Starting phenix.real_space_refine on Sun Jun 22 15:02:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rbo_19033/06_2025/8rbo_19033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rbo_19033/06_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_19033/06_2025/8rbo_19033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rbo_19033/06_2025/8rbo_19033.map" model { file = "/net/cci-nas-00/data/ceres_data/8rbo_19033/06_2025/8rbo_19033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rbo_19033/06_2025/8rbo_19033.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.93, per 1000 atoms: 0.57 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: 7.44 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 70 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 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: 3.31 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: 12.50 Time building geometry restraints manager: 8.34 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 67.940 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.000 ------------------------------------------------------------------------------- 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 : 9.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (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 TRP 0.015 0.001 TRP A 163 HIS 0.007 0.001 HIS B 911 PHE 0.034 0.001 PHE E 95 TYR 0.016 0.001 TYR F 38 ARG 0.010 0.000 ARG F 50 Details of bonding type rmsd hydrogen bonds : bond 0.17905 ( 1191) hydrogen bonds : angle 6.74642 ( 3357) metal coordination : bond 0.00773 ( 20) metal coordination : angle 6.63463 ( 27) covalent geometry : bond 0.00334 (26864) covalent geometry : angle 0.55805 (36266) *********************** 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 : 3.226 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: 0.4309 time to fit residues: 492.1439 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 : 2.900 ------------------------------------------------------------------------------- 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 272 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 135 optimal weight: 0.1980 chunk 83 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 253 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 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 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 B1000 HIS ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN F 105 GLN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.107968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.085841 restraints weight = 94378.491| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 4.65 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26884 Z= 0.178 Angle : 0.714 17.426 36293 Z= 0.359 Chirality : 0.048 0.268 4021 Planarity : 0.005 0.070 4702 Dihedral : 4.343 41.181 3645 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.10 % Allowed : 25.25 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 3266 helix: 1.28 (0.14), residues: 1274 sheet: -0.53 (0.24), residues: 440 loop : -0.23 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B1057 HIS 0.009 0.001 HIS A 818 PHE 0.039 0.002 PHE B 273 TYR 0.020 0.002 TYR E 134 ARG 0.013 0.001 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 1191) hydrogen bonds : angle 5.25804 ( 3357) metal coordination : bond 0.00844 ( 20) metal coordination : angle 6.34243 ( 27) covalent geometry : bond 0.00380 (26864) covalent geometry : angle 0.69305 (36266) *********************** 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 571 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 454 time to evaluate : 3.070 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: A 114 MET cc_start: 0.8516 (mtt) cc_final: 0.8312 (mmt) REVERT: A 203 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8643 (mp0) REVERT: A 332 ASP cc_start: 0.8560 (t0) cc_final: 0.7907 (t70) REVERT: A 544 ASP cc_start: 0.8197 (p0) cc_final: 0.7979 (p0) REVERT: A 592 MET cc_start: 0.9235 (mtm) cc_final: 0.9030 (mpp) REVERT: A 758 LEU cc_start: 0.8225 (tp) cc_final: 0.7993 (tp) REVERT: A 766 LEU cc_start: 0.7357 (pp) cc_final: 0.6690 (pp) REVERT: B 293 TYR cc_start: 0.8398 (t80) cc_final: 0.8135 (t80) REVERT: B 500 MET cc_start: 0.7390 (mmm) cc_final: 0.6356 (mmm) REVERT: B 750 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8121 (p) REVERT: B 766 GLN cc_start: 0.8672 (mm110) cc_final: 0.8280 (pm20) REVERT: B 905 ASP cc_start: 0.8815 (m-30) cc_final: 0.8600 (m-30) REVERT: B 948 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8112 (pp20) REVERT: B 1057 TRP cc_start: 0.7432 (m-90) cc_final: 0.6632 (t-100) REVERT: E 59 ILE cc_start: 0.7198 (mp) cc_final: 0.6927 (mp) REVERT: E 68 HIS cc_start: 0.6469 (m-70) cc_final: 0.5989 (m-70) REVERT: E 92 VAL cc_start: 0.4975 (OUTLIER) cc_final: 0.3591 (m) REVERT: E 143 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7403 (ptm160) REVERT: F 21 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7575 (mm) REVERT: F 25 ARG cc_start: 0.8841 (mmm-85) cc_final: 0.8627 (mmm-85) REVERT: F 42 ARG cc_start: 0.6965 (ptt-90) cc_final: 0.5848 (ptt-90) REVERT: F 45 LEU cc_start: 0.7336 (tp) cc_final: 0.7018 (mt) REVERT: F 51 PHE cc_start: 0.0451 (OUTLIER) cc_final: -0.0524 (p90) REVERT: H 44 LYS cc_start: 0.5954 (ptmt) cc_final: 0.5664 (mtpp) REVERT: K 26 VAL cc_start: 0.6811 (OUTLIER) cc_final: 0.6497 (t) REVERT: P 18 ASP cc_start: 0.8163 (t70) cc_final: 0.7650 (t70) outliers start: 117 outliers final: 43 residues processed: 540 average time/residue: 0.4105 time to fit residues: 355.0010 Evaluate side-chains 428 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 378 time to evaluate : 3.074 ------------------------------------------------------------------------------- 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 276 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 409 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 772 ILE Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 828 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 199 ARG Chi-restraints excluded: chain B residue 450 PHE 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 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 985 VAL Chi-restraints excluded: chain B residue 1052 ASP Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 356 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 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 143 ARG 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 N residue 20 GLU Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 42 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 255 optimal weight: 4.9990 chunk 241 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 180 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 292 optimal weight: 0.0030 chunk 248 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.1794 ------------------------------------------------------------------------------- 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 730 ASN A 818 HIS A 867 GLN B 297 ASN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 HIS B 921 GLN B1000 HIS ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.101983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.078350 restraints weight = 89305.373| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 4.81 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 26884 Z= 0.219 Angle : 0.757 20.280 36293 Z= 0.381 Chirality : 0.049 0.501 4021 Planarity : 0.006 0.091 4702 Dihedral : 4.628 41.725 3645 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.24 % Allowed : 25.43 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3266 helix: 1.06 (0.14), residues: 1277 sheet: -0.78 (0.23), residues: 470 loop : -0.30 (0.17), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B1057 HIS 0.010 0.002 HIS A 292 PHE 0.030 0.002 PHE B 273 TYR 0.043 0.002 TYR B 286 ARG 0.020 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 1191) hydrogen bonds : angle 5.14071 ( 3357) metal coordination : bond 0.00944 ( 20) metal coordination : angle 7.30922 ( 27) covalent geometry : bond 0.00500 (26864) covalent geometry : angle 0.73063 (36266) *********************** 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 536 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 415 time to evaluate : 3.041 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: A 71 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.6617 (t80) REVERT: A 114 MET cc_start: 0.8633 (mtt) cc_final: 0.8375 (mmt) REVERT: A 179 MET cc_start: 0.8168 (mmm) cc_final: 0.7955 (mmm) REVERT: A 279 TYR cc_start: 0.8709 (t80) cc_final: 0.8468 (t80) REVERT: A 464 MET cc_start: 0.8043 (mtp) cc_final: 0.7836 (mtp) REVERT: A 503 ASP cc_start: 0.9042 (m-30) cc_final: 0.8775 (m-30) REVERT: A 592 MET cc_start: 0.9299 (mtm) cc_final: 0.9059 (mpp) REVERT: A 799 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7686 (mmmm) REVERT: B 74 PHE cc_start: 0.8170 (t80) cc_final: 0.7793 (t80) REVERT: B 500 MET cc_start: 0.7317 (mmm) cc_final: 0.6756 (mtt) REVERT: B 640 MET cc_start: 0.5235 (tpp) cc_final: 0.3877 (mmm) REVERT: B 705 MET cc_start: 0.5981 (OUTLIER) cc_final: 0.5675 (mpp) REVERT: B 731 MET cc_start: 0.8140 (mtm) cc_final: 0.7526 (mtm) REVERT: B 857 THR cc_start: 0.8835 (p) cc_final: 0.8603 (p) REVERT: B 905 ASP cc_start: 0.9072 (m-30) cc_final: 0.8659 (m-30) REVERT: B 1057 TRP cc_start: 0.7471 (m-90) cc_final: 0.7227 (m-90) REVERT: B 1093 TYR cc_start: 0.7863 (m-10) cc_final: 0.7597 (m-10) REVERT: B 1097 LEU cc_start: 0.9221 (tp) cc_final: 0.8807 (tp) REVERT: C 80 MET cc_start: 0.7336 (pmm) cc_final: 0.6676 (pmm) REVERT: C 147 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7997 (pp) REVERT: C 175 THR cc_start: 0.6001 (OUTLIER) cc_final: 0.5692 (p) REVERT: C 312 MET cc_start: 0.8167 (tpp) cc_final: 0.7839 (tpt) REVERT: D 65 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8888 (mm) REVERT: D 169 GLU cc_start: 0.8710 (mp0) cc_final: 0.8453 (mp0) REVERT: F 22 LEU cc_start: 0.9372 (mt) cc_final: 0.9096 (pp) REVERT: F 25 ARG cc_start: 0.9067 (mmm-85) cc_final: 0.8813 (mmm-85) REVERT: F 42 ARG cc_start: 0.6826 (ptt-90) cc_final: 0.6377 (ptt-90) REVERT: F 51 PHE cc_start: 0.1033 (OUTLIER) cc_final: -0.0053 (p90) REVERT: F 90 MET cc_start: 0.8490 (tpp) cc_final: 0.8285 (tpp) REVERT: N 22 LYS cc_start: 0.8475 (ttpt) cc_final: 0.8265 (ttpp) REVERT: N 60 MET cc_start: 0.7493 (ppp) cc_final: 0.7163 (mtp) REVERT: P 15 VAL cc_start: 0.7455 (t) cc_final: 0.7212 (m) outliers start: 121 outliers final: 50 residues processed: 500 average time/residue: 0.3885 time to fit residues: 305.6971 Evaluate side-chains 395 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 339 time to evaluate : 3.155 ------------------------------------------------------------------------------- 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 103 ILE Chi-restraints excluded: chain A residue 129 GLU 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 305 LEU Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 447 LEU 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 772 ILE Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 733 ASP Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 1052 ASP 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 117 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 191 VAL 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 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 75 TYR Chi-restraints excluded: chain K residue 3 LYS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain P residue 20 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 272 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 273 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 HIS C 157 ASN E 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.095074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.070258 restraints weight = 92180.446| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.50 r_work: 0.3228 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.6682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 26884 Z= 0.188 Angle : 0.667 15.204 36293 Z= 0.336 Chirality : 0.046 0.257 4021 Planarity : 0.005 0.061 4702 Dihedral : 4.350 23.474 3643 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.57 % Allowed : 26.83 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3266 helix: 1.12 (0.14), residues: 1289 sheet: -0.79 (0.22), residues: 498 loop : -0.26 (0.17), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 628 HIS 0.031 0.002 HIS A 818 PHE 0.027 0.002 PHE E 95 TYR 0.021 0.002 TYR B 520 ARG 0.007 0.001 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 1191) hydrogen bonds : angle 4.95946 ( 3357) metal coordination : bond 0.00660 ( 20) metal coordination : angle 6.29978 ( 27) covalent geometry : bond 0.00442 (26864) covalent geometry : angle 0.64462 (36266) *********************** 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 464 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 362 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.6607 (t80) REVERT: A 113 TYR cc_start: 0.8046 (m-80) cc_final: 0.7821 (m-10) REVERT: A 114 MET cc_start: 0.8759 (mtt) cc_final: 0.8538 (mmt) REVERT: A 179 MET cc_start: 0.8105 (mmm) cc_final: 0.7843 (mmm) REVERT: A 201 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6816 (p0) REVERT: A 464 MET cc_start: 0.8729 (mtp) cc_final: 0.8411 (mtp) REVERT: A 503 ASP cc_start: 0.9144 (m-30) cc_final: 0.8935 (m-30) REVERT: A 520 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8378 (ttt-90) REVERT: A 592 MET cc_start: 0.9501 (mtm) cc_final: 0.9260 (mpp) REVERT: A 721 MET cc_start: 0.8465 (mmm) cc_final: 0.8259 (tpp) REVERT: B 74 PHE cc_start: 0.8121 (t80) cc_final: 0.7732 (t80) REVERT: B 122 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6389 (pp20) REVERT: B 286 TYR cc_start: 0.9269 (t80) cc_final: 0.8924 (t80) REVERT: B 500 MET cc_start: 0.7732 (mmm) cc_final: 0.7222 (mmm) REVERT: B 640 MET cc_start: 0.6949 (tpp) cc_final: 0.5634 (ttt) REVERT: B 731 MET cc_start: 0.8837 (mtm) cc_final: 0.8378 (mtm) REVERT: B 1057 TRP cc_start: 0.7809 (m-90) cc_final: 0.7573 (m-90) REVERT: B 1093 TYR cc_start: 0.8078 (m-10) cc_final: 0.7750 (m-10) REVERT: C 147 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8021 (pp) REVERT: C 238 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7889 (mm-30) REVERT: C 307 MET cc_start: 0.8650 (mmm) cc_final: 0.8401 (mtt) REVERT: C 383 MET cc_start: 0.8729 (ptp) cc_final: 0.8527 (ptp) REVERT: D 65 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9063 (mm) REVERT: D 169 GLU cc_start: 0.8841 (mp0) cc_final: 0.8601 (mp0) REVERT: F 42 ARG cc_start: 0.6855 (ptt-90) cc_final: 0.6405 (ptt-90) REVERT: F 51 PHE cc_start: 0.1394 (OUTLIER) cc_final: 0.0136 (p90) REVERT: F 108 MET cc_start: 0.8976 (tmm) cc_final: 0.8712 (tmm) REVERT: P 15 VAL cc_start: 0.7667 (t) cc_final: 0.7372 (m) outliers start: 102 outliers final: 51 residues processed: 442 average time/residue: 0.3850 time to fit residues: 269.2322 Evaluate side-chains 368 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 310 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 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 85 PHE Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 129 GLU 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 278 THR Chi-restraints excluded: chain A residue 420 LEU 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 616 SER Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 69 VAL 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 450 PHE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 733 ASP Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 864 VAL 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 303 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 76 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 72 VAL 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 P residue 46 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 63 optimal weight: 0.5980 chunk 305 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 overall best weight: 1.3364 ------------------------------------------------------------------------------- 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 A 818 HIS B 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.093029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.068214 restraints weight = 90542.075| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 4.41 r_work: 0.3179 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.7456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26884 Z= 0.140 Angle : 0.635 13.284 36293 Z= 0.317 Chirality : 0.046 0.231 4021 Planarity : 0.005 0.057 4702 Dihedral : 4.233 23.332 3643 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.40 % Allowed : 26.65 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3266 helix: 1.24 (0.15), residues: 1291 sheet: -0.67 (0.22), residues: 485 loop : -0.21 (0.17), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1057 HIS 0.009 0.001 HIS A 176 PHE 0.018 0.001 PHE B 356 TYR 0.029 0.001 TYR E 134 ARG 0.013 0.000 ARG F 93 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 1191) hydrogen bonds : angle 4.80379 ( 3357) metal coordination : bond 0.01535 ( 20) metal coordination : angle 5.67486 ( 27) covalent geometry : bond 0.00321 (26864) covalent geometry : angle 0.61560 (36266) *********************** 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 442 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 345 time to evaluate : 3.056 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 63 ARG cc_start: 0.8012 (tpp-160) cc_final: 0.7637 (tpp-160) REVERT: A 71 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.6430 (t80) REVERT: A 88 THR cc_start: 0.8327 (m) cc_final: 0.8070 (p) REVERT: A 89 ILE cc_start: 0.8504 (mt) cc_final: 0.8281 (mt) REVERT: A 312 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7529 (t80) REVERT: A 426 SER cc_start: 0.9036 (m) cc_final: 0.8835 (p) REVERT: A 464 MET cc_start: 0.8636 (mtp) cc_final: 0.8332 (mtp) REVERT: A 520 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8318 (ttt-90) REVERT: A 592 MET cc_start: 0.9480 (mtm) cc_final: 0.9256 (mpp) REVERT: A 721 MET cc_start: 0.8530 (mmm) cc_final: 0.8115 (tpp) REVERT: B 122 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: B 286 TYR cc_start: 0.9238 (t80) cc_final: 0.9015 (t80) REVERT: B 293 TYR cc_start: 0.8535 (t80) cc_final: 0.8257 (t80) REVERT: B 444 ASP cc_start: 0.8453 (p0) cc_final: 0.7889 (p0) REVERT: B 500 MET cc_start: 0.7583 (mmm) cc_final: 0.7013 (mmm) REVERT: B 625 MET cc_start: 0.8260 (tpp) cc_final: 0.8042 (tpp) REVERT: B 640 MET cc_start: 0.7257 (tpp) cc_final: 0.6233 (ttt) REVERT: B 731 MET cc_start: 0.8940 (mtm) cc_final: 0.8611 (mtm) REVERT: B 1044 ILE cc_start: 0.8474 (mm) cc_final: 0.8189 (mt) REVERT: B 1057 TRP cc_start: 0.7671 (m-90) cc_final: 0.6887 (m100) REVERT: B 1093 TYR cc_start: 0.8156 (m-10) cc_final: 0.7817 (m-10) REVERT: C 238 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7976 (mm-30) REVERT: D 65 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9061 (mm) REVERT: D 191 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8399 (m) REVERT: F 25 ARG cc_start: 0.9049 (mmm-85) cc_final: 0.8845 (mmm-85) REVERT: F 42 ARG cc_start: 0.6911 (ptt-90) cc_final: 0.6281 (ptt-90) REVERT: F 51 PHE cc_start: 0.1706 (OUTLIER) cc_final: 0.0404 (p90) REVERT: H 39 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7660 (mt0) REVERT: N 34 VAL cc_start: 0.9012 (t) cc_final: 0.8781 (m) REVERT: P 14 GLU cc_start: 0.8607 (mp0) cc_final: 0.8255 (mp0) REVERT: P 15 VAL cc_start: 0.7641 (t) cc_final: 0.7368 (m) REVERT: P 18 ASP cc_start: 0.8405 (t70) cc_final: 0.7888 (t70) outliers start: 97 outliers final: 56 residues processed: 420 average time/residue: 0.3700 time to fit residues: 247.7015 Evaluate side-chains 371 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 308 time to evaluate : 2.892 ------------------------------------------------------------------------------- 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 129 GLU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 185 ASP 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 292 HIS 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 520 ARG 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 777 LEU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ILE 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 282 GLN Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 356 PHE Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1060 GLU Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 76 VAL 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 38 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain H residue 51 LYS 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 P residue 42 VAL Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 187 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 66 optimal weight: 0.0670 chunk 68 optimal weight: 7.9990 chunk 296 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS B 911 HIS ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.091739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066410 restraints weight = 89585.606| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 4.51 r_work: 0.3185 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.7842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26884 Z= 0.123 Angle : 0.624 15.443 36293 Z= 0.310 Chirality : 0.045 0.238 4021 Planarity : 0.004 0.054 4702 Dihedral : 4.124 21.495 3643 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.05 % Allowed : 26.94 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3266 helix: 1.26 (0.15), residues: 1289 sheet: -0.82 (0.22), residues: 503 loop : -0.10 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B1057 HIS 0.026 0.001 HIS A 292 PHE 0.024 0.001 PHE B 74 TYR 0.022 0.001 TYR E 38 ARG 0.014 0.000 ARG E 157 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 1191) hydrogen bonds : angle 4.69367 ( 3357) metal coordination : bond 0.00684 ( 20) metal coordination : angle 5.65429 ( 27) covalent geometry : bond 0.00284 (26864) covalent geometry : angle 0.60530 (36266) *********************** 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 411 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 324 time to evaluate : 2.988 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: A 44 MET cc_start: 0.8972 (mmm) cc_final: 0.8727 (mmm) REVERT: A 63 ARG cc_start: 0.8145 (tpp-160) cc_final: 0.7797 (tpp-160) REVERT: A 71 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.6478 (t80) REVERT: A 88 THR cc_start: 0.8345 (m) cc_final: 0.8073 (p) REVERT: A 89 ILE cc_start: 0.8619 (mt) cc_final: 0.8416 (mt) REVERT: A 312 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7453 (t80) REVERT: A 426 SER cc_start: 0.9081 (m) cc_final: 0.8865 (p) REVERT: A 464 MET cc_start: 0.8697 (mtp) cc_final: 0.8292 (mtp) REVERT: A 520 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8232 (ttt-90) REVERT: A 592 MET cc_start: 0.9489 (mtm) cc_final: 0.9226 (mpp) REVERT: A 721 MET cc_start: 0.8428 (mmm) cc_final: 0.8073 (tpp) REVERT: A 741 MET cc_start: 0.8195 (mmm) cc_final: 0.7805 (tpt) REVERT: B 74 PHE cc_start: 0.7990 (t80) cc_final: 0.7754 (t80) REVERT: B 122 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7560 (mm-30) REVERT: B 293 TYR cc_start: 0.8613 (t80) cc_final: 0.8339 (t80) REVERT: B 500 MET cc_start: 0.7663 (mmm) cc_final: 0.7097 (mmm) REVERT: B 625 MET cc_start: 0.8360 (tpp) cc_final: 0.7786 (tpp) REVERT: B 640 MET cc_start: 0.7329 (tpp) cc_final: 0.6341 (ttt) REVERT: B 1044 ILE cc_start: 0.8416 (mm) cc_final: 0.8156 (mt) REVERT: B 1093 TYR cc_start: 0.8137 (m-10) cc_final: 0.7794 (m-10) REVERT: C 294 MET cc_start: 0.8811 (mmp) cc_final: 0.8584 (mmt) REVERT: C 359 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8258 (mt) REVERT: D 65 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9020 (mm) REVERT: E 12 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8199 (ttp80) REVERT: F 42 ARG cc_start: 0.6858 (ptt-90) cc_final: 0.6141 (ptp90) REVERT: F 51 PHE cc_start: 0.1815 (OUTLIER) cc_final: 0.0482 (p90) REVERT: H 27 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8006 (mmtt) REVERT: H 39 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7717 (mt0) REVERT: P 6 TYR cc_start: 0.8380 (m-10) cc_final: 0.8152 (m-10) REVERT: P 15 VAL cc_start: 0.7531 (t) cc_final: 0.7271 (m) REVERT: P 18 ASP cc_start: 0.8406 (t70) cc_final: 0.7853 (t70) outliers start: 87 outliers final: 60 residues processed: 390 average time/residue: 0.3727 time to fit residues: 230.8585 Evaluate side-chains 370 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 303 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 31 THR 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 163 TRP Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 520 ARG 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 865 ILE Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 165 ILE 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 327 LEU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1080 CYS 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 96 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 76 VAL 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 E residue 170 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 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 P residue 42 VAL 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 179 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 241 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 271 optimal weight: 30.0000 chunk 237 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 256 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 611 ASN F 68 ASN F 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.089437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.064677 restraints weight = 87816.224| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 4.47 r_work: 0.3009 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.9061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 26884 Z= 0.191 Angle : 0.688 16.421 36293 Z= 0.346 Chirality : 0.047 0.410 4021 Planarity : 0.005 0.067 4702 Dihedral : 4.261 23.036 3643 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.05 % Allowed : 26.76 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3266 helix: 1.09 (0.15), residues: 1299 sheet: -0.75 (0.23), residues: 501 loop : -0.15 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B1057 HIS 0.026 0.001 HIS A 292 PHE 0.018 0.002 PHE B 356 TYR 0.031 0.002 TYR B 194 ARG 0.024 0.001 ARG B 199 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 1191) hydrogen bonds : angle 4.74853 ( 3357) metal coordination : bond 0.00798 ( 20) metal coordination : angle 5.92300 ( 27) covalent geometry : bond 0.00430 (26864) covalent geometry : angle 0.66902 (36266) *********************** 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 386 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 299 time to evaluate : 2.891 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: A 37 TYR cc_start: 0.8815 (m-80) cc_final: 0.8499 (m-80) REVERT: A 44 MET cc_start: 0.9032 (mmm) cc_final: 0.8802 (mmm) REVERT: A 63 ARG cc_start: 0.8288 (tpp-160) cc_final: 0.7990 (tpp-160) REVERT: A 71 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.6652 (t80) REVERT: A 88 THR cc_start: 0.8648 (m) cc_final: 0.8438 (p) REVERT: A 114 MET cc_start: 0.8726 (mtt) cc_final: 0.8492 (mmm) REVERT: A 315 ASN cc_start: 0.8229 (m110) cc_final: 0.8001 (m110) REVERT: A 426 SER cc_start: 0.9293 (m) cc_final: 0.9054 (p) REVERT: A 464 MET cc_start: 0.8946 (mtp) cc_final: 0.8310 (mtp) REVERT: A 741 MET cc_start: 0.8419 (mmm) cc_final: 0.8099 (tpt) REVERT: B 74 PHE cc_start: 0.8040 (t80) cc_final: 0.7811 (t80) REVERT: B 122 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7683 (mm-30) REVERT: B 286 TYR cc_start: 0.9266 (t80) cc_final: 0.9004 (t80) REVERT: B 293 TYR cc_start: 0.8579 (t80) cc_final: 0.8270 (t80) REVERT: B 500 MET cc_start: 0.7851 (mmm) cc_final: 0.7303 (mmm) REVERT: B 625 MET cc_start: 0.8903 (tpp) cc_final: 0.8270 (tpp) REVERT: B 640 MET cc_start: 0.7779 (tpp) cc_final: 0.7292 (ttt) REVERT: B 756 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8831 (mm-30) REVERT: B 791 GLU cc_start: 0.9187 (mp0) cc_final: 0.8668 (tp30) REVERT: B 1044 ILE cc_start: 0.8545 (mm) cc_final: 0.8337 (mt) REVERT: B 1086 ILE cc_start: 0.8473 (mm) cc_final: 0.8255 (mm) REVERT: B 1091 MET cc_start: 0.6252 (tpp) cc_final: 0.5985 (ttt) REVERT: B 1093 TYR cc_start: 0.8218 (m-80) cc_final: 0.7832 (m-80) REVERT: D 65 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9131 (mm) REVERT: F 42 ARG cc_start: 0.7173 (ptt-90) cc_final: 0.6933 (ptt-90) REVERT: F 51 PHE cc_start: 0.2026 (OUTLIER) cc_final: 0.0606 (p90) REVERT: H 27 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8311 (mmtt) REVERT: H 47 ASP cc_start: 0.7968 (t0) cc_final: 0.7741 (t0) REVERT: H 67 SER cc_start: 0.8942 (m) cc_final: 0.8447 (p) REVERT: L 8 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8512 (tptp) REVERT: N 1 MET cc_start: 0.8875 (mmp) cc_final: 0.8588 (mmp) REVERT: P 15 VAL cc_start: 0.7406 (t) cc_final: 0.7123 (m) REVERT: P 18 ASP cc_start: 0.8449 (t70) cc_final: 0.7843 (t70) outliers start: 87 outliers final: 62 residues processed: 370 average time/residue: 0.4075 time to fit residues: 242.0723 Evaluate side-chains 347 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 280 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 71 PHE 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 278 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 473 GLU 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 690 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 165 ILE 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 327 LEU Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 968 MET Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1060 GLU Chi-restraints excluded: chain B residue 1080 CYS Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 217 ILE 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 147 ILE 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 75 TYR Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 46 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 319 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 276 optimal weight: 30.0000 chunk 135 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 315 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 911 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.084525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.059110 restraints weight = 89000.016| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 4.22 r_work: 0.2950 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.9930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26884 Z= 0.169 Angle : 0.661 16.498 36293 Z= 0.331 Chirality : 0.046 0.233 4021 Planarity : 0.005 0.065 4702 Dihedral : 4.236 19.247 3643 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.91 % Allowed : 27.57 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3266 helix: 1.11 (0.15), residues: 1294 sheet: -0.55 (0.24), residues: 459 loop : -0.18 (0.17), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1057 HIS 0.013 0.001 HIS A 292 PHE 0.026 0.002 PHE F 96 TYR 0.017 0.001 TYR A 113 ARG 0.014 0.001 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 1191) hydrogen bonds : angle 4.75675 ( 3357) metal coordination : bond 0.00860 ( 20) metal coordination : angle 6.19318 ( 27) covalent geometry : bond 0.00391 (26864) covalent geometry : angle 0.63923 (36266) *********************** 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 381 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 298 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8843 (m-80) cc_final: 0.8526 (m-80) REVERT: A 44 MET cc_start: 0.9117 (mmm) cc_final: 0.8856 (mmm) REVERT: A 71 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.6600 (t80) REVERT: A 88 THR cc_start: 0.8915 (m) cc_final: 0.8675 (p) REVERT: A 114 MET cc_start: 0.8634 (mtt) cc_final: 0.8294 (mmm) REVERT: A 315 ASN cc_start: 0.8375 (m110) cc_final: 0.8169 (m110) REVERT: A 464 MET cc_start: 0.8998 (mtp) cc_final: 0.8490 (mtp) REVERT: A 592 MET cc_start: 0.9564 (mtt) cc_final: 0.9276 (mpp) REVERT: A 884 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8015 (mttt) REVERT: A 899 MET cc_start: 0.8711 (ptp) cc_final: 0.8450 (ptp) REVERT: B 74 PHE cc_start: 0.8205 (t80) cc_final: 0.7901 (t80) REVERT: B 179 GLU cc_start: 0.8079 (mp0) cc_final: 0.7609 (pm20) REVERT: B 286 TYR cc_start: 0.9228 (t80) cc_final: 0.9025 (t80) REVERT: B 293 TYR cc_start: 0.8502 (t80) cc_final: 0.8129 (t80) REVERT: B 320 MET cc_start: 0.7312 (mmp) cc_final: 0.7034 (mmp) REVERT: B 500 MET cc_start: 0.8044 (mmm) cc_final: 0.7527 (mmm) REVERT: B 557 TYR cc_start: 0.7272 (m-10) cc_final: 0.7004 (m-80) REVERT: B 616 GLU cc_start: 0.8642 (tt0) cc_final: 0.8398 (tp30) REVERT: B 640 MET cc_start: 0.8173 (tpp) cc_final: 0.7830 (ttt) REVERT: B 756 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8867 (mt-10) REVERT: B 791 GLU cc_start: 0.9173 (mp0) cc_final: 0.8833 (tp30) REVERT: B 1057 TRP cc_start: 0.8318 (m100) cc_final: 0.7889 (m100) REVERT: B 1060 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: B 1093 TYR cc_start: 0.8362 (m-80) cc_final: 0.7981 (m-80) REVERT: B 1103 LYS cc_start: 0.7619 (mttt) cc_final: 0.7264 (mtmm) REVERT: D 65 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9198 (mm) REVERT: E 47 SER cc_start: 0.8123 (p) cc_final: 0.7918 (m) REVERT: E 60 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8823 (tp) REVERT: E 136 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.5824 (pp) REVERT: F 51 PHE cc_start: 0.2379 (OUTLIER) cc_final: 0.0979 (p90) REVERT: F 68 ASN cc_start: 0.8624 (m110) cc_final: 0.7958 (p0) REVERT: H 39 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8108 (mt0) REVERT: H 67 SER cc_start: 0.9161 (m) cc_final: 0.8697 (p) REVERT: N 1 MET cc_start: 0.8929 (mmp) cc_final: 0.8663 (mmp) REVERT: N 33 LYS cc_start: 0.9289 (tppt) cc_final: 0.8988 (mmtm) REVERT: N 34 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8965 (p) REVERT: P 15 VAL cc_start: 0.7541 (t) cc_final: 0.7243 (m) outliers start: 83 outliers final: 55 residues processed: 364 average time/residue: 0.3961 time to fit residues: 228.0243 Evaluate side-chains 334 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 271 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 185 ASP 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 305 LEU Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 473 GLU 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 865 ILE Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 885 THR 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 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 548 ILE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1060 GLU Chi-restraints excluded: chain B residue 1080 CYS Chi-restraints excluded: chain B residue 1099 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 303 ILE 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 217 ILE 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 75 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 136 LEU Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain F residue 38 TYR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 1 MET 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 N residue 34 VAL 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 51 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 214 optimal weight: 0.0470 chunk 105 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 279 optimal weight: 0.2980 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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** A 292 HIS B 447 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.085088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.059637 restraints weight = 88735.647| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 4.23 r_work: 0.2969 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 1.0105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26884 Z= 0.117 Angle : 0.656 14.542 36293 Z= 0.323 Chirality : 0.045 0.225 4021 Planarity : 0.005 0.056 4702 Dihedral : 4.111 19.192 3643 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.07 % Allowed : 28.72 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 3266 helix: 1.24 (0.15), residues: 1279 sheet: -0.50 (0.24), residues: 459 loop : -0.07 (0.17), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.007 0.001 HIS B 302 PHE 0.035 0.001 PHE F 96 TYR 0.023 0.001 TYR B 315 ARG 0.006 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 1191) hydrogen bonds : angle 4.61475 ( 3357) metal coordination : bond 0.00530 ( 20) metal coordination : angle 5.63385 ( 27) covalent geometry : bond 0.00270 (26864) covalent geometry : angle 0.63811 (36266) *********************** 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 347 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 288 time to evaluate : 3.417 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: 0.8840 (m-80) cc_final: 0.8522 (m-80) REVERT: A 44 MET cc_start: 0.9091 (mmm) cc_final: 0.8807 (mmm) REVERT: A 71 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6510 (t80) REVERT: A 114 MET cc_start: 0.8669 (mtt) cc_final: 0.8314 (mmm) REVERT: A 210 MET cc_start: 0.8207 (ttp) cc_final: 0.7886 (ttm) REVERT: A 464 MET cc_start: 0.8921 (mtp) cc_final: 0.8353 (mtp) REVERT: A 592 MET cc_start: 0.9517 (mtt) cc_final: 0.9195 (mpp) REVERT: A 627 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8509 (tm-30) REVERT: B 74 PHE cc_start: 0.8208 (t80) cc_final: 0.7881 (t80) REVERT: B 166 VAL cc_start: 0.9117 (t) cc_final: 0.8881 (m) REVERT: B 286 TYR cc_start: 0.9254 (t80) cc_final: 0.8991 (t80) REVERT: B 293 TYR cc_start: 0.8535 (t80) cc_final: 0.8192 (t80) REVERT: B 402 GLU cc_start: 0.8006 (tp30) cc_final: 0.7714 (pt0) REVERT: B 500 MET cc_start: 0.8081 (mmm) cc_final: 0.7588 (mmm) REVERT: B 557 TYR cc_start: 0.7257 (m-10) cc_final: 0.6932 (m-80) REVERT: B 640 MET cc_start: 0.8064 (tpp) cc_final: 0.7739 (ttt) REVERT: B 756 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8948 (mm-30) REVERT: B 1093 TYR cc_start: 0.8397 (m-80) cc_final: 0.7965 (m-80) REVERT: B 1103 LYS cc_start: 0.7596 (mttt) cc_final: 0.7242 (mtmm) REVERT: D 65 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9214 (mm) REVERT: E 47 SER cc_start: 0.8066 (p) cc_final: 0.7834 (m) REVERT: F 51 PHE cc_start: 0.1442 (OUTLIER) cc_final: -0.0018 (p90) REVERT: H 39 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8208 (mt0) REVERT: H 67 SER cc_start: 0.9205 (m) cc_final: 0.8775 (p) REVERT: N 1 MET cc_start: 0.8885 (mmp) cc_final: 0.8655 (mmp) REVERT: P 14 GLU cc_start: 0.8702 (mp0) cc_final: 0.8395 (mp0) REVERT: P 15 VAL cc_start: 0.7575 (t) cc_final: 0.7303 (m) outliers start: 59 outliers final: 47 residues processed: 334 average time/residue: 0.3874 time to fit residues: 206.7713 Evaluate side-chains 311 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 3.322 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 185 ASP 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 292 HIS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 473 GLU 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 865 ILE Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 1037 HIS Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1080 CYS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 17 MET 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 147 ILE 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 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 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 177 optimal weight: 0.0470 chunk 26 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 293 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 295 optimal weight: 0.0020 chunk 131 optimal weight: 4.9990 chunk 316 optimal weight: 7.9990 chunk 320 optimal weight: 7.9990 chunk 194 optimal weight: 20.0000 overall best weight: 2.4092 ------------------------------------------------------------------------------- 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** F 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.081571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055795 restraints weight = 89046.071| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 4.19 r_work: 0.2871 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 1.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26884 Z= 0.183 Angle : 0.697 14.972 36293 Z= 0.351 Chirality : 0.046 0.260 4021 Planarity : 0.005 0.072 4702 Dihedral : 4.314 36.413 3643 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.10 % Allowed : 28.90 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3266 helix: 1.18 (0.15), residues: 1278 sheet: -0.50 (0.24), residues: 444 loop : -0.13 (0.17), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.010 0.001 HIS H 18 PHE 0.031 0.002 PHE F 96 TYR 0.017 0.001 TYR B 316 ARG 0.011 0.001 ARG E 145 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 1191) hydrogen bonds : angle 4.74183 ( 3357) metal coordination : bond 0.00756 ( 20) metal coordination : angle 5.99719 ( 27) covalent geometry : bond 0.00433 (26864) covalent geometry : angle 0.67817 (36266) ********************** 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 331 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 271 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8827 (m-80) cc_final: 0.8526 (m-80) REVERT: A 44 MET cc_start: 0.9087 (mmm) cc_final: 0.8804 (mmm) REVERT: A 63 ARG cc_start: 0.8288 (tpp-160) cc_final: 0.7959 (tpp-160) REVERT: A 71 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.6503 (t80) REVERT: A 114 MET cc_start: 0.8710 (mtt) cc_final: 0.8020 (mmm) REVERT: A 210 MET cc_start: 0.8443 (ttp) cc_final: 0.8137 (ttm) REVERT: A 464 MET cc_start: 0.9070 (mtp) cc_final: 0.8455 (mtp) REVERT: A 592 MET cc_start: 0.9538 (mtt) cc_final: 0.9226 (mpp) REVERT: A 627 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8507 (tm-30) REVERT: A 714 ASP cc_start: 0.8631 (m-30) cc_final: 0.8132 (t70) REVERT: A 884 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8083 (mttp) REVERT: B 18 MET cc_start: 0.9429 (tpp) cc_final: 0.9128 (tpt) REVERT: B 56 ASP cc_start: 0.8502 (m-30) cc_final: 0.8253 (p0) REVERT: B 74 PHE cc_start: 0.8405 (t80) cc_final: 0.8038 (t80) REVERT: B 286 TYR cc_start: 0.9221 (t80) cc_final: 0.8942 (t80) REVERT: B 483 MET cc_start: 0.7904 (mtm) cc_final: 0.7585 (ptp) REVERT: B 497 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8358 (pp20) REVERT: B 500 MET cc_start: 0.8288 (mmm) cc_final: 0.7760 (mmm) REVERT: B 731 MET cc_start: 0.8993 (mtm) cc_final: 0.8516 (mtm) REVERT: B 756 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8907 (mt-10) REVERT: B 1093 TYR cc_start: 0.8503 (m-80) cc_final: 0.8109 (m-80) REVERT: B 1103 LYS cc_start: 0.7838 (mttt) cc_final: 0.7313 (mtmm) REVERT: C 80 MET cc_start: 0.8642 (ptp) cc_final: 0.8229 (pmm) REVERT: D 65 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9187 (mm) REVERT: D 257 GLN cc_start: 0.9388 (tm-30) cc_final: 0.8898 (pt0) REVERT: E 47 SER cc_start: 0.8404 (p) cc_final: 0.8155 (m) REVERT: E 60 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8938 (tp) REVERT: F 51 PHE cc_start: 0.1183 (OUTLIER) cc_final: -0.0297 (p90) REVERT: F 68 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8012 (p0) REVERT: H 39 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8345 (mt0) REVERT: H 67 SER cc_start: 0.9264 (m) cc_final: 0.8861 (p) REVERT: P 14 GLU cc_start: 0.8725 (mp0) cc_final: 0.8445 (mp0) REVERT: P 15 VAL cc_start: 0.7596 (t) cc_final: 0.7290 (m) outliers start: 60 outliers final: 46 residues processed: 319 average time/residue: 0.3993 time to fit residues: 201.9317 Evaluate side-chains 312 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 3.330 ------------------------------------------------------------------------------- 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 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 292 HIS Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 1037 HIS Chi-restraints excluded: chain B residue 1053 LYS Chi-restraints excluded: chain B residue 1080 CYS Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 235 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 217 ILE 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 110 ILE Chi-restraints excluded: chain E residue 147 ILE 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 F residue 68 ASN Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 75 TYR Chi-restraints excluded: chain K residue 1 MET 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 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 263 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 overall best weight: 2.4584 ------------------------------------------------------------------------------- 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 370 GLN F 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.081005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.055668 restraints weight = 88998.313| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 4.07 r_work: 0.2863 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 1.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26884 Z= 0.177 Angle : 0.678 14.729 36293 Z= 0.340 Chirality : 0.046 0.175 4021 Planarity : 0.005 0.057 4702 Dihedral : 4.211 20.772 3643 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.14 % Allowed : 28.76 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 3266 helix: 1.15 (0.15), residues: 1279 sheet: -0.46 (0.24), residues: 434 loop : -0.13 (0.17), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.009 0.001 HIS A 292 PHE 0.032 0.001 PHE F 96 TYR 0.018 0.001 TYR B 315 ARG 0.011 0.001 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 1191) hydrogen bonds : angle 4.73392 ( 3357) metal coordination : bond 0.00741 ( 20) metal coordination : angle 5.95697 ( 27) covalent geometry : bond 0.00414 (26864) covalent geometry : angle 0.65890 (36266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16840.23 seconds wall clock time: 288 minutes 19.25 seconds (17299.25 seconds total)