chain 'A' and resid 123 through 141 removed outlier: 3.558A pdb=" N PHE A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 179 through 189 removed outlier: 3.517A pdb=" N LYS A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 206 through 209 Processing helix chain 'A' and resid 236 through 259 Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.631A pdb=" N ILE A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 344 through 350 removed outlier: 3.503A pdb=" N GLU A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.606A pdb=" N GLY A 371 " --> pdb=" O MET A 367 " (cutoff:3.500A) 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: 3.814A 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: 3.955A 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 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 576 through 590 removed outlier: 3.804A pdb=" N CYS A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 Processing helix chain 'A' and resid 620 through 625 removed outlier: 4.134A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 640 through 663 removed outlier: 3.890A pdb=" N LYS A 653 " --> pdb=" O ASP A 649 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.871A pdb=" N GLU A 671 " --> pdb=" O ILE A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 701 Processing helix chain 'A' and resid 711 through 738 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 756 through 765 removed outlier: 3.634A 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 847 removed outlier: 3.901A pdb=" N GLU A 824 " --> pdb=" O MET A 820 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 887 through 901 Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.794A pdb=" N SER B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 51 removed outlier: 3.901A pdb=" N SER B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU B 43 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.537A pdb=" N ILE B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) 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: 3.861A pdb=" N LEU B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) removed outlier: 3.824A 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 347 through 378 removed outlier: 3.582A pdb=" N GLN B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 removed outlier: 4.351A pdb=" N ASN B 386 " --> pdb=" O TYR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 394 Processing helix chain 'B' and resid 397 through 411 removed outlier: 3.512A 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: 3.734A pdb=" N ASP B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 460 removed outlier: 3.580A pdb=" N TRP B 460 " --> pdb=" O GLY B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 503 removed outlier: 3.637A pdb=" N ILE B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 546 Processing helix chain 'B' and resid 587 through 596 Processing helix chain 'B' and resid 600 through 607 Processing helix chain 'B' and resid 616 through 621 Processing helix chain 'B' and resid 626 through 630 removed outlier: 3.680A pdb=" N VAL B 630 " --> pdb=" O PRO B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 645 removed outlier: 3.989A pdb=" N LEU B 645 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 652 removed outlier: 3.615A pdb=" N VAL B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.667A pdb=" N ASN B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 670 Processing helix chain 'B' and resid 702 through 708 removed outlier: 4.222A pdb=" N LYS B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.768A 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 739 through 744 Processing helix chain 'B' and resid 891 through 895 Processing helix chain 'B' and resid 909 through 913 removed outlier: 3.543A pdb=" N ILE B 913 " --> pdb=" O PRO B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 935 removed outlier: 3.963A pdb=" N LEU B 922 " --> pdb=" O THR B 918 " (cutoff:3.500A) removed outlier: 3.575A 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 1093 through 1105 removed outlier: 3.584A pdb=" N MET B1105 " --> pdb=" O GLU B1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 18 through 36 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 98 through 108 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 173 removed outlier: 4.405A 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: 3.833A pdb=" N LYS C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 222 removed outlier: 3.687A pdb=" N HIS C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.865A pdb=" N LEU C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 277 Processing helix chain 'C' and resid 278 through 298 removed outlier: 3.596A pdb=" N ASN C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 removed outlier: 4.158A 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 341 removed outlier: 3.535A pdb=" N PHE C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 361 through 369 removed outlier: 3.665A pdb=" N ASN C 365 " --> pdb=" O GLY C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.536A 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: 3.616A pdb=" N HIS D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE D 68 " --> pdb=" O ARG D 64 " (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: 3.717A pdb=" N LEU D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 209 removed outlier: 4.024A pdb=" N GLU D 207 " --> pdb=" O ASP D 204 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 111 through 114 Processing helix chain 'E' and resid 172 through 189 Processing helix chain 'F' and resid 13 through 16 Processing helix chain 'F' and resid 17 through 31 Processing helix chain 'F' and resid 41 through 51 removed outlier: 3.533A pdb=" N HIS F 47 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE F 51 " --> pdb=" O HIS F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 70 removed outlier: 3.598A pdb=" N PHE F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 85 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 104 through 116 removed outlier: 3.714A pdb=" N MET F 108 " --> pdb=" O THR F 104 " (cutoff:3.500A) removed outlier: 3.606A 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 removed outlier: 3.557A pdb=" N TYR H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.704A 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 47 Processing helix chain 'L' and resid 21 through 33 removed outlier: 4.018A pdb=" N LEU L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 94 removed outlier: 3.542A pdb=" N GLU L 72 " --> pdb=" O GLU L 68 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS L 94 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 16 No H-bonds generated for 'chain 'N' and resid 14 through 16' Processing helix chain 'N' and resid 17 through 28 Processing helix chain 'N' and resid 30 through 38 Processing helix chain 'N' and resid 42 through 51 removed outlier: 3.815A pdb=" N MET N 48 " --> pdb=" O CYS N 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU N 49 " --> pdb=" O CYS N 45 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 1107 through 1114 removed outlier: 5.952A pdb=" N SER B1114 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 5.111A 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: 6.713A pdb=" N THR A 213 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N ARG A 78 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N VAL A 211 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 321 removed outlier: 3.968A pdb=" N LEU B1024 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1000 through 1002 removed outlier: 5.935A pdb=" N VAL A 340 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET A 440 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL A 342 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.899A pdb=" N TYR A 380 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N HIS A 412 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA A 378 " --> pdb=" O HIS A 412 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 517 through 518 Processing sheet with id=AA8, first strand: chain 'A' and resid 566 through 570 removed outlier: 6.808A pdb=" N TYR A 608 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 768 through 769 Processing sheet with id=AB1, first strand: chain 'A' and resid 771 through 772 Processing sheet with id=AB2, first strand: chain 'A' and resid 851 through 852 removed outlier: 4.416A pdb=" N LYS A 851 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 859 " --> pdb=" O LYS A 851 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 52 through 53 removed outlier: 6.441A pdb=" N GLU B 103 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE B 67 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR B 101 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL B 69 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 52 through 53 removed outlier: 6.441A pdb=" N GLU B 103 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE B 67 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR B 101 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL B 69 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY B 121 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 102 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ARG B 119 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET B 104 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU B 117 " --> pdb=" O MET B 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AB6, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB7, first strand: chain 'B' and resid 343 through 346 removed outlier: 6.313A pdb=" N SER B 167 " --> pdb=" O THR B 440 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 177 through 181 Processing sheet with id=AB9, first strand: chain 'B' and resid 485 through 486 Processing sheet with id=AC1, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AC2, first strand: chain 'B' and resid 505 through 506 removed outlier: 5.644A pdb=" N LEU B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU B 521 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY B 527 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 688 through 692 removed outlier: 3.553A pdb=" N SER B 749 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 859 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 850 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS B 861 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 848 " --> pdb=" O LYS B 861 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR B 863 " --> pdb=" O ASP B 846 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 688 through 692 removed outlier: 3.553A pdb=" N SER B 749 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU B 859 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 850 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS B 861 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 848 " --> pdb=" O LYS B 861 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR B 863 " --> pdb=" O ASP B 846 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AC6, first strand: chain 'B' and resid 965 through 966 removed outlier: 7.148A pdb=" N ILE B 735 " --> pdb=" O GLY B 887 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 889 " --> pdb=" O ILE B 735 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE B 737 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N LEU B 906 " --> pdb=" O ASN B 718 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL B 720 " --> pdb=" O LEU B 906 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL B 908 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 722 " --> pdb=" O VAL B 908 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE B 982 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 769 through 770 removed outlier: 3.520A pdb=" N LYS B 769 " --> pdb=" O THR B 811 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 806 through 808 removed outlier: 6.809A pdb=" N VAL B 835 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 897 through 898 Processing sheet with id=AD1, first strand: chain 'B' and resid 1053 through 1059 Processing sheet with id=AD2, first strand: chain 'B' and resid 1067 through 1069 Processing sheet with id=AD3, first strand: chain 'C' and resid 233 through 238 removed outlier: 3.600A pdb=" N THR C 246 " --> pdb=" O MET C 117 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 142 through 143 removed outlier: 3.844A pdb=" N THR C 142 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 148 through 154 removed outlier: 3.876A pdb=" N VAL C 162 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C 199 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 37 through 39 removed outlier: 3.747A pdb=" N THR E 37 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N SER E 47 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N TRP E 77 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU E 49 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N LEU E 75 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL E 51 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP E 73 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP E 53 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL E 71 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLU E 69 " --> pdb=" O LYS E 55 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY E 57 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR E 67 " --> pdb=" O GLY E 57 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY F 8 " --> pdb=" O THR E 6 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS E 8 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS F 6 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 37 through 39 removed outlier: 3.747A pdb=" N THR E 37 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY E 57 " --> pdb=" O MET C 383 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET C 383 " --> pdb=" O GLY E 57 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU C 381 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS C 380 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 5 through 11 removed outlier: 7.009A pdb=" N LYS D 17 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS D 11 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR D 158 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N ASN D 220 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N LYS D 156 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N TYR D 222 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N TYR D 154 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N PHE D 224 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 11.453A pdb=" N PHE D 152 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 107 through 108 removed outlier: 6.522A pdb=" N ARG D 130 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU D 51 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL D 132 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N PHE D 49 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN D 134 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL D 47 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR D 136 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 43 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 99 through 102 removed outlier: 6.690A pdb=" N GLY D 99 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS D 124 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL D 101 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 85 through 93 removed outlier: 5.007A pdb=" N VAL E 92 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE E 161 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS E 109 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY E 162 " --> pdb=" O ILE E 147 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.715A pdb=" N GLU H 17 " --> pdb=" O LYS H 64 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR H 73 " --> pdb=" O ARG H 65 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 2 through 9 removed outlier: 6.787A pdb=" N GLU L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS L 8 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU L 12 " --> pdb=" O LYS L 8 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 5 through 7 1217 hydrogen bonds defined for protein. 3357 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: 5.35 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8806 1.34 - 1.46: 5438 1.46 - 1.58: 12422 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 26864 Sorted by residual: bond pdb=" CA ILE A 165 " pdb=" CB ILE A 165 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.31e-02 5.83e+03 2.15e+00 bond pdb=" CG1 ILE F 95 " pdb=" CD1 ILE F 95 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.42e+00 bond pdb=" N HIS C 86 " pdb=" CA HIS C 86 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.32e+00 bond pdb=" CA ASP A 52 " pdb=" CB ASP A 52 " ideal model delta sigma weight residual 1.525 1.541 -0.016 1.52e-02 4.33e+03 1.11e+00 bond pdb=" CG1 ILE K 41 " pdb=" CD1 ILE K 41 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.09e+00 ... (remaining 26859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 35750 2.00 - 4.00: 455 4.00 - 5.99: 43 5.99 - 7.99: 14 7.99 - 9.99: 4 Bond angle restraints: 36266 Sorted by residual: angle pdb=" N GLY D 151 " pdb=" CA GLY D 151 " pdb=" C GLY D 151 " ideal model delta sigma weight residual 111.56 115.46 -3.90 1.01e+00 9.80e-01 1.49e+01 angle pdb=" CB MET F 108 " pdb=" CG MET F 108 " pdb=" SD MET F 108 " ideal model delta sigma weight residual 112.70 122.69 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA ARG F 50 " pdb=" CB ARG F 50 " pdb=" CG ARG F 50 " ideal model delta sigma weight residual 114.10 120.63 -6.53 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA MET B 483 " pdb=" CB MET B 483 " pdb=" CG MET B 483 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.87e+00 angle pdb=" CA MET E 1 " pdb=" CB MET E 1 " pdb=" CG MET E 1 " ideal model delta sigma weight residual 114.10 120.34 -6.24 2.00e+00 2.50e-01 9.75e+00 ... (remaining 36261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 14154 18.00 - 35.99: 1824 35.99 - 53.99: 441 53.99 - 71.99: 88 71.99 - 89.99: 48 Dihedral angle restraints: 16555 sinusoidal: 7046 harmonic: 9509 Sorted by residual: dihedral pdb=" CA GLN A 848 " pdb=" C GLN A 848 " pdb=" N ASP A 849 " pdb=" CA ASP A 849 " ideal model delta harmonic sigma weight residual -180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PRO E 94 " pdb=" C PRO E 94 " pdb=" N PHE E 95 " pdb=" CA PHE E 95 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASP E 21 " pdb=" CB ASP E 21 " pdb=" CG ASP E 21 " pdb=" OD1 ASP E 21 " ideal model delta sinusoidal sigma weight residual -30.00 -89.24 59.24 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 16552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2564 0.032 - 0.065: 920 0.065 - 0.097: 321 0.097 - 0.130: 205 0.130 - 0.162: 11 Chirality restraints: 4021 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 2.56 0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA MET E 93 " pdb=" N MET E 93 " pdb=" C MET E 93 " pdb=" CB MET E 93 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA GLN F 110 " pdb=" N GLN F 110 " pdb=" C GLN F 110 " pdb=" CB GLN F 110 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 4018 not shown) Planarity restraints: 4702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 93 " 0.046 5.00e-02 4.00e+02 6.90e-02 7.62e+00 pdb=" N PRO E 94 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 94 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 94 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 47 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO H 48 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO H 48 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 48 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 260 " -0.035 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO A 261 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " -0.030 5.00e-02 4.00e+02 ... (remaining 4699 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 332 2.64 - 3.21: 24759 3.21 - 3.77: 41013 3.77 - 4.34: 56219 4.34 - 4.90: 93541 Nonbonded interactions: 215864 Sorted by model distance: nonbonded pdb=" OD1 ASP A 462 " pdb="MG MG A1002 " model vdw 2.081 2.170 nonbonded pdb=" O TYR A 279 " pdb=" OG1 THR A 300 " model vdw 2.168 3.040 nonbonded pdb=" OG SER A 14 " pdb=" OE1 GLN A 16 " model vdw 2.183 3.040 nonbonded pdb=" O ALA C 91 " pdb=" NH1 ARG C 236 " model vdw 2.216 3.120 nonbonded pdb=" OH TYR A 113 " pdb=" OE1 GLU A 133 " model vdw 2.224 3.040 ... (remaining 215859 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.090 Set scattering table: 0.040 Process input model: 24.230 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4315 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 0.047 26884 Z= 0.146 Angle : 0.586 19.023 36293 Z= 0.296 Chirality : 0.043 0.162 4021 Planarity : 0.004 0.069 4702 Dihedral : 17.235 89.986 10447 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.07 % Allowed : 24.73 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.49 (0.15), residues: 3266 helix: 1.49 (0.15), residues: 1246 sheet: -0.64 (0.23), residues: 496 loop : -0.23 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 50 TYR 0.016 0.001 TYR F 38 PHE 0.034 0.001 PHE E 95 TRP 0.015 0.001 TRP A 163 HIS 0.007 0.001 HIS B 911 Details of bonding type rmsd covalent geometry : bond 0.00334 (26864) covalent geometry : angle 0.55805 (36266) hydrogen bonds : bond 0.17905 ( 1191) hydrogen bonds : angle 6.74642 ( 3357) metal coordination : bond 0.00773 ( 20) metal coordination : angle 6.63463 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 759 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 70 PHE cc_start: 0.4648 (p90) cc_final: 0.4274 (p90) outliers start: 2 outliers final: 1 residues processed: 761 average time/residue: 0.1745 time to fit residues: 202.1573 Evaluate side-chains 426 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 425 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 786 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.0370 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN A 424 GLN A 730 ASN A 818 HIS A 867 GLN B 36 ASN B 459 HIS ** B 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN B 690 HIS B 921 GLN B1000 HIS ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN C 365 ASN F 105 GLN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN N 52 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.103218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.080125 restraints weight = 93310.721| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 4.55 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26884 Z= 0.223 Angle : 0.817 16.826 36293 Z= 0.410 Chirality : 0.051 0.293 4021 Planarity : 0.007 0.096 4702 Dihedral : 4.750 41.689 3645 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.01 % Allowed : 24.69 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.01 (0.15), residues: 3266 helix: 0.85 (0.14), residues: 1261 sheet: -0.80 (0.23), residues: 450 loop : -0.33 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 331 TYR 0.036 0.002 TYR E 134 PHE 0.038 0.003 PHE B 273 TRP 0.032 0.003 TRP B1057 HIS 0.008 0.002 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00505 (26864) covalent geometry : angle 0.79647 (36266) hydrogen bonds : bond 0.04748 ( 1191) hydrogen bonds : angle 5.35666 ( 3357) metal coordination : bond 0.00896 ( 20) metal coordination : angle 6.67201 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 470 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LEU cc_start: 0.8429 (mt) cc_final: 0.8079 (mt) REVERT: A 114 MET cc_start: 0.8610 (mtt) cc_final: 0.8403 (mmt) REVERT: A 203 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8681 (mp0) REVERT: A 279 TYR cc_start: 0.8571 (t80) cc_final: 0.8304 (t80) REVERT: A 312 PHE cc_start: 0.7652 (m-80) cc_final: 0.7281 (m-10) REVERT: A 332 ASP cc_start: 0.8674 (t0) cc_final: 0.7992 (t70) REVERT: A 503 ASP cc_start: 0.9097 (m-30) cc_final: 0.8854 (m-30) REVERT: A 758 LEU cc_start: 0.8338 (tp) cc_final: 0.8113 (tp) REVERT: A 820 MET cc_start: 0.6957 (mtp) cc_final: 0.6717 (mtt) REVERT: B 18 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6722 (ttm) REVERT: B 157 ILE cc_start: 0.6761 (mp) cc_final: 0.6418 (mt) REVERT: B 188 ILE cc_start: 0.7101 (mt) cc_final: 0.6680 (tp) REVERT: B 286 TYR cc_start: 0.9260 (t80) cc_final: 0.9007 (t80) REVERT: B 293 TYR cc_start: 0.8436 (t80) cc_final: 0.8172 (t80) REVERT: B 303 MET cc_start: 0.5680 (mmm) cc_final: 0.5444 (mmp) REVERT: B 384 PHE cc_start: 0.3755 (m-80) cc_final: 0.3426 (m-80) REVERT: B 413 TRP cc_start: 0.5798 (t-100) cc_final: 0.4878 (t-100) REVERT: B 500 MET cc_start: 0.7177 (mmm) cc_final: 0.5706 (mmm) REVERT: B 616 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6427 (mt-10) REVERT: B 625 MET cc_start: 0.6298 (ttp) cc_final: 0.5780 (tpp) REVERT: B 665 TYR cc_start: 0.8131 (m-10) cc_final: 0.7889 (m-10) REVERT: B 731 MET cc_start: 0.7906 (mtm) cc_final: 0.7228 (mtm) REVERT: B 750 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8032 (p) REVERT: B 905 ASP cc_start: 0.8937 (m-30) cc_final: 0.8702 (m-30) REVERT: B 948 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8343 (pp20) REVERT: B 968 MET cc_start: 0.8552 (ptp) cc_final: 0.8263 (mtp) REVERT: B 1053 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7086 (mtmm) REVERT: B 1057 TRP cc_start: 0.7682 (m-90) cc_final: 0.7035 (t-100) REVERT: B 1093 TYR cc_start: 0.7921 (m-80) cc_final: 0.7606 (m-80) REVERT: C 147 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7965 (pp) REVERT: E 59 ILE cc_start: 0.8056 (mp) cc_final: 0.7747 (mp) REVERT: E 92 VAL cc_start: 0.5381 (OUTLIER) cc_final: 0.5072 (m) REVERT: E 143 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7364 (ptm160) REVERT: F 21 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7690 (mm) REVERT: F 25 ARG cc_start: 0.8936 (mmm-85) cc_final: 0.8641 (mmm-85) REVERT: F 51 PHE cc_start: 0.0333 (OUTLIER) cc_final: -0.0530 (p90) REVERT: K 26 VAL cc_start: 0.7283 (OUTLIER) cc_final: 0.6972 (t) REVERT: P 35 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7576 (mm) outliers start: 143 outliers final: 52 residues processed: 576 average time/residue: 0.1559 time to fit residues: 142.3585 Evaluate side-chains 414 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 351 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 520 TYR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 786 TYR Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 944 ILE Chi-restraints excluded: chain B residue 948 GLU Chi-restraints excluded: chain B residue 1052 ASP Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 196 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 259 optimal weight: 9.9990 chunk 269 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 255 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 693 ASN A 730 ASN ** A 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 818 HIS B 297 ASN B 298 ASN B 388 HIS B 620 ASN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.086780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061134 restraints weight = 91579.175| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 4.33 r_work: 0.3026 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.8986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 26884 Z= 0.367 Angle : 1.006 21.316 36293 Z= 0.510 Chirality : 0.057 0.387 4021 Planarity : 0.008 0.085 4702 Dihedral : 5.597 47.131 3645 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 6.80 % Allowed : 23.99 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.66 (0.14), residues: 3266 helix: 0.15 (0.14), residues: 1278 sheet: -0.95 (0.24), residues: 450 loop : -0.66 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 573 TYR 0.059 0.004 TYR B 557 PHE 0.046 0.003 PHE B 360 TRP 0.044 0.004 TRP B 628 HIS 0.012 0.002 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00843 (26864) covalent geometry : angle 0.98240 (36266) hydrogen bonds : bond 0.06691 ( 1191) hydrogen bonds : angle 5.89704 ( 3357) metal coordination : bond 0.02738 ( 20) metal coordination : angle 7.96704 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 354 time to evaluate : 0.926 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 37 TYR cc_start: 0.8842 (m-80) cc_final: 0.8598 (m-80) REVERT: A 44 MET cc_start: 0.9230 (mmm) cc_final: 0.8969 (mmm) REVERT: A 71 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.6774 (t80) REVERT: A 114 MET cc_start: 0.8810 (mtt) cc_final: 0.8539 (mmt) REVERT: A 203 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8791 (mp0) REVERT: A 279 TYR cc_start: 0.9093 (t80) cc_final: 0.8848 (t80) REVERT: A 326 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7810 (ttm170) REVERT: A 426 SER cc_start: 0.9354 (m) cc_final: 0.9146 (p) REVERT: A 520 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8458 (ttt-90) REVERT: A 775 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8035 (tptp) REVERT: A 828 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8614 (m-30) REVERT: A 884 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8376 (mttt) REVERT: B 74 PHE cc_start: 0.8305 (t80) cc_final: 0.7892 (t80) REVERT: B 122 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: B 286 TYR cc_start: 0.9220 (t80) cc_final: 0.8966 (t80) REVERT: B 303 MET cc_start: 0.6445 (mmm) cc_final: 0.6097 (mmm) REVERT: B 500 MET cc_start: 0.7920 (mmm) cc_final: 0.7112 (mpp) REVERT: B 552 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6915 (mt) REVERT: B 616 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7924 (tp30) REVERT: B 731 MET cc_start: 0.8876 (mtm) cc_final: 0.8344 (mtm) REVERT: B 786 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.8345 (m-80) REVERT: B 791 GLU cc_start: 0.9204 (mp0) cc_final: 0.8892 (tm-30) REVERT: B 990 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8621 (ttt180) REVERT: B 1057 TRP cc_start: 0.8417 (OUTLIER) cc_final: 0.7860 (m100) REVERT: B 1093 TYR cc_start: 0.8112 (m-80) cc_final: 0.7780 (m-80) REVERT: D 127 GLU cc_start: 0.8608 (tp30) cc_final: 0.8262 (pp20) REVERT: D 187 THR cc_start: 0.6459 (OUTLIER) cc_final: 0.6097 (p) REVERT: E 9 ASP cc_start: 0.7398 (t0) cc_final: 0.5929 (t0) REVERT: E 47 SER cc_start: 0.8011 (p) cc_final: 0.7385 (m) REVERT: F 22 LEU cc_start: 0.9421 (mt) cc_final: 0.9203 (pp) REVERT: F 51 PHE cc_start: 0.3184 (OUTLIER) cc_final: 0.1713 (p90) REVERT: F 85 MET cc_start: 0.2936 (tpt) cc_final: 0.2715 (tpt) REVERT: F 108 MET cc_start: 0.8857 (tmm) cc_final: 0.8516 (tmm) REVERT: H 39 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8286 (mp10) REVERT: H 62 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8192 (tm-30) REVERT: H 63 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8001 (mt) REVERT: H 67 SER cc_start: 0.8989 (m) cc_final: 0.8574 (p) REVERT: L 13 LEU cc_start: 0.8986 (tp) cc_final: 0.8656 (tt) REVERT: N 32 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8305 (tm-30) REVERT: N 33 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8849 (mmtm) REVERT: P 18 ASP cc_start: 0.8559 (t70) cc_final: 0.7972 (t70) outliers start: 194 outliers final: 73 residues processed: 511 average time/residue: 0.1664 time to fit residues: 133.2982 Evaluate side-chains 367 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 280 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 520 ARG Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 775 LYS Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 533 LYS Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain B residue 733 ASP Chi-restraints excluded: chain B residue 786 TYR Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 990 ARG Chi-restraints excluded: chain B residue 1052 ASP Chi-restraints excluded: chain B residue 1057 TRP Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 133 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 315 ASN B 620 ASN C 157 ASN C 370 GLN F 102 GLN F 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.086111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.060097 restraints weight = 89526.695| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 4.45 r_work: 0.3037 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.9359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26884 Z= 0.143 Angle : 0.668 15.598 36293 Z= 0.333 Chirality : 0.046 0.258 4021 Planarity : 0.005 0.054 4702 Dihedral : 4.677 42.821 3645 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.26 % Allowed : 26.30 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: -0.01 (0.15), residues: 3266 helix: 0.88 (0.14), residues: 1286 sheet: -0.83 (0.24), residues: 464 loop : -0.41 (0.17), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 93 TYR 0.023 0.002 TYR B 520 PHE 0.019 0.001 PHE E 173 TRP 0.060 0.002 TRP B1057 HIS 0.017 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00326 (26864) covalent geometry : angle 0.64487 (36266) hydrogen bonds : bond 0.04325 ( 1191) hydrogen bonds : angle 5.13738 ( 3357) metal coordination : bond 0.00734 ( 20) metal coordination : angle 6.44338 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 326 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8886 (m-80) cc_final: 0.8628 (m-80) REVERT: A 44 MET cc_start: 0.9192 (mmm) cc_final: 0.8942 (mmm) REVERT: A 71 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.6644 (t80) REVERT: A 114 MET cc_start: 0.8841 (mtt) cc_final: 0.8587 (mmt) REVERT: A 203 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8816 (mp0) REVERT: A 308 LYS cc_start: 0.9212 (tppt) cc_final: 0.8764 (tppt) REVERT: A 392 MET cc_start: 0.8892 (mmm) cc_final: 0.8688 (mmt) REVERT: A 464 MET cc_start: 0.9112 (mmm) cc_final: 0.8578 (mmm) REVERT: A 721 MET cc_start: 0.8700 (tpp) cc_final: 0.8486 (tpp) REVERT: A 741 MET cc_start: 0.8677 (mmm) cc_final: 0.8259 (tpt) REVERT: B 74 PHE cc_start: 0.8405 (t80) cc_final: 0.7956 (t80) REVERT: B 122 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7710 (mm-30) REVERT: B 129 SER cc_start: 0.8457 (t) cc_final: 0.8168 (m) REVERT: B 205 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6683 (pm20) REVERT: B 286 TYR cc_start: 0.9246 (t80) cc_final: 0.9003 (t80) REVERT: B 303 MET cc_start: 0.6697 (mmm) cc_final: 0.6182 (mmp) REVERT: B 500 MET cc_start: 0.7806 (mmm) cc_final: 0.7062 (mtp) REVERT: B 616 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8193 (tp30) REVERT: B 756 GLU cc_start: 0.9330 (pm20) cc_final: 0.8788 (pt0) REVERT: B 791 GLU cc_start: 0.9191 (mp0) cc_final: 0.8917 (tm-30) REVERT: B 1093 TYR cc_start: 0.8258 (m-80) cc_final: 0.7928 (m-80) REVERT: D 187 THR cc_start: 0.6421 (OUTLIER) cc_final: 0.6124 (p) REVERT: D 246 MET cc_start: 0.8536 (mtp) cc_final: 0.8287 (mtp) REVERT: E 60 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8695 (tp) REVERT: F 42 ARG cc_start: 0.6650 (ptt-90) cc_final: 0.6182 (ptt-90) REVERT: F 51 PHE cc_start: 0.2161 (OUTLIER) cc_final: 0.0726 (p90) REVERT: F 90 MET cc_start: 0.8258 (tpp) cc_final: 0.7147 (ttt) REVERT: F 93 ARG cc_start: 0.8289 (mmm-85) cc_final: 0.7915 (mmm-85) REVERT: H 39 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7990 (mt0) REVERT: H 67 SER cc_start: 0.9075 (m) cc_final: 0.8587 (p) REVERT: K 51 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8978 (mt) REVERT: L 77 LYS cc_start: 0.9245 (mmmm) cc_final: 0.8951 (mtmt) REVERT: N 1 MET cc_start: 0.8998 (mmp) cc_final: 0.8796 (mmp) REVERT: N 20 GLU cc_start: 0.8695 (tp30) cc_final: 0.8410 (tp30) REVERT: N 32 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8352 (tm-30) REVERT: P 15 VAL cc_start: 0.7486 (t) cc_final: 0.7158 (m) REVERT: P 18 ASP cc_start: 0.8438 (t70) cc_final: 0.7827 (t70) outliers start: 93 outliers final: 49 residues processed: 398 average time/residue: 0.1639 time to fit residues: 102.7346 Evaluate side-chains 334 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 356 PHE Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1057 TRP Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 117 TYR Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain P residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 258 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 289 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 296 optimal weight: 0.0000 chunk 186 optimal weight: 0.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.084938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.059207 restraints weight = 88866.794| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.26 r_work: 0.2969 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.9687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26884 Z= 0.133 Angle : 0.617 16.245 36293 Z= 0.307 Chirality : 0.045 0.198 4021 Planarity : 0.004 0.056 4702 Dihedral : 4.318 24.120 3643 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.01 % Allowed : 26.23 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.15), residues: 3266 helix: 1.05 (0.15), residues: 1292 sheet: -0.69 (0.25), residues: 440 loop : -0.28 (0.17), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 157 TYR 0.018 0.001 TYR B 293 PHE 0.018 0.001 PHE E 127 TRP 0.052 0.001 TRP B1057 HIS 0.006 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00309 (26864) covalent geometry : angle 0.59346 (36266) hydrogen bonds : bond 0.03916 ( 1191) hydrogen bonds : angle 4.89348 ( 3357) metal coordination : bond 0.00602 ( 20) metal coordination : angle 6.20110 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 294 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8886 (m-80) cc_final: 0.8601 (m-80) REVERT: A 44 MET cc_start: 0.9239 (mmm) cc_final: 0.8928 (mmm) REVERT: A 71 PHE cc_start: 0.7472 (OUTLIER) cc_final: 0.6529 (t80) REVERT: A 201 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6396 (p0) REVERT: A 203 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8896 (mp0) REVERT: A 210 MET cc_start: 0.8169 (ttp) cc_final: 0.7916 (ttm) REVERT: A 392 MET cc_start: 0.8910 (mmm) cc_final: 0.8680 (mmt) REVERT: A 464 MET cc_start: 0.9274 (mmm) cc_final: 0.8705 (mmm) REVERT: A 695 LEU cc_start: 0.8355 (mm) cc_final: 0.8072 (mp) REVERT: A 704 LEU cc_start: 0.8121 (tp) cc_final: 0.7886 (mt) REVERT: A 721 MET cc_start: 0.8780 (tpp) cc_final: 0.8573 (tpp) REVERT: A 741 MET cc_start: 0.8701 (mmm) cc_final: 0.8320 (tpt) REVERT: B 74 PHE cc_start: 0.8351 (t80) cc_final: 0.7901 (t80) REVERT: B 129 SER cc_start: 0.8375 (t) cc_final: 0.8059 (m) REVERT: B 179 GLU cc_start: 0.7631 (mp0) cc_final: 0.6821 (mp0) REVERT: B 188 ILE cc_start: 0.8242 (mm) cc_final: 0.7505 (mm) REVERT: B 205 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6738 (pt0) REVERT: B 286 TYR cc_start: 0.9273 (t80) cc_final: 0.9029 (t80) REVERT: B 293 TYR cc_start: 0.8590 (t80) cc_final: 0.8347 (t80) REVERT: B 303 MET cc_start: 0.6851 (mmm) cc_final: 0.6376 (mmp) REVERT: B 500 MET cc_start: 0.7769 (mmm) cc_final: 0.6990 (mtp) REVERT: B 616 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8295 (tp30) REVERT: B 625 MET cc_start: 0.8863 (tpp) cc_final: 0.7939 (tpp) REVERT: B 756 GLU cc_start: 0.9327 (pm20) cc_final: 0.8881 (pt0) REVERT: B 791 GLU cc_start: 0.9196 (mp0) cc_final: 0.8923 (tm-30) REVERT: B 1093 TYR cc_start: 0.8261 (m-80) cc_final: 0.7956 (m-80) REVERT: C 82 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6478 (pt) REVERT: D 65 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9172 (mm) REVERT: D 187 THR cc_start: 0.6784 (OUTLIER) cc_final: 0.6469 (p) REVERT: E 47 SER cc_start: 0.8180 (p) cc_final: 0.7958 (m) REVERT: E 60 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8785 (tp) REVERT: E 141 LEU cc_start: 0.5794 (tt) cc_final: 0.5528 (tt) REVERT: F 42 ARG cc_start: 0.6763 (ptt-90) cc_final: 0.5821 (ptt-90) REVERT: F 51 PHE cc_start: 0.1447 (OUTLIER) cc_final: 0.0058 (p90) REVERT: H 27 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8494 (mmtt) REVERT: H 39 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8079 (mt0) REVERT: H 67 SER cc_start: 0.9202 (m) cc_final: 0.8804 (p) REVERT: L 77 LYS cc_start: 0.9277 (mmmm) cc_final: 0.8974 (mtmt) REVERT: N 1 MET cc_start: 0.9055 (mmp) cc_final: 0.8817 (mmp) REVERT: N 20 GLU cc_start: 0.8644 (tp30) cc_final: 0.8348 (tp30) REVERT: N 32 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8526 (tm-30) REVERT: P 15 VAL cc_start: 0.7637 (t) cc_final: 0.7320 (m) outliers start: 86 outliers final: 49 residues processed: 363 average time/residue: 0.1516 time to fit residues: 87.7950 Evaluate side-chains 331 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 274 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 973 THR Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 114 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 chunk 246 optimal weight: 0.3980 chunk 130 optimal weight: 0.3980 chunk 244 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 117 optimal weight: 20.0000 chunk 222 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.082635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.056966 restraints weight = 88500.719| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.19 r_work: 0.2944 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 1.0273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26884 Z= 0.154 Angle : 0.616 13.904 36293 Z= 0.308 Chirality : 0.045 0.197 4021 Planarity : 0.005 0.076 4702 Dihedral : 4.197 21.859 3643 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.22 % Allowed : 25.81 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.34 (0.15), residues: 3266 helix: 1.19 (0.15), residues: 1288 sheet: -0.68 (0.24), residues: 434 loop : -0.23 (0.17), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 25 TYR 0.021 0.001 TYR E 134 PHE 0.014 0.001 PHE F 70 TRP 0.036 0.002 TRP A 163 HIS 0.010 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00358 (26864) covalent geometry : angle 0.59492 (36266) hydrogen bonds : bond 0.03822 ( 1191) hydrogen bonds : angle 4.74210 ( 3357) metal coordination : bond 0.00594 ( 20) metal coordination : angle 5.93177 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 287 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8873 (m-80) cc_final: 0.8602 (m-80) REVERT: A 44 MET cc_start: 0.9228 (mmm) cc_final: 0.8916 (mmm) REVERT: A 63 ARG cc_start: 0.8291 (tpp-160) cc_final: 0.7881 (tpp-160) REVERT: A 71 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6422 (t80) REVERT: A 210 MET cc_start: 0.8337 (ttp) cc_final: 0.7947 (ttm) REVERT: A 433 MET cc_start: 0.8818 (mmm) cc_final: 0.8501 (mtt) REVERT: A 464 MET cc_start: 0.9328 (mmm) cc_final: 0.8718 (mmm) REVERT: A 559 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9256 (mm) REVERT: A 714 ASP cc_start: 0.8545 (m-30) cc_final: 0.8031 (t70) REVERT: B 56 ASP cc_start: 0.8410 (m-30) cc_final: 0.8066 (p0) REVERT: B 74 PHE cc_start: 0.8530 (t80) cc_final: 0.8017 (t80) REVERT: B 286 TYR cc_start: 0.9282 (t80) cc_final: 0.9020 (t80) REVERT: B 293 TYR cc_start: 0.8603 (t80) cc_final: 0.8360 (t80) REVERT: B 303 MET cc_start: 0.7200 (mmm) cc_final: 0.6707 (mmp) REVERT: B 446 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8779 (pm20) REVERT: B 500 MET cc_start: 0.8089 (mmm) cc_final: 0.7303 (mtp) REVERT: B 616 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8546 (tp30) REVERT: B 625 MET cc_start: 0.8928 (tpp) cc_final: 0.8052 (tpp) REVERT: B 756 GLU cc_start: 0.9332 (pm20) cc_final: 0.9119 (pm20) REVERT: B 1028 GLU cc_start: 0.8286 (pm20) cc_final: 0.7621 (pt0) REVERT: B 1029 MET cc_start: 0.8505 (mmt) cc_final: 0.8304 (mmm) REVERT: B 1057 TRP cc_start: 0.8562 (m-90) cc_final: 0.7661 (m100) REVERT: B 1088 LYS cc_start: 0.8686 (ttmt) cc_final: 0.8219 (ttmm) REVERT: B 1093 TYR cc_start: 0.8333 (m-80) cc_final: 0.7957 (m-80) REVERT: D 65 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9161 (mm) REVERT: D 67 MET cc_start: 0.9620 (tpp) cc_final: 0.9340 (tpp) REVERT: E 47 SER cc_start: 0.8396 (p) cc_final: 0.8145 (m) REVERT: E 60 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8838 (tp) REVERT: F 42 ARG cc_start: 0.7112 (ptt-90) cc_final: 0.6333 (ptt-90) REVERT: F 51 PHE cc_start: 0.1742 (OUTLIER) cc_final: 0.0285 (p90) REVERT: F 68 ASN cc_start: 0.8581 (m-40) cc_final: 0.7928 (p0) REVERT: F 88 ASP cc_start: 0.8769 (t0) cc_final: 0.7924 (t0) REVERT: F 90 MET cc_start: 0.8148 (tpp) cc_final: 0.6698 (ttt) REVERT: H 27 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8550 (mmtt) REVERT: H 39 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8199 (mt0) REVERT: H 67 SER cc_start: 0.9224 (m) cc_final: 0.8863 (p) REVERT: L 77 LYS cc_start: 0.9259 (mmmm) cc_final: 0.8908 (mtmt) REVERT: N 1 MET cc_start: 0.9033 (mmp) cc_final: 0.8800 (mmp) REVERT: N 20 GLU cc_start: 0.8647 (tp30) cc_final: 0.8384 (tp30) REVERT: N 32 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8476 (tm-30) REVERT: P 15 VAL cc_start: 0.7652 (t) cc_final: 0.7337 (m) outliers start: 92 outliers final: 56 residues processed: 361 average time/residue: 0.1600 time to fit residues: 92.6200 Evaluate side-chains 321 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 260 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1016 GLU Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 212 optimal weight: 3.9990 chunk 295 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 chunk 173 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 234 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 215 optimal weight: 0.0570 chunk 23 optimal weight: 20.0000 chunk 179 optimal weight: 3.9990 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 GLN B 485 GLN C 295 GLN F 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.079051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.053214 restraints weight = 87524.281| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.14 r_work: 0.2854 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 1.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26884 Z= 0.215 Angle : 0.669 13.738 36293 Z= 0.335 Chirality : 0.047 0.191 4021 Planarity : 0.005 0.055 4702 Dihedral : 4.360 20.821 3643 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.36 % Allowed : 26.41 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.26 (0.15), residues: 3266 helix: 1.14 (0.15), residues: 1282 sheet: -0.83 (0.24), residues: 439 loop : -0.23 (0.17), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 251 TYR 0.017 0.002 TYR A 375 PHE 0.014 0.002 PHE B 50 TRP 0.016 0.001 TRP B 15 HIS 0.014 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00507 (26864) covalent geometry : angle 0.64436 (36266) hydrogen bonds : bond 0.04261 ( 1191) hydrogen bonds : angle 4.90699 ( 3357) metal coordination : bond 0.00838 ( 20) metal coordination : angle 6.60773 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 283 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8862 (m-80) cc_final: 0.8576 (m-80) REVERT: A 44 MET cc_start: 0.9194 (mmm) cc_final: 0.8888 (mmm) REVERT: A 114 MET cc_start: 0.8823 (mtt) cc_final: 0.8402 (mtt) REVERT: A 142 MET cc_start: 0.6378 (tmm) cc_final: 0.5328 (mmm) REVERT: A 311 ARG cc_start: 0.8774 (tpp80) cc_final: 0.8563 (tpp80) REVERT: A 433 MET cc_start: 0.8848 (mmm) cc_final: 0.8525 (mtt) REVERT: A 464 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.8977 (mmm) REVERT: A 559 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9268 (mm) REVERT: A 714 ASP cc_start: 0.8730 (m-30) cc_final: 0.8221 (t70) REVERT: B 56 ASP cc_start: 0.8529 (m-30) cc_final: 0.8223 (p0) REVERT: B 74 PHE cc_start: 0.8680 (t80) cc_final: 0.8330 (t80) REVERT: B 286 TYR cc_start: 0.9245 (t80) cc_final: 0.8970 (t80) REVERT: B 340 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8376 (t80) REVERT: B 430 MET cc_start: 0.9367 (mmm) cc_final: 0.8995 (mmm) REVERT: B 446 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8953 (pm20) REVERT: B 500 MET cc_start: 0.8568 (mmm) cc_final: 0.7652 (mtp) REVERT: B 616 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8900 (tp30) REVERT: B 618 GLU cc_start: 0.9271 (tp30) cc_final: 0.8880 (tp30) REVERT: B 625 MET cc_start: 0.9009 (tpp) cc_final: 0.8241 (tpp) REVERT: B 756 GLU cc_start: 0.9309 (pm20) cc_final: 0.9022 (pm20) REVERT: B 1028 GLU cc_start: 0.8369 (pm20) cc_final: 0.7774 (pt0) REVERT: B 1029 MET cc_start: 0.8542 (mmt) cc_final: 0.8328 (mmm) REVERT: B 1057 TRP cc_start: 0.8663 (m-90) cc_final: 0.8009 (m100) REVERT: B 1088 LYS cc_start: 0.8773 (ttmt) cc_final: 0.8466 (ttmt) REVERT: B 1093 TYR cc_start: 0.8464 (m-80) cc_final: 0.8037 (m-80) REVERT: D 65 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9165 (mm) REVERT: E 2 TYR cc_start: 0.8982 (m-10) cc_final: 0.8761 (m-10) REVERT: E 46 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7608 (mm) REVERT: E 47 SER cc_start: 0.8703 (p) cc_final: 0.8331 (m) REVERT: E 60 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8935 (tp) REVERT: F 42 ARG cc_start: 0.7232 (ptt-90) cc_final: 0.6044 (ptp90) REVERT: F 51 PHE cc_start: 0.1570 (OUTLIER) cc_final: -0.0143 (p90) REVERT: F 88 ASP cc_start: 0.8554 (t0) cc_final: 0.8183 (t70) REVERT: H 39 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8323 (mt0) REVERT: H 67 SER cc_start: 0.9205 (m) cc_final: 0.8872 (p) REVERT: L 77 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8873 (mtmt) REVERT: N 1 MET cc_start: 0.9074 (mmp) cc_final: 0.8771 (mmp) REVERT: N 20 GLU cc_start: 0.8753 (tp30) cc_final: 0.8447 (tp30) REVERT: N 32 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8527 (tm-30) REVERT: P 15 VAL cc_start: 0.7745 (t) cc_final: 0.7398 (m) outliers start: 96 outliers final: 58 residues processed: 363 average time/residue: 0.1714 time to fit residues: 97.0001 Evaluate side-chains 320 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 255 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 733 ASP Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1052 ASP Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1059 CYS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 93 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain P residue 35 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 299 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 303 optimal weight: 1.9990 chunk 206 optimal weight: 0.4980 chunk 31 optimal weight: 10.0000 chunk 265 optimal weight: 3.9990 chunk 288 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.079020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053272 restraints weight = 87590.573| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 4.11 r_work: 0.2857 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 1.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26884 Z= 0.160 Angle : 0.635 14.067 36293 Z= 0.314 Chirality : 0.046 0.234 4021 Planarity : 0.004 0.058 4702 Dihedral : 4.209 19.051 3643 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.66 % Allowed : 27.29 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.35 (0.15), residues: 3266 helix: 1.17 (0.15), residues: 1288 sheet: -0.71 (0.24), residues: 447 loop : -0.18 (0.17), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 389 TYR 0.018 0.001 TYR B 315 PHE 0.016 0.001 PHE B 390 TRP 0.016 0.001 TRP A 163 HIS 0.008 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00377 (26864) covalent geometry : angle 0.60937 (36266) hydrogen bonds : bond 0.03906 ( 1191) hydrogen bonds : angle 4.74460 ( 3357) metal coordination : bond 0.00870 ( 20) metal coordination : angle 6.58625 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 267 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8884 (m-80) cc_final: 0.8613 (m-80) REVERT: A 44 MET cc_start: 0.9206 (mmm) cc_final: 0.8842 (mmm) REVERT: A 63 ARG cc_start: 0.8290 (tpp-160) cc_final: 0.7929 (tpp-160) REVERT: A 142 MET cc_start: 0.6420 (tmm) cc_final: 0.5462 (mmm) REVERT: A 433 MET cc_start: 0.8834 (mmm) cc_final: 0.8579 (mtt) REVERT: A 464 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8994 (mmm) REVERT: A 559 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9315 (mm) REVERT: A 714 ASP cc_start: 0.8731 (m-30) cc_final: 0.8132 (t0) REVERT: A 721 MET cc_start: 0.9054 (tpp) cc_final: 0.8694 (mmt) REVERT: B 56 ASP cc_start: 0.8541 (m-30) cc_final: 0.8246 (p0) REVERT: B 74 PHE cc_start: 0.8694 (t80) cc_final: 0.8116 (t80) REVERT: B 286 TYR cc_start: 0.9241 (t80) cc_final: 0.8955 (t80) REVERT: B 340 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8253 (t80) REVERT: B 446 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8975 (pm20) REVERT: B 496 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7004 (tpm170) REVERT: B 500 MET cc_start: 0.8592 (mmm) cc_final: 0.7681 (mtt) REVERT: B 616 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8838 (tp30) REVERT: B 618 GLU cc_start: 0.9247 (tp30) cc_final: 0.9018 (tp30) REVERT: B 625 MET cc_start: 0.8989 (tpp) cc_final: 0.8292 (tpp) REVERT: B 731 MET cc_start: 0.9122 (mtm) cc_final: 0.8446 (mtm) REVERT: B 1028 GLU cc_start: 0.8259 (pm20) cc_final: 0.7693 (pt0) REVERT: B 1088 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8389 (mttm) REVERT: B 1093 TYR cc_start: 0.8428 (m-80) cc_final: 0.7978 (m-80) REVERT: C 80 MET cc_start: 0.8760 (ptp) cc_final: 0.7957 (pmm) REVERT: D 65 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9182 (mm) REVERT: E 46 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7677 (mm) REVERT: E 47 SER cc_start: 0.8654 (p) cc_final: 0.8211 (m) REVERT: F 42 ARG cc_start: 0.7295 (ptt-90) cc_final: 0.6551 (ptp90) REVERT: F 51 PHE cc_start: 0.1121 (OUTLIER) cc_final: -0.0050 (p90) REVERT: F 68 ASN cc_start: 0.8769 (m110) cc_final: 0.8236 (p0) REVERT: H 27 LYS cc_start: 0.8896 (mmtm) cc_final: 0.8674 (mtmm) REVERT: H 39 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8314 (mt0) REVERT: H 67 SER cc_start: 0.9290 (m) cc_final: 0.8947 (p) REVERT: K 51 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9115 (mt) REVERT: L 77 LYS cc_start: 0.9198 (mmmm) cc_final: 0.8830 (mtmt) REVERT: N 1 MET cc_start: 0.9007 (mmp) cc_final: 0.8683 (mmp) REVERT: N 20 GLU cc_start: 0.8739 (tp30) cc_final: 0.8437 (tp30) REVERT: N 32 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8537 (tm-30) REVERT: P 15 VAL cc_start: 0.7736 (t) cc_final: 0.7367 (m) outliers start: 76 outliers final: 48 residues processed: 330 average time/residue: 0.1659 time to fit residues: 85.9338 Evaluate side-chains 309 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 253 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1016 GLU Chi-restraints excluded: chain B residue 1059 CYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 86 optimal weight: 4.9990 chunk 219 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 304 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN C 346 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.078949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.053277 restraints weight = 87672.864| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 4.12 r_work: 0.2848 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 1.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26884 Z= 0.133 Angle : 0.626 13.696 36293 Z= 0.309 Chirality : 0.045 0.212 4021 Planarity : 0.004 0.052 4702 Dihedral : 4.092 19.297 3643 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.45 % Allowed : 27.64 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.42 (0.15), residues: 3266 helix: 1.21 (0.15), residues: 1297 sheet: -0.69 (0.24), residues: 454 loop : -0.12 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 389 TYR 0.019 0.001 TYR B 382 PHE 0.030 0.001 PHE P 9 TRP 0.015 0.001 TRP A 209 HIS 0.009 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00313 (26864) covalent geometry : angle 0.60153 (36266) hydrogen bonds : bond 0.03719 ( 1191) hydrogen bonds : angle 4.67304 ( 3357) metal coordination : bond 0.00767 ( 20) metal coordination : angle 6.34774 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 266 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8892 (m-80) cc_final: 0.8622 (m-80) REVERT: A 44 MET cc_start: 0.9209 (mmm) cc_final: 0.8944 (mmm) REVERT: A 63 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.7954 (tpp-160) REVERT: A 142 MET cc_start: 0.6660 (tmm) cc_final: 0.5779 (mmm) REVERT: A 433 MET cc_start: 0.8808 (mmm) cc_final: 0.8538 (mtt) REVERT: A 464 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.8995 (mmm) REVERT: A 559 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9305 (mm) REVERT: A 616 SER cc_start: 0.9172 (OUTLIER) cc_final: 0.8970 (t) REVERT: A 721 MET cc_start: 0.9056 (tpp) cc_final: 0.8747 (mmt) REVERT: B 56 ASP cc_start: 0.8644 (m-30) cc_final: 0.8332 (p0) REVERT: B 74 PHE cc_start: 0.8760 (t80) cc_final: 0.8126 (t80) REVERT: B 218 ASN cc_start: 0.9266 (m-40) cc_final: 0.8162 (t0) REVERT: B 286 TYR cc_start: 0.9263 (t80) cc_final: 0.8997 (t80) REVERT: B 340 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8211 (t80) REVERT: B 446 GLU cc_start: 0.9238 (mm-30) cc_final: 0.9004 (pm20) REVERT: B 496 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6751 (tpp-160) REVERT: B 500 MET cc_start: 0.8675 (mmm) cc_final: 0.8177 (mmm) REVERT: B 616 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8855 (tp30) REVERT: B 625 MET cc_start: 0.9054 (tpp) cc_final: 0.8390 (tpp) REVERT: B 731 MET cc_start: 0.9101 (mtm) cc_final: 0.8445 (mtm) REVERT: B 1028 GLU cc_start: 0.8197 (pm20) cc_final: 0.7663 (pt0) REVERT: B 1057 TRP cc_start: 0.8772 (m-90) cc_final: 0.8290 (m-90) REVERT: B 1088 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8200 (mtpp) REVERT: B 1093 TYR cc_start: 0.8440 (m-80) cc_final: 0.7956 (m-80) REVERT: D 65 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9179 (mm) REVERT: E 47 SER cc_start: 0.8716 (p) cc_final: 0.8183 (m) REVERT: F 51 PHE cc_start: 0.1021 (OUTLIER) cc_final: -0.0117 (p90) REVERT: H 27 LYS cc_start: 0.8950 (mmtm) cc_final: 0.8725 (mtmm) REVERT: H 39 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8286 (mt0) REVERT: H 67 SER cc_start: 0.9354 (m) cc_final: 0.9049 (p) REVERT: K 51 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9137 (mt) REVERT: L 14 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8947 (mt-10) REVERT: L 77 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8820 (mtmt) REVERT: N 1 MET cc_start: 0.8996 (mmp) cc_final: 0.8675 (mmp) REVERT: N 20 GLU cc_start: 0.8704 (tp30) cc_final: 0.8385 (tp30) REVERT: N 32 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8481 (tm-30) REVERT: P 15 VAL cc_start: 0.7870 (t) cc_final: 0.7522 (m) outliers start: 70 outliers final: 49 residues processed: 322 average time/residue: 0.1669 time to fit residues: 85.1669 Evaluate side-chains 311 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 253 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 340 TYR Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1016 GLU Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1059 CYS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 117 optimal weight: 20.0000 chunk 290 optimal weight: 20.0000 chunk 233 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 182 optimal weight: 0.0570 chunk 129 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 147 optimal weight: 0.1980 chunk 179 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 245 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN B 882 GLN C 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.079606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.054016 restraints weight = 87115.197| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.10 r_work: 0.2876 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 1.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26884 Z= 0.112 Angle : 0.631 14.086 36293 Z= 0.309 Chirality : 0.045 0.261 4021 Planarity : 0.004 0.052 4702 Dihedral : 3.999 19.547 3643 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.96 % Allowed : 27.92 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.52 (0.15), residues: 3266 helix: 1.28 (0.15), residues: 1289 sheet: -0.54 (0.24), residues: 444 loop : -0.08 (0.17), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 389 TYR 0.017 0.001 TYR B 315 PHE 0.020 0.001 PHE P 9 TRP 0.014 0.001 TRP B1057 HIS 0.008 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00260 (26864) covalent geometry : angle 0.61066 (36266) hydrogen bonds : bond 0.03569 ( 1191) hydrogen bonds : angle 4.61063 ( 3357) metal coordination : bond 0.00691 ( 20) metal coordination : angle 5.87811 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6532 Ramachandran restraints generated. 3266 Oldfield, 0 Emsley, 3266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 271 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8887 (m-80) cc_final: 0.8622 (m-80) REVERT: A 44 MET cc_start: 0.9207 (mmm) cc_final: 0.8941 (mmm) REVERT: A 63 ARG cc_start: 0.8344 (tpp-160) cc_final: 0.7965 (tpp-160) REVERT: A 142 MET cc_start: 0.6740 (tmm) cc_final: 0.5854 (mmm) REVERT: A 433 MET cc_start: 0.8778 (mmm) cc_final: 0.8544 (mtt) REVERT: A 464 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.9003 (mmm) REVERT: A 559 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9288 (mm) REVERT: A 721 MET cc_start: 0.9071 (tpp) cc_final: 0.8762 (mmt) REVERT: B 56 ASP cc_start: 0.8592 (m-30) cc_final: 0.8259 (p0) REVERT: B 74 PHE cc_start: 0.8775 (t80) cc_final: 0.8095 (t80) REVERT: B 218 ASN cc_start: 0.9296 (m-40) cc_final: 0.8187 (t0) REVERT: B 286 TYR cc_start: 0.9227 (t80) cc_final: 0.8956 (t80) REVERT: B 320 MET cc_start: 0.7576 (mmt) cc_final: 0.6820 (mpp) REVERT: B 446 GLU cc_start: 0.9211 (mm-30) cc_final: 0.9001 (pm20) REVERT: B 496 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6732 (tpp-160) REVERT: B 500 MET cc_start: 0.8687 (mmm) cc_final: 0.8193 (mmm) REVERT: B 616 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8774 (tp30) REVERT: B 625 MET cc_start: 0.9015 (tpp) cc_final: 0.8387 (tpp) REVERT: B 731 MET cc_start: 0.9064 (mtm) cc_final: 0.8509 (mtm) REVERT: B 1028 GLU cc_start: 0.8176 (pm20) cc_final: 0.7674 (pt0) REVERT: B 1057 TRP cc_start: 0.8751 (m-90) cc_final: 0.8351 (m-90) REVERT: B 1088 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8279 (mtpp) REVERT: B 1093 TYR cc_start: 0.8492 (m-80) cc_final: 0.8032 (m-80) REVERT: C 80 MET cc_start: 0.8532 (ptp) cc_final: 0.7936 (pmm) REVERT: C 288 ASP cc_start: 0.9311 (t0) cc_final: 0.9096 (t0) REVERT: D 65 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9190 (mm) REVERT: E 47 SER cc_start: 0.8689 (p) cc_final: 0.8142 (m) REVERT: F 51 PHE cc_start: 0.0804 (OUTLIER) cc_final: -0.0271 (p90) REVERT: F 85 MET cc_start: 0.3546 (tpt) cc_final: 0.2818 (mmm) REVERT: H 39 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8315 (mt0) REVERT: H 67 SER cc_start: 0.9384 (m) cc_final: 0.9108 (p) REVERT: K 51 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9144 (mt) REVERT: L 14 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8877 (mt-10) REVERT: L 77 LYS cc_start: 0.9191 (mmmm) cc_final: 0.8843 (mtmt) REVERT: N 1 MET cc_start: 0.8966 (mmp) cc_final: 0.8644 (mmp) REVERT: N 20 GLU cc_start: 0.8649 (tp30) cc_final: 0.8348 (tp30) REVERT: N 32 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8380 (tm-30) REVERT: P 14 GLU cc_start: 0.8715 (mp0) cc_final: 0.8389 (mp0) REVERT: P 15 VAL cc_start: 0.7862 (t) cc_final: 0.7526 (m) outliers start: 56 outliers final: 41 residues processed: 318 average time/residue: 0.1588 time to fit residues: 80.1735 Evaluate side-chains 301 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 253 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 574 CYS Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 496 ARG Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1059 CYS Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 54 GLU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 279 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 30 optimal weight: 0.2980 chunk 107 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 137 optimal weight: 0.2980 chunk 287 optimal weight: 30.0000 chunk 104 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 320 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 882 GLN E 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.077818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.052240 restraints weight = 87776.300| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.09 r_work: 0.2836 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 1.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26884 Z= 0.157 Angle : 0.644 12.727 36293 Z= 0.316 Chirality : 0.045 0.234 4021 Planarity : 0.005 0.078 4702 Dihedral : 4.069 19.383 3643 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.14 % Allowed : 27.71 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.52 (0.15), residues: 3266 helix: 1.30 (0.15), residues: 1284 sheet: -0.52 (0.24), residues: 477 loop : -0.08 (0.17), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 320 TYR 0.017 0.001 TYR B 316 PHE 0.018 0.001 PHE E 95 TRP 0.013 0.001 TRP B 15 HIS 0.010 0.001 HIS B 302 Details of bonding type rmsd covalent geometry : bond 0.00371 (26864) covalent geometry : angle 0.62263 (36266) hydrogen bonds : bond 0.03833 ( 1191) hydrogen bonds : angle 4.67839 ( 3357) metal coordination : bond 0.00793 ( 20) metal coordination : angle 6.05449 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6958.31 seconds wall clock time: 119 minutes 28.36 seconds (7168.36 seconds total)