Starting phenix.real_space_refine on Thu Mar 5 17:32:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xyu_72341/03_2026/9xyu_72341.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xyu_72341/03_2026/9xyu_72341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xyu_72341/03_2026/9xyu_72341.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xyu_72341/03_2026/9xyu_72341.map" model { file = "/net/cci-nas-00/data/ceres_data/9xyu_72341/03_2026/9xyu_72341.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xyu_72341/03_2026/9xyu_72341.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 P 49 5.49 5 S 146 5.16 5 C 14758 2.51 5 N 4043 2.21 5 O 4400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23406 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4882 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 2 Chain: "B" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5659 Classifications: {'peptide': 702} Link IDs: {'PTRANS': 29, 'TRANS': 672} Chain breaks: 1 Chain: "C" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1234 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 147} Chain: "D" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3483 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain breaks: 1 Chain: "E" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2896 Classifications: {'peptide': 369} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Chain: "F" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2034 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 1 Chain: "G" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "H" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 332 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain breaks: 1 Chain: "K" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1348 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 154} Chain breaks: 1 Chain: "L" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 548 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "M" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 454 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" 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 5825 SG CYS B 116 104.911 112.224 124.878 1.00215.07 S ATOM 6134 SG CYS B 155 109.864 112.712 129.150 1.00237.11 S ATOM 5965 SG CYS B 134 109.648 116.075 123.489 1.00231.89 S ATOM 6423 SG CYS B 190 110.793 109.752 123.711 1.00211.24 S ATOM 17832 SG CYS E 345 65.668 35.272 86.037 1.00132.03 S ATOM 17854 SG CYS E 348 63.250 37.315 83.882 1.00124.01 S ATOM 18011 SG CYS E 368 66.907 38.318 84.116 1.00125.02 S ATOM 18032 SG CYS E 371 64.515 38.764 87.079 1.00124.77 S ATOM 17952 SG CYS E 360 69.287 37.467 97.798 1.00140.77 S ATOM 17970 SG CYS E 363 66.452 35.005 98.469 1.00136.58 S ATOM 18119 SG CYS E 382 65.937 37.976 96.106 1.00123.54 S ATOM 18136 SG CYS E 385 66.095 38.450 99.830 1.00124.16 S ATOM 17396 SG CYS E 291 40.772 62.965 112.469 1.00144.02 S ATOM 17418 SG CYS E 294 38.012 64.909 114.197 1.00155.44 S ATOM 17507 SG CYS E 305 40.644 66.804 112.270 1.00145.39 S ATOM 17530 SG CYS E 308 41.511 65.140 115.570 1.00157.34 S ATOM 20032 SG CYS F 268 62.248 58.979 114.126 1.00121.82 S ATOM 20051 SG CYS F 271 62.786 56.045 111.729 1.00121.83 S ATOM 20136 SG CYS F 282 62.669 55.433 115.479 1.00143.02 S ATOM 20156 SG CYS F 285 65.619 57.234 113.991 1.00147.41 S ATOM 19924 SG CYS F 255 52.299 48.694 115.457 1.00130.62 S ATOM 19941 SG CYS F 257 54.538 47.487 118.249 1.00135.71 S ATOM 20090 SG CYS F 276 51.172 49.214 119.114 1.00135.42 S ATOM 21075 SG CYS K 105 127.762 131.662 64.982 1.00317.24 S ATOM 21099 SG CYS K 108 130.473 134.149 65.973 1.00318.15 S ATOM 21247 SG CYS K 126 127.257 134.003 67.974 1.00302.96 S ATOM 21269 SG CYS K 129 127.292 135.428 64.452 1.00294.44 S Time building chain proxies: 4.85, per 1000 atoms: 0.21 Number of scatterers: 23406 At special positions: 0 Unit cell: (145.176, 159.904, 152.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 146 16.00 P 49 15.00 O 4400 8.00 N 4043 7.00 C 14758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 368 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb=" ZN F 402 " pdb="ZN ZN F 402 " - pdb=" NE2 HIS F 258 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 255 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 257 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 276 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 108 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 129 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 126 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 105 " Number of angles added : 33 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5304 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 25 sheets defined 44.8% alpha, 12.3% beta 18 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 150 through 158 Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.958A pdb=" N GLN A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.663A pdb=" N GLU A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 196' Processing helix chain 'A' and resid 277 through 286 removed outlier: 4.084A pdb=" N ILE A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 368 through 381 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 421 through 432 Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.889A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 removed outlier: 3.756A pdb=" N LEU A 483 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 516 through 522 removed outlier: 3.628A pdb=" N GLU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 534 No H-bonds generated for 'chain 'A' and resid 531 through 534' Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 586 through 598 removed outlier: 3.930A pdb=" N LYS A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N HIS A 598 " --> pdb=" O GLN A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 641 Processing helix chain 'A' and resid 669 through 676 Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 706 through 718 Processing helix chain 'B' and resid 19 through 34 Processing helix chain 'B' and resid 48 through 59 Processing helix chain 'B' and resid 77 through 98 Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 142 through 148 removed outlier: 3.642A pdb=" N TYR B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 148' Processing helix chain 'B' and resid 156 through 162 removed outlier: 3.722A pdb=" N ASP B 162 " --> pdb=" O TYR B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 191 through 197 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 215 through 221 removed outlier: 4.404A pdb=" N LEU B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 247 Processing helix chain 'B' and resid 253 through 283 Processing helix chain 'B' and resid 322 through 345 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 375 through 385 Processing helix chain 'B' and resid 395 through 409 Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.551A pdb=" N ARG B 450 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 Proline residue: B 468 - end of helix No H-bonds generated for 'chain 'B' and resid 464 through 470' Processing helix chain 'B' and resid 514 through 527 Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 558 through 564 Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 604 through 607 No H-bonds generated for 'chain 'B' and resid 604 through 607' Processing helix chain 'B' and resid 633 through 642 Processing helix chain 'B' and resid 648 through 667 removed outlier: 4.869A pdb=" N ALA B 667 " --> pdb=" O CYS B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 687 through 690 No H-bonds generated for 'chain 'B' and resid 687 through 690' Processing helix chain 'B' and resid 695 through 701 removed outlier: 4.665A pdb=" N HIS B 700 " --> pdb=" O TRP B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 725 Processing helix chain 'B' and resid 730 through 736 removed outlier: 3.616A pdb=" N LEU B 736 " --> pdb=" O ASP B 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 412 Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 455 through 478 Processing helix chain 'C' and resid 484 through 515 removed outlier: 4.812A pdb=" N CYS C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Proline residue: C 507 - end of helix Processing helix chain 'C' and resid 521 through 546 removed outlier: 3.574A pdb=" N HIS C 524 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 546 " --> pdb=" O ARG C 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 28 through 36 Processing helix chain 'D' and resid 38 through 47 Processing helix chain 'D' and resid 50 through 58 Processing helix chain 'D' and resid 68 through 74 Processing helix chain 'D' and resid 80 through 93 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 145 through 164 Processing helix chain 'D' and resid 173 through 182 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 222 Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 232 through 241 Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 285 through 288 No H-bonds generated for 'chain 'D' and resid 285 through 288' Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 348 through 357 Processing helix chain 'D' and resid 361 through 371 Processing helix chain 'D' and resid 374 through 376 No H-bonds generated for 'chain 'D' and resid 374 through 376' Processing helix chain 'D' and resid 385 through 397 Processing helix chain 'D' and resid 415 through 428 Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 30 through 41 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 80 through 98 Processing helix chain 'E' and resid 124 through 136 removed outlier: 4.387A pdb=" N ASP E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 156 Processing helix chain 'E' and resid 182 through 191 Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 225 through 234 Processing helix chain 'E' and resid 273 through 277 Processing helix chain 'E' and resid 315 through 325 removed outlier: 4.513A pdb=" N SER E 321 " --> pdb=" O HIS E 317 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N HIS E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N HIS E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 378 Processing helix chain 'E' and resid 383 through 386 No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'F' and resid 19 through 27 Processing helix chain 'F' and resid 34 through 51 Processing helix chain 'F' and resid 102 through 120 Processing helix chain 'F' and resid 133 through 150 Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'F' and resid 220 through 231 removed outlier: 4.397A pdb=" N LEU F 224 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE F 231 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 240 removed outlier: 3.954A pdb=" N GLN F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 288 Processing helix chain 'G' and resid 14 through 26 Processing helix chain 'G' and resid 47 through 63 removed outlier: 3.798A pdb=" N VAL G 50 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASN G 51 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP G 62 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN G 63 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 890 through 901 Processing helix chain 'H' and resid 904 through 914 removed outlier: 3.935A pdb=" N ARG H 908 " --> pdb=" O TRP H 904 " (cutoff:3.500A) Processing helix chain 'H' and resid 927 through 933 Processing helix chain 'H' and resid 936 through 938 No H-bonds generated for 'chain 'H' and resid 936 through 938' Processing helix chain 'K' and resid 116 through 120 Processing helix chain 'K' and resid 141 through 147 Processing helix chain 'K' and resid 153 through 156 No H-bonds generated for 'chain 'K' and resid 153 through 156' Processing helix chain 'K' and resid 183 through 194 Processing helix chain 'K' and resid 197 through 229 removed outlier: 3.852A pdb=" N ARG K 228 " --> pdb=" O LYS K 224 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ALA K 229 " --> pdb=" O GLU K 225 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 61 removed outlier: 6.589A pdb=" N LYS A 59 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ARG D 337 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N MET D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 317 " --> pdb=" O VAL D 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.509A pdb=" N PHE A 85 " --> pdb=" O TRP A 77 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 113 through 117 current: chain 'A' and resid 105 through 108 Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 171 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 167 through 171 current: chain 'A' and resid 174 through 179 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 174 through 179 current: chain 'A' and resid 268 through 271 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 392 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 389 through 392 current: chain 'A' and resid 405 through 409 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 405 through 409 current: chain 'A' and resid 361 through 365 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 361 through 365 current: chain 'A' and resid 438 through 441 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 438 through 441 current: chain 'A' and resid 463 through 467 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 463 through 467 current: chain 'A' and resid 336 through 339 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 336 through 339 current: chain 'A' and resid 487 through 490 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 690 removed outlier: 3.529A pdb=" N LYS A 688 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 690 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP A 511 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ALA A 657 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ALA A 508 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE A 659 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL A 510 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N SER A 661 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N CYS A 512 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL A 663 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.976A pdb=" N LEU B 8 " --> pdb=" O VAL B 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 479 through 481 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 479 through 481 current: chain 'B' and resid 36 through 41 removed outlier: 5.004A pdb=" N VAL B 454 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 38 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 453 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS B 69 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL B 232 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE B 71 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASP B 234 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N CYS B 73 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 249 through 252 removed outlier: 7.085A pdb=" N VAL B 249 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU B 433 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU B 251 " --> pdb=" O PRO B 431 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE B 432 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 436 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE B 418 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU B 352 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 490 through 495 removed outlier: 8.303A pdb=" N GLY B 675 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N MET B 493 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET B 677 " --> pdb=" O MET B 493 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE B 495 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE B 679 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 96 through 100 removed outlier: 3.646A pdb=" N ILE D 109 " --> pdb=" O HIS D 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 248 through 251 removed outlier: 7.819A pdb=" N ARG D 279 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU D 270 " --> pdb=" O THR D 284 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 402 through 409 removed outlier: 3.646A pdb=" N TYR D 409 " --> pdb=" O MET D 441 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N MET D 441 " --> pdb=" O TYR D 409 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE D 433 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 184 through 186 removed outlier: 7.197A pdb=" N LEU D 184 " --> pdb=" O THR D 197 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 113 through 118 removed outlier: 6.819A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N SER E 164 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N TYR E 62 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLU E 166 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL E 64 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU E 168 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ASP E 66 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE E 170 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG E 195 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ILE E 169 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER E 197 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N PHE E 171 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE E 199 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS E 220 " --> pdb=" O VAL E 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 289 through 291 removed outlier: 4.079A pdb=" N ALA E 296 " --> pdb=" O CYS E 291 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 332 through 335 removed outlier: 3.529A pdb=" N GLN E 332 " --> pdb=" O VAL E 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 303 through 305 removed outlier: 4.077A pdb=" N LEU E 310 " --> pdb=" O CYS E 305 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 343 through 345 removed outlier: 6.902A pdb=" N ARG E 343 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY E 350 " --> pdb=" O CYS E 345 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 67 through 69 removed outlier: 3.606A pdb=" N ALA F 58 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE F 13 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU F 156 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU F 10 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS F 158 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N VAL F 12 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG F 160 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL F 14 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU F 162 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ASP F 16 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE F 164 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU F 190 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL F 163 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP F 192 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LYS F 165 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N CYS F 194 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 253 through 255 removed outlier: 3.562A pdb=" N ALA F 253 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN F 260 " --> pdb=" O CYS F 255 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 273 through 275 removed outlier: 3.722A pdb=" N SER F 273 " --> pdb=" O CYS F 268 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR F 266 " --> pdb=" O PHE F 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 5 through 11 removed outlier: 6.791A pdb=" N PHE G 44 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP G 37 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 103 through 105 removed outlier: 3.744A pdb=" N CYS K 105 " --> pdb=" O LYS K 110 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS K 110 " --> pdb=" O CYS K 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 138 through 140 removed outlier: 3.629A pdb=" N ILE K 139 " --> pdb=" O TYR K 181 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET K 178 " --> pdb=" O LYS K 167 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS K 167 " --> pdb=" O MET K 178 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE K 165 " --> pdb=" O LEU K 180 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 248 through 252 removed outlier: 4.998A pdb=" N THR K 260 " --> pdb=" O PRO K 248 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2436 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 10081 1.43 - 1.64: 13681 1.64 - 1.86: 214 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 23988 Sorted by residual: bond pdb=" C SER B 462 " pdb=" N PRO B 463 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.23e-02 6.61e+03 1.51e+00 bond pdb=" C3' DG L 49 " pdb=" O3' DG L 49 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" C PRO B 354 " pdb=" N PRO B 355 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.42e+00 bond pdb=" C3' DA L 46 " pdb=" O3' DA L 46 " ideal model delta sigma weight residual 1.422 1.448 -0.026 3.00e-02 1.11e+03 7.50e-01 bond pdb=" C3' DA L 51 " pdb=" O3' DA L 51 " ideal model delta sigma weight residual 1.422 1.448 -0.026 3.00e-02 1.11e+03 7.36e-01 ... (remaining 23983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 32167 1.37 - 2.74: 353 2.74 - 4.12: 93 4.12 - 5.49: 16 5.49 - 6.86: 7 Bond angle restraints: 32636 Sorted by residual: angle pdb=" N THR B 122 " pdb=" CA THR B 122 " pdb=" C THR B 122 " ideal model delta sigma weight residual 109.81 114.78 -4.97 2.21e+00 2.05e-01 5.05e+00 angle pdb=" CA VAL C 453 " pdb=" CB VAL C 453 " pdb=" CG1 VAL C 453 " ideal model delta sigma weight residual 110.40 114.13 -3.73 1.70e+00 3.46e-01 4.80e+00 angle pdb=" C ASP A 474 " pdb=" N ASP A 475 " pdb=" CA ASP A 475 " ideal model delta sigma weight residual 121.54 125.41 -3.87 1.91e+00 2.74e-01 4.10e+00 angle pdb=" C MET C 452 " pdb=" N VAL C 453 " pdb=" CA VAL C 453 " ideal model delta sigma weight residual 122.13 125.78 -3.65 1.85e+00 2.92e-01 3.90e+00 angle pdb=" CA LEU B 271 " pdb=" CB LEU B 271 " pdb=" CG LEU B 271 " ideal model delta sigma weight residual 116.30 123.16 -6.86 3.50e+00 8.16e-02 3.84e+00 ... (remaining 32631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 14158 35.09 - 70.18: 262 70.18 - 105.28: 6 105.28 - 140.37: 1 140.37 - 175.46: 2 Dihedral angle restraints: 14429 sinusoidal: 6249 harmonic: 8180 Sorted by residual: dihedral pdb=" C4' DG L 49 " pdb=" C3' DG L 49 " pdb=" O3' DG L 49 " pdb=" P DC L 50 " ideal model delta sinusoidal sigma weight residual -140.00 35.46 -175.46 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT L 47 " pdb=" C3' DT L 47 " pdb=" O3' DT L 47 " pdb=" P DT L 48 " ideal model delta sinusoidal sigma weight residual 220.00 75.36 144.64 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DA L 51 " pdb=" C3' DA L 51 " pdb=" O3' DA L 51 " pdb=" P DC L 52 " ideal model delta sinusoidal sigma weight residual -140.00 -2.42 -137.58 1 3.50e+01 8.16e-04 1.36e+01 ... (remaining 14426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2376 0.027 - 0.054: 810 0.054 - 0.081: 249 0.081 - 0.108: 175 0.108 - 0.135: 47 Chirality restraints: 3657 Sorted by residual: chirality pdb=" CA THR B 122 " pdb=" N THR B 122 " pdb=" C THR B 122 " pdb=" CB THR B 122 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CB VAL C 453 " pdb=" CA VAL C 453 " pdb=" CG1 VAL C 453 " pdb=" CG2 VAL C 453 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA TRP H 904 " pdb=" N TRP H 904 " pdb=" C TRP H 904 " pdb=" CB TRP H 904 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 3654 not shown) Planarity restraints: 3996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 583 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 353 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 354 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 354 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 354 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 102 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO B 103 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " 0.019 5.00e-02 4.00e+02 ... (remaining 3993 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2759 2.75 - 3.29: 23659 3.29 - 3.83: 39953 3.83 - 4.36: 45100 4.36 - 4.90: 77285 Nonbonded interactions: 188756 Sorted by model distance: nonbonded pdb=" O ILE E 194 " pdb=" OG1 THR E 215 " model vdw 2.217 3.040 nonbonded pdb=" O SER H 903 " pdb=" ND2 ASN H 907 " model vdw 2.245 3.120 nonbonded pdb=" OD2 ASP F 208 " pdb=" OH TYR F 251 " model vdw 2.246 3.040 nonbonded pdb=" OD1 ASN E 79 " pdb=" OG1 THR E 82 " model vdw 2.270 3.040 nonbonded pdb=" O ALA A 125 " pdb=" OG SER A 128 " model vdw 2.274 3.040 ... (remaining 188751 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 group one per residue 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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.700 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.002 0.037 24016 Z= 0.082 Angle : 0.423 6.862 32681 Z= 0.215 Chirality : 0.037 0.135 3657 Planarity : 0.003 0.054 3996 Dihedral : 12.292 175.462 9125 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.53 % Allowed : 6.28 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.17), residues: 2755 helix: 2.31 (0.15), residues: 1350 sheet: 0.35 (0.30), residues: 364 loop : -0.86 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 425 TYR 0.009 0.001 TYR A 534 PHE 0.007 0.001 PHE C 475 TRP 0.008 0.001 TRP H 904 HIS 0.002 0.000 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00160 (23988) covalent geometry : angle 0.41673 (32636) hydrogen bonds : bond 0.16026 ( 936) hydrogen bonds : angle 4.71141 ( 2522) metal coordination : bond 0.00266 ( 28) metal coordination : angle 2.04832 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 398 GLN cc_start: 0.8574 (pp30) cc_final: 0.8254 (pp30) REVERT: C 470 GLU cc_start: 0.9047 (pp20) cc_final: 0.8792 (pp20) REVERT: C 527 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8788 (pp20) REVERT: F 157 MET cc_start: 0.8305 (tpp) cc_final: 0.7759 (tpt) REVERT: K 118 MET cc_start: 0.8642 (mmm) cc_final: 0.8304 (mmm) REVERT: K 257 TYR cc_start: 0.8219 (m-80) cc_final: 0.8004 (m-80) outliers start: 13 outliers final: 2 residues processed: 180 average time/residue: 0.1548 time to fit residues: 44.5132 Evaluate side-chains 119 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain B residue 5 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN A 506 GLN A 677 GLN B 118 HIS B 154 HIS B 187 GLN B 543 GLN B 555 GLN B 700 HIS C 405 GLN C 458 GLN D 97 HIS D 273 GLN D 390 GLN E 99 ASN E 154 GLN ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS E 227 HIS E 340 ASN ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN F 204 GLN K 169 ASN K 208 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.055543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.040544 restraints weight = 147798.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.041870 restraints weight = 77174.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.042709 restraints weight = 52536.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.043215 restraints weight = 41901.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.043386 restraints weight = 36656.735| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24016 Z= 0.121 Angle : 0.508 10.818 32681 Z= 0.259 Chirality : 0.038 0.142 3657 Planarity : 0.004 0.057 3996 Dihedral : 12.778 175.664 3582 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.13 % Allowed : 9.16 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2755 helix: 1.98 (0.15), residues: 1341 sheet: 0.32 (0.29), residues: 366 loop : -0.85 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 898 TYR 0.013 0.001 TYR K 270 PHE 0.017 0.001 PHE F 231 TRP 0.017 0.001 TRP B 342 HIS 0.004 0.001 HIS G 42 Details of bonding type rmsd covalent geometry : bond 0.00265 (23988) covalent geometry : angle 0.49460 (32636) hydrogen bonds : bond 0.03701 ( 936) hydrogen bonds : angle 3.90575 ( 2522) metal coordination : bond 0.00874 ( 28) metal coordination : angle 3.18734 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8854 (ttm) cc_final: 0.8599 (ptm) REVERT: B 25 MET cc_start: 0.9010 (mmm) cc_final: 0.8743 (mmm) REVERT: B 57 MET cc_start: 0.9587 (tpt) cc_final: 0.9260 (mmm) REVERT: B 676 LEU cc_start: 0.8836 (tp) cc_final: 0.8577 (tp) REVERT: C 398 GLN cc_start: 0.8899 (pp30) cc_final: 0.8583 (pp30) REVERT: C 452 MET cc_start: 0.6952 (ppp) cc_final: 0.6702 (ppp) REVERT: C 492 LYS cc_start: 0.9298 (ptpt) cc_final: 0.9079 (pttp) REVERT: C 493 MET cc_start: 0.8947 (mmm) cc_final: 0.8695 (mmm) REVERT: C 527 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8975 (tm-30) REVERT: C 528 MET cc_start: 0.8197 (tpp) cc_final: 0.7695 (mmm) REVERT: E 71 MET cc_start: 0.8354 (mmm) cc_final: 0.7932 (mmm) REVERT: F 147 MET cc_start: 0.8730 (mmm) cc_final: 0.8431 (mmm) REVERT: F 157 MET cc_start: 0.8655 (tpp) cc_final: 0.8298 (tpt) REVERT: H 904 TRP cc_start: 0.8161 (OUTLIER) cc_final: 0.7453 (t-100) REVERT: H 909 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8573 (mm-30) REVERT: H 912 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7773 (pp20) REVERT: K 118 MET cc_start: 0.8303 (mmm) cc_final: 0.8088 (mmm) REVERT: K 257 TYR cc_start: 0.8503 (m-80) cc_final: 0.8302 (m-80) outliers start: 28 outliers final: 15 residues processed: 142 average time/residue: 0.1490 time to fit residues: 35.2922 Evaluate side-chains 131 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 511 TRP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain H residue 891 SER Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 116 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 40 optimal weight: 0.9980 chunk 277 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 210 optimal weight: 0.0370 chunk 191 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 118 optimal weight: 0.0070 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 HIS ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.055611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.040619 restraints weight = 146342.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.041932 restraints weight = 76071.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.042762 restraints weight = 51854.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.043243 restraints weight = 41311.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.043572 restraints weight = 36160.267| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24016 Z= 0.097 Angle : 0.484 9.540 32681 Z= 0.245 Chirality : 0.038 0.148 3657 Planarity : 0.003 0.058 3996 Dihedral : 12.743 175.986 3582 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.09 % Allowed : 9.56 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2755 helix: 1.86 (0.15), residues: 1334 sheet: 0.28 (0.29), residues: 363 loop : -0.84 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 473 TYR 0.014 0.001 TYR D 281 PHE 0.014 0.001 PHE G 33 TRP 0.011 0.001 TRP B 342 HIS 0.005 0.000 HIS K 244 Details of bonding type rmsd covalent geometry : bond 0.00206 (23988) covalent geometry : angle 0.47106 (32636) hydrogen bonds : bond 0.03328 ( 936) hydrogen bonds : angle 3.76274 ( 2522) metal coordination : bond 0.00474 ( 28) metal coordination : angle 2.99030 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8841 (ttm) cc_final: 0.8577 (ptm) REVERT: B 25 MET cc_start: 0.9032 (mmm) cc_final: 0.8766 (mmm) REVERT: B 57 MET cc_start: 0.9617 (tpt) cc_final: 0.9295 (mmm) REVERT: B 676 LEU cc_start: 0.8928 (tp) cc_final: 0.8717 (tp) REVERT: C 398 GLN cc_start: 0.8868 (pp30) cc_final: 0.8556 (pp30) REVERT: C 452 MET cc_start: 0.6828 (ppp) cc_final: 0.6552 (ppp) REVERT: C 527 GLU cc_start: 0.9276 (tm-30) cc_final: 0.8995 (tm-30) REVERT: C 528 MET cc_start: 0.8366 (tpp) cc_final: 0.7936 (mmm) REVERT: E 71 MET cc_start: 0.8414 (mmm) cc_final: 0.7908 (mmm) REVERT: F 157 MET cc_start: 0.8655 (tpp) cc_final: 0.8057 (tpt) REVERT: H 904 TRP cc_start: 0.8271 (OUTLIER) cc_final: 0.7432 (t-100) REVERT: H 909 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8559 (mm-30) REVERT: H 912 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7738 (pp20) REVERT: K 118 MET cc_start: 0.8331 (mmm) cc_final: 0.8109 (mmm) REVERT: K 263 MET cc_start: 0.6996 (ptt) cc_final: 0.6460 (ptt) outliers start: 27 outliers final: 14 residues processed: 143 average time/residue: 0.1398 time to fit residues: 33.2298 Evaluate side-chains 128 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 511 TRP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 116 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 40 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 HIS B 519 ASN B 659 HIS ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.051953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.036540 restraints weight = 146672.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.037707 restraints weight = 78127.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.038497 restraints weight = 54404.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.038933 restraints weight = 43851.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.039241 restraints weight = 38767.936| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 24016 Z= 0.252 Angle : 0.634 10.920 32681 Z= 0.315 Chirality : 0.041 0.272 3657 Planarity : 0.004 0.054 3996 Dihedral : 13.069 175.193 3582 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.99 % Allowed : 9.93 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2755 helix: 1.64 (0.15), residues: 1341 sheet: -0.08 (0.29), residues: 375 loop : -0.83 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 514 TYR 0.027 0.002 TYR A 581 PHE 0.021 0.002 PHE B 508 TRP 0.021 0.002 TRP A 511 HIS 0.007 0.001 HIS B 612 Details of bonding type rmsd covalent geometry : bond 0.00556 (23988) covalent geometry : angle 0.61364 (32636) hydrogen bonds : bond 0.03833 ( 936) hydrogen bonds : angle 3.85116 ( 2522) metal coordination : bond 0.01184 ( 28) metal coordination : angle 4.31834 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8881 (ttm) cc_final: 0.8647 (ttm) REVERT: A 490 GLU cc_start: 0.8220 (tp30) cc_final: 0.7896 (tm-30) REVERT: C 452 MET cc_start: 0.6952 (ppp) cc_final: 0.6625 (ppp) REVERT: C 514 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8280 (ptt90) REVERT: C 527 GLU cc_start: 0.9368 (tm-30) cc_final: 0.8787 (tm-30) REVERT: C 528 MET cc_start: 0.8600 (tpp) cc_final: 0.7962 (mmm) REVERT: D 380 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8955 (p) REVERT: D 427 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8434 (pp20) REVERT: F 147 MET cc_start: 0.8785 (mmm) cc_final: 0.8513 (mmm) REVERT: K 118 MET cc_start: 0.8267 (mmm) cc_final: 0.7998 (mmm) REVERT: K 263 MET cc_start: 0.7412 (ptt) cc_final: 0.6653 (ptt) outliers start: 49 outliers final: 27 residues processed: 156 average time/residue: 0.1416 time to fit residues: 37.1161 Evaluate side-chains 135 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 421 TRP Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 514 ARG Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain H residue 891 SER Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 116 TYR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 165 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 229 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 258 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 274 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.052626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.037360 restraints weight = 145318.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.038574 restraints weight = 76563.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.039373 restraints weight = 52790.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.039856 restraints weight = 42463.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.040092 restraints weight = 37370.655| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24016 Z= 0.129 Angle : 0.521 8.978 32681 Z= 0.259 Chirality : 0.038 0.151 3657 Planarity : 0.003 0.069 3996 Dihedral : 13.080 175.768 3582 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.50 % Allowed : 10.86 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.17), residues: 2755 helix: 1.63 (0.15), residues: 1339 sheet: -0.06 (0.29), residues: 363 loop : -0.82 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 676 TYR 0.015 0.001 TYR A 534 PHE 0.016 0.001 PHE G 33 TRP 0.016 0.001 TRP D 55 HIS 0.007 0.001 HIS B 613 Details of bonding type rmsd covalent geometry : bond 0.00287 (23988) covalent geometry : angle 0.50027 (32636) hydrogen bonds : bond 0.03181 ( 936) hydrogen bonds : angle 3.69511 ( 2522) metal coordination : bond 0.00648 ( 28) metal coordination : angle 3.92985 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8927 (ttm) cc_final: 0.8672 (ttm) REVERT: A 427 MET cc_start: 0.8258 (tmm) cc_final: 0.7918 (tmm) REVERT: A 490 GLU cc_start: 0.8276 (tp30) cc_final: 0.7878 (tm-30) REVERT: B 620 MET cc_start: 0.8421 (mmm) cc_final: 0.8176 (mmm) REVERT: C 452 MET cc_start: 0.6996 (ppp) cc_final: 0.6669 (ppp) REVERT: C 527 GLU cc_start: 0.9378 (tm-30) cc_final: 0.8768 (tm-30) REVERT: C 528 MET cc_start: 0.8667 (tpp) cc_final: 0.8193 (mmm) REVERT: E 71 MET cc_start: 0.8630 (mmm) cc_final: 0.8090 (mmm) REVERT: F 157 MET cc_start: 0.8637 (tpp) cc_final: 0.8385 (mmm) REVERT: K 118 MET cc_start: 0.8236 (mmm) cc_final: 0.7987 (mmm) REVERT: K 263 MET cc_start: 0.7241 (ptt) cc_final: 0.6466 (ptt) outliers start: 37 outliers final: 21 residues processed: 136 average time/residue: 0.1436 time to fit residues: 32.9639 Evaluate side-chains 126 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 421 TRP Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain H residue 891 SER Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 165 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 58 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 276 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 225 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.052805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.037600 restraints weight = 145406.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.038815 restraints weight = 76299.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.039617 restraints weight = 52372.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.040096 restraints weight = 42061.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.040291 restraints weight = 36963.317| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24016 Z= 0.111 Angle : 0.518 16.543 32681 Z= 0.253 Chirality : 0.038 0.146 3657 Planarity : 0.003 0.058 3996 Dihedral : 13.089 173.507 3582 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.50 % Allowed : 11.14 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.17), residues: 2755 helix: 1.62 (0.15), residues: 1342 sheet: 0.05 (0.30), residues: 349 loop : -0.81 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 514 TYR 0.016 0.001 TYR A 534 PHE 0.012 0.001 PHE B 421 TRP 0.055 0.001 TRP D 55 HIS 0.008 0.001 HIS B 613 Details of bonding type rmsd covalent geometry : bond 0.00247 (23988) covalent geometry : angle 0.49326 (32636) hydrogen bonds : bond 0.03097 ( 936) hydrogen bonds : angle 3.62383 ( 2522) metal coordination : bond 0.00738 ( 28) metal coordination : angle 4.32886 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8920 (ttm) cc_final: 0.8643 (ttm) REVERT: A 427 MET cc_start: 0.8236 (tmm) cc_final: 0.7930 (tmm) REVERT: A 437 LEU cc_start: 0.8977 (tt) cc_final: 0.8645 (tt) REVERT: A 490 GLU cc_start: 0.8285 (tp30) cc_final: 0.7870 (tm-30) REVERT: B 620 MET cc_start: 0.8414 (mmm) cc_final: 0.8165 (mmm) REVERT: C 452 MET cc_start: 0.6995 (ppp) cc_final: 0.6670 (ppp) REVERT: C 527 GLU cc_start: 0.9348 (tm-30) cc_final: 0.8770 (tm-30) REVERT: C 528 MET cc_start: 0.8645 (tpp) cc_final: 0.8151 (mmm) REVERT: D 185 MET cc_start: 0.8806 (mmm) cc_final: 0.7846 (mmm) REVERT: D 380 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8953 (p) REVERT: D 441 MET cc_start: 0.7688 (tmm) cc_final: 0.7375 (tmm) REVERT: F 147 MET cc_start: 0.8722 (mmm) cc_final: 0.8427 (mmm) REVERT: H 909 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8521 (mm-30) REVERT: K 118 MET cc_start: 0.8273 (mmm) cc_final: 0.8024 (mmm) REVERT: K 263 MET cc_start: 0.7014 (ptt) cc_final: 0.6230 (ptt) outliers start: 37 outliers final: 27 residues processed: 141 average time/residue: 0.1429 time to fit residues: 33.9925 Evaluate side-chains 133 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 891 SER Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 116 TYR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 165 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 153 optimal weight: 0.0980 chunk 251 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 184 optimal weight: 0.0470 chunk 114 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.052349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.037022 restraints weight = 144528.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.038280 restraints weight = 75025.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.039083 restraints weight = 51208.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.039578 restraints weight = 40910.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.039798 restraints weight = 35886.503| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24016 Z= 0.135 Angle : 0.532 15.144 32681 Z= 0.260 Chirality : 0.038 0.151 3657 Planarity : 0.003 0.066 3996 Dihedral : 13.164 174.185 3582 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.46 % Allowed : 11.10 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.17), residues: 2755 helix: 1.65 (0.15), residues: 1334 sheet: -0.06 (0.30), residues: 361 loop : -0.77 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 514 TYR 0.015 0.001 TYR A 534 PHE 0.013 0.001 PHE B 421 TRP 0.081 0.002 TRP D 55 HIS 0.008 0.001 HIS B 613 Details of bonding type rmsd covalent geometry : bond 0.00302 (23988) covalent geometry : angle 0.50874 (32636) hydrogen bonds : bond 0.03141 ( 936) hydrogen bonds : angle 3.62178 ( 2522) metal coordination : bond 0.00806 ( 28) metal coordination : angle 4.20912 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.902 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 380 MET cc_start: 0.8910 (ttm) cc_final: 0.8636 (ttm) REVERT: A 427 MET cc_start: 0.8260 (tmm) cc_final: 0.7935 (tmm) REVERT: A 490 GLU cc_start: 0.8256 (tp30) cc_final: 0.7900 (tm-30) REVERT: A 658 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8588 (p90) REVERT: B 438 MET cc_start: 0.9043 (mmt) cc_final: 0.8691 (mmm) REVERT: B 620 MET cc_start: 0.8441 (mmm) cc_final: 0.8234 (mmm) REVERT: C 452 MET cc_start: 0.6916 (ppp) cc_final: 0.6655 (ppp) REVERT: C 527 GLU cc_start: 0.9364 (tm-30) cc_final: 0.8778 (tm-30) REVERT: C 528 MET cc_start: 0.8665 (tpp) cc_final: 0.8200 (mmm) REVERT: D 185 MET cc_start: 0.8818 (mmm) cc_final: 0.7777 (mmm) REVERT: D 341 MET cc_start: 0.8261 (ptm) cc_final: 0.7932 (tmm) REVERT: D 380 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8964 (p) REVERT: H 909 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8540 (mm-30) REVERT: K 118 MET cc_start: 0.8285 (mmm) cc_final: 0.8037 (mmm) REVERT: K 256 MET cc_start: 0.8536 (tpp) cc_final: 0.8309 (tpp) REVERT: K 263 MET cc_start: 0.7005 (ptt) cc_final: 0.6212 (ptt) outliers start: 36 outliers final: 28 residues processed: 140 average time/residue: 0.1424 time to fit residues: 33.7071 Evaluate side-chains 136 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 891 SER Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 165 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 190 optimal weight: 2.9990 chunk 273 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 244 optimal weight: 0.8980 chunk 277 optimal weight: 6.9990 chunk 259 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.052267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.036925 restraints weight = 144632.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.038192 restraints weight = 74787.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.039003 restraints weight = 51042.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.039471 restraints weight = 40834.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.039791 restraints weight = 35823.119| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24016 Z= 0.128 Angle : 0.538 14.322 32681 Z= 0.262 Chirality : 0.038 0.248 3657 Planarity : 0.003 0.057 3996 Dihedral : 13.205 173.326 3582 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.38 % Allowed : 11.51 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.17), residues: 2755 helix: 1.60 (0.15), residues: 1330 sheet: -0.08 (0.30), residues: 357 loop : -0.74 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 514 TYR 0.016 0.001 TYR A 534 PHE 0.013 0.001 PHE B 421 TRP 0.053 0.001 TRP D 55 HIS 0.008 0.001 HIS B 613 Details of bonding type rmsd covalent geometry : bond 0.00284 (23988) covalent geometry : angle 0.51657 (32636) hydrogen bonds : bond 0.03059 ( 936) hydrogen bonds : angle 3.60734 ( 2522) metal coordination : bond 0.00720 ( 28) metal coordination : angle 4.09701 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8907 (ttm) cc_final: 0.8596 (ttp) REVERT: A 427 MET cc_start: 0.8301 (tmm) cc_final: 0.7939 (tmm) REVERT: A 490 GLU cc_start: 0.8258 (tp30) cc_final: 0.7960 (tm-30) REVERT: A 658 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8552 (p90) REVERT: C 452 MET cc_start: 0.6818 (ppp) cc_final: 0.6553 (ppp) REVERT: C 527 GLU cc_start: 0.9383 (tm-30) cc_final: 0.8818 (tm-30) REVERT: C 528 MET cc_start: 0.8668 (tpp) cc_final: 0.8208 (mmm) REVERT: D 185 MET cc_start: 0.8801 (mmm) cc_final: 0.8291 (mmm) REVERT: D 341 MET cc_start: 0.8419 (ptm) cc_final: 0.8033 (tmm) REVERT: D 441 MET cc_start: 0.7567 (tmm) cc_final: 0.7166 (tmm) REVERT: F 147 MET cc_start: 0.8747 (mmm) cc_final: 0.8466 (mmm) REVERT: H 909 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8536 (mm-30) REVERT: K 118 MET cc_start: 0.8322 (mmm) cc_final: 0.8078 (mmm) REVERT: K 256 MET cc_start: 0.8666 (tpp) cc_final: 0.8446 (tpp) REVERT: K 263 MET cc_start: 0.7043 (ptt) cc_final: 0.6233 (ptt) outliers start: 34 outliers final: 27 residues processed: 138 average time/residue: 0.1383 time to fit residues: 32.3008 Evaluate side-chains 133 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain H residue 891 SER Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 119 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 68 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 274 optimal weight: 7.9990 chunk 250 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.051841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.036668 restraints weight = 146601.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.037932 restraints weight = 75880.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.038747 restraints weight = 51718.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.039245 restraints weight = 41197.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.039481 restraints weight = 36074.691| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24016 Z= 0.142 Angle : 0.552 14.184 32681 Z= 0.269 Chirality : 0.038 0.290 3657 Planarity : 0.003 0.068 3996 Dihedral : 13.256 172.950 3582 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.34 % Allowed : 11.79 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.17), residues: 2755 helix: 1.62 (0.15), residues: 1334 sheet: -0.14 (0.30), residues: 362 loop : -0.72 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 514 TYR 0.014 0.001 TYR A 534 PHE 0.013 0.001 PHE B 421 TRP 0.051 0.001 TRP D 55 HIS 0.008 0.001 HIS B 613 Details of bonding type rmsd covalent geometry : bond 0.00315 (23988) covalent geometry : angle 0.53092 (32636) hydrogen bonds : bond 0.03110 ( 936) hydrogen bonds : angle 3.61873 ( 2522) metal coordination : bond 0.00773 ( 28) metal coordination : angle 4.14756 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.890 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 380 MET cc_start: 0.8930 (ttm) cc_final: 0.8608 (ttp) REVERT: A 427 MET cc_start: 0.8371 (tmm) cc_final: 0.7987 (tmm) REVERT: A 490 GLU cc_start: 0.8279 (tp30) cc_final: 0.7978 (tm-30) REVERT: A 658 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8616 (p90) REVERT: B 42 MET cc_start: 0.8827 (mmm) cc_final: 0.8444 (mmm) REVERT: B 57 MET cc_start: 0.9618 (tpt) cc_final: 0.9296 (mmm) REVERT: B 438 MET cc_start: 0.9087 (mmt) cc_final: 0.8605 (mmt) REVERT: B 620 MET cc_start: 0.8314 (mmm) cc_final: 0.8110 (mmm) REVERT: C 452 MET cc_start: 0.6895 (ppp) cc_final: 0.6653 (ppp) REVERT: C 527 GLU cc_start: 0.9370 (tm-30) cc_final: 0.8880 (tm-30) REVERT: C 528 MET cc_start: 0.8687 (tpp) cc_final: 0.8228 (mmm) REVERT: D 185 MET cc_start: 0.8814 (mmm) cc_final: 0.8368 (mmm) REVERT: D 341 MET cc_start: 0.8458 (ptm) cc_final: 0.8019 (tmm) REVERT: D 441 MET cc_start: 0.7600 (tmm) cc_final: 0.7219 (tmm) REVERT: F 147 MET cc_start: 0.8737 (mmm) cc_final: 0.8444 (mmm) REVERT: H 909 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8526 (mm-30) REVERT: K 118 MET cc_start: 0.8350 (mmm) cc_final: 0.8105 (mmm) REVERT: K 256 MET cc_start: 0.8705 (tpp) cc_final: 0.8492 (tpp) REVERT: K 263 MET cc_start: 0.7152 (ptt) cc_final: 0.6309 (ptt) outliers start: 33 outliers final: 29 residues processed: 137 average time/residue: 0.1357 time to fit residues: 31.6541 Evaluate side-chains 135 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain H residue 891 SER Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 67 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 277 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 564 ASN ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.051075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.035805 restraints weight = 147288.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.037027 restraints weight = 76313.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.037837 restraints weight = 52161.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.038323 restraints weight = 41654.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.038591 restraints weight = 36534.243| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24016 Z= 0.172 Angle : 0.578 15.023 32681 Z= 0.280 Chirality : 0.039 0.265 3657 Planarity : 0.003 0.052 3996 Dihedral : 13.450 172.932 3582 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.46 % Allowed : 11.91 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.17), residues: 2755 helix: 1.56 (0.15), residues: 1334 sheet: -0.27 (0.30), residues: 369 loop : -0.67 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 514 TYR 0.019 0.001 TYR A 581 PHE 0.016 0.001 PHE B 508 TRP 0.050 0.002 TRP D 55 HIS 0.008 0.001 HIS B 613 Details of bonding type rmsd covalent geometry : bond 0.00381 (23988) covalent geometry : angle 0.55355 (32636) hydrogen bonds : bond 0.03260 ( 936) hydrogen bonds : angle 3.69186 ( 2522) metal coordination : bond 0.00966 ( 28) metal coordination : angle 4.54311 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.8971 (ttm) cc_final: 0.8700 (ttp) REVERT: A 427 MET cc_start: 0.8462 (tmm) cc_final: 0.8039 (tmm) REVERT: A 490 GLU cc_start: 0.8227 (tp30) cc_final: 0.7952 (tm-30) REVERT: A 658 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8655 (p90) REVERT: B 25 MET cc_start: 0.9120 (mmm) cc_final: 0.8762 (mmt) REVERT: B 438 MET cc_start: 0.8960 (mmt) cc_final: 0.8514 (mmt) REVERT: C 452 MET cc_start: 0.6834 (ppp) cc_final: 0.6239 (ppp) REVERT: C 465 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.6398 (m-10) REVERT: C 528 MET cc_start: 0.8776 (tpp) cc_final: 0.8508 (mmm) REVERT: D 185 MET cc_start: 0.8823 (mmm) cc_final: 0.8516 (mmm) REVERT: D 341 MET cc_start: 0.8522 (ptm) cc_final: 0.8263 (tmm) REVERT: D 441 MET cc_start: 0.7650 (tmm) cc_final: 0.7204 (tmm) REVERT: F 147 MET cc_start: 0.8710 (mmm) cc_final: 0.8412 (mmm) REVERT: G 61 MET cc_start: 0.9057 (mmm) cc_final: 0.8752 (mmt) REVERT: H 909 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8519 (mm-30) REVERT: K 118 MET cc_start: 0.8287 (mmm) cc_final: 0.8035 (mmm) REVERT: K 181 TYR cc_start: 0.8699 (m-80) cc_final: 0.8350 (m-80) REVERT: K 263 MET cc_start: 0.7252 (ptt) cc_final: 0.6339 (ptt) REVERT: K 273 MET cc_start: 0.6637 (mpp) cc_final: 0.6347 (mtm) outliers start: 36 outliers final: 32 residues processed: 137 average time/residue: 0.1440 time to fit residues: 33.0585 Evaluate side-chains 135 residues out of total 2468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 273 MET Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain H residue 891 SER Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 116 TYR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 22 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.051209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.035916 restraints weight = 146075.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.037130 restraints weight = 75929.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.037963 restraints weight = 52303.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.038452 restraints weight = 41700.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.038750 restraints weight = 36542.094| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24016 Z= 0.142 Angle : 0.562 14.854 32681 Z= 0.271 Chirality : 0.039 0.280 3657 Planarity : 0.003 0.072 3996 Dihedral : 13.437 172.405 3582 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.42 % Allowed : 12.24 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2755 helix: 1.53 (0.15), residues: 1333 sheet: -0.17 (0.30), residues: 362 loop : -0.63 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 514 TYR 0.030 0.001 TYR F 101 PHE 0.014 0.001 PHE B 508 TRP 0.045 0.001 TRP D 55 HIS 0.008 0.001 HIS B 613 Details of bonding type rmsd covalent geometry : bond 0.00317 (23988) covalent geometry : angle 0.53789 (32636) hydrogen bonds : bond 0.03128 ( 936) hydrogen bonds : angle 3.66354 ( 2522) metal coordination : bond 0.00838 ( 28) metal coordination : angle 4.40567 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4794.36 seconds wall clock time: 83 minutes 22.92 seconds (5002.92 seconds total)