Starting phenix.real_space_refine on Sat Mar 7 00:36:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pd3_71524/03_2026/9pd3_71524.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pd3_71524/03_2026/9pd3_71524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pd3_71524/03_2026/9pd3_71524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pd3_71524/03_2026/9pd3_71524.map" model { file = "/net/cci-nas-00/data/ceres_data/9pd3_71524/03_2026/9pd3_71524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pd3_71524/03_2026/9pd3_71524.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.002 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 7 6.06 5 P 70 5.49 5 S 202 5.16 5 C 22133 2.51 5 N 6056 2.21 5 O 6600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 35072 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 4947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4947 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 1 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: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1076 Classifications: {'peptide': 133} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain breaks: 2 Chain: "D" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3441 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 406} Chain breaks: 2 Chain: "E" Number of atoms: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2677 Classifications: {'peptide': 342} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 323} Chain breaks: 2 Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2013 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} 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: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "K" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1716 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 201} Chain breaks: 3 Chain: "L" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 770 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "M" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 665 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "N" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1459 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain: "O" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1485 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain breaks: 1 Chain: "P" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 950 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "Q" Number of atoms: 5461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5461 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 34, 'TRANS': 678} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 21, 'ARG:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 174 Chain: "R" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1400 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 11, 'TRANS': 184} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 8, 'GLN:plan1': 5, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "S" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 685 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain breaks: 1 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} Chain: "N" 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 5890 SG CYS B 116 121.456 51.064 64.043 1.00196.95 S ATOM 6199 SG CYS B 155 126.851 47.186 63.271 1.00224.61 S ATOM 6030 SG CYS B 134 122.807 46.289 67.942 1.00217.31 S ATOM 6488 SG CYS B 190 126.934 51.553 67.484 1.00207.57 S ATOM 17042 SG CYS E 291 97.868 103.067 30.683 1.00407.29 S ATOM 17064 SG CYS E 294 98.878 100.473 28.142 1.00425.82 S ATOM 17153 SG CYS E 305 98.092 99.366 31.715 1.00411.76 S ATOM 17176 SG CYS E 308 101.236 101.361 31.054 1.00421.57 S ATOM 17478 SG CYS E 345 74.311 141.198 51.472 1.00352.10 S ATOM 17500 SG CYS E 348 72.916 137.845 52.380 1.00328.63 S ATOM 17657 SG CYS E 368 75.107 139.908 54.994 1.00359.63 S ATOM 17678 SG CYS E 371 76.612 138.151 52.199 1.00366.92 S ATOM 17598 SG CYS E 360 88.165 140.865 48.543 1.00370.71 S ATOM 17616 SG CYS E 363 85.923 141.166 45.513 1.00365.51 S ATOM 17765 SG CYS E 382 85.495 138.232 47.891 1.00356.62 S ATOM 17782 SG CYS E 385 88.585 138.404 45.682 1.00371.76 S ATOM 19657 SG CYS F 268 104.226 118.228 46.080 1.00390.26 S ATOM 19676 SG CYS F 271 102.443 121.506 46.840 1.00386.66 S ATOM 19761 SG CYS F 282 104.467 121.203 43.645 1.00404.34 S ATOM 19781 SG CYS F 285 106.234 121.287 46.999 1.00416.01 S ATOM 19549 SG CYS F 255 99.407 121.293 35.101 1.00389.85 S ATOM 19566 SG CYS F 257 101.396 123.337 32.835 1.00397.99 S ATOM 19715 SG CYS F 276 100.269 119.691 31.753 1.00391.15 S ATOM 20801 SG CYS K 105 106.307 93.291 159.777 1.00328.96 S ATOM 20825 SG CYS K 108 108.769 92.319 162.517 1.00340.03 S ATOM 20973 SG CYS K 126 108.709 90.440 159.178 1.00305.23 S ATOM 20995 SG CYS K 129 106.015 89.906 161.730 1.00333.50 S ATOM 23958 SG CYS N 481 116.269 58.409 159.219 1.00470.61 S ATOM 23995 SG CYS N 486 117.115 58.268 155.451 1.00461.39 S ATOM 24111 SG CYS N 500 113.477 59.073 156.329 1.00480.15 S Time building chain proxies: 7.14, per 1000 atoms: 0.20 Number of scatterers: 35072 At special positions: 0 Unit cell: (181.594, 164.934, 183.26, 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 7 29.99 Fe 4 26.01 S 202 16.00 P 70 15.00 O 6600 8.00 N 6056 7.00 C 22133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 291 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 345 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 368 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 348 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 360 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 385 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 382 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb=" ZN F 402 " pdb="ZN ZN F 402 " - pdb=" ND1 HIS F 258 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 257 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 255 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 276 " pdb=" ZN K 300 " pdb="ZN ZN K 300 " - pdb=" SG CYS K 126 " pdb="ZN ZN K 300 " - pdb=" SG CYS K 108 " pdb="ZN ZN K 300 " - pdb=" SG CYS K 129 " pdb="ZN ZN K 300 " - pdb=" SG CYS K 105 " pdb=" ZN N1000 " pdb="ZN ZN N1000 " - pdb=" SG CYS N 500 " pdb="ZN ZN N1000 " - pdb=" SG CYS N 486 " pdb="ZN ZN N1000 " - pdb=" SG CYS N 481 " Number of angles added : 33 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8098 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 39 sheets defined 43.6% alpha, 13.7% beta 23 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 4.72 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 Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 277 through 286 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: 3.780A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 removed outlier: 3.563A 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: 3.878A 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 Processing helix chain 'A' and resid 633 through 641 removed outlier: 4.104A pdb=" N GLY A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) 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 33 Processing helix chain 'B' and resid 48 through 59 Processing helix chain 'B' and resid 77 through 98 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 127 through 138 removed outlier: 3.699A pdb=" N LEU B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 148 removed outlier: 3.862A pdb=" N TYR B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 5.312A 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: 3.658A 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: 3.846A pdb=" N ASP B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 247 removed outlier: 3.716A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) 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 removed outlier: 3.517A pdb=" N ALA B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 375 through 386 Processing helix chain 'B' and resid 395 through 409 removed outlier: 3.593A pdb=" N THR B 409 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 442 No H-bonds generated for 'chain 'B' and resid 440 through 442' Processing helix chain 'B' and resid 444 through 450 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 removed outlier: 3.618A pdb=" N ASN B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) 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: 3.698A pdb=" N LEU B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS B 663 " --> pdb=" O HIS B 659 " (cutoff:3.500A) removed outlier: 4.057A 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: 5.146A pdb=" N HIS B 700 " --> pdb=" O TRP B 696 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'B' and resid 710 through 725 Processing helix chain 'B' and resid 730 through 736 removed outlier: 3.928A 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 removed outlier: 3.768A pdb=" N SER C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 478 Processing helix chain 'C' and resid 484 through 515 removed outlier: 4.191A 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 541 removed outlier: 4.256A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (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 removed outlier: 3.603A pdb=" N TRP D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) 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 removed outlier: 3.724A pdb=" N PHE D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) 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 69 through 72 Processing helix chain 'E' and resid 80 through 98 removed outlier: 3.531A pdb=" N TYR E 90 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 136 removed outlier: 3.610A pdb=" N VAL E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 4.898A 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 186 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: 4.526A pdb=" N ALA E 319 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG E 320 " --> pdb=" O PRO E 316 " (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: 6.636A pdb=" N LEU F 224 " --> pdb=" O MET F 220 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TYR F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 240 removed outlier: 3.767A pdb=" N SER F 239 " --> pdb=" O GLN F 235 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 235 through 240' 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: 3.847A pdb=" N VAL G 50 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN G 51 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP G 62 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN G 63 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 892 through 901 Processing helix chain 'K' and resid 27 through 40 removed outlier: 3.571A pdb=" N ARG K 34 " --> pdb=" O ARG K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 120 removed outlier: 4.067A pdb=" N HIS K 120 " --> pdb=" O TYR K 116 " (cutoff:3.500A) No H-bonds generated for '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 230 removed outlier: 3.789A pdb=" N GLU K 201 " --> pdb=" O GLN K 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 444 through 450 Processing helix chain 'N' and resid 532 through 539 Processing helix chain 'N' and resid 543 through 552 Processing helix chain 'N' and resid 554 through 564 removed outlier: 4.015A pdb=" N PHE N 558 " --> pdb=" O ASN N 554 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE N 562 " --> pdb=" O PHE N 558 " (cutoff:3.500A) Processing helix chain 'N' and resid 599 through 615 Processing helix chain 'O' and resid 51 through 55 Processing helix chain 'O' and resid 152 through 169 removed outlier: 4.269A pdb=" N LEU O 169 " --> pdb=" O HIS O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 218 Processing helix chain 'O' and resid 227 through 232 Processing helix chain 'O' and resid 242 through 252 removed outlier: 3.993A pdb=" N ASP O 247 " --> pdb=" O LYS O 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 14 through 19 removed outlier: 4.626A pdb=" N ALA P 18 " --> pdb=" O GLY P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 108 Processing helix chain 'Q' and resid 17 through 28 removed outlier: 3.754A pdb=" N ASP Q 28 " --> pdb=" O LEU Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 51 Processing helix chain 'Q' and resid 66 through 79 Processing helix chain 'Q' and resid 94 through 103 Processing helix chain 'Q' and resid 111 through 119 Processing helix chain 'Q' and resid 136 through 140 Processing helix chain 'Q' and resid 144 through 155 removed outlier: 4.516A pdb=" N GLN Q 154 " --> pdb=" O ARG Q 150 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LYS Q 155 " --> pdb=" O LEU Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 169 through 172 No H-bonds generated for 'chain 'Q' and resid 169 through 172' Processing helix chain 'Q' and resid 178 through 185 Processing helix chain 'Q' and resid 201 through 206 Processing helix chain 'Q' and resid 223 through 243 Processing helix chain 'Q' and resid 260 through 269 removed outlier: 3.912A pdb=" N ILE Q 266 " --> pdb=" O ASP Q 263 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR Q 269 " --> pdb=" O ILE Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 274 through 276 No H-bonds generated for 'chain 'Q' and resid 274 through 276' Processing helix chain 'Q' and resid 280 through 300 removed outlier: 3.537A pdb=" N GLN Q 286 " --> pdb=" O LYS Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 303 through 319 removed outlier: 3.516A pdb=" N ASN Q 308 " --> pdb=" O VAL Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 334 through 342 removed outlier: 3.911A pdb=" N ARG Q 342 " --> pdb=" O ASN Q 338 " (cutoff:3.500A) Processing helix chain 'Q' and resid 379 through 397 Processing helix chain 'Q' and resid 414 through 425 Processing helix chain 'Q' and resid 428 through 439 removed outlier: 3.680A pdb=" N THR Q 439 " --> pdb=" O LEU Q 435 " (cutoff:3.500A) Processing helix chain 'Q' and resid 563 through 572 removed outlier: 4.604A pdb=" N LEU Q 566 " --> pdb=" O PRO Q 563 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR Q 567 " --> pdb=" O TYR Q 564 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL Q 569 " --> pdb=" O LEU Q 566 " (cutoff:3.500A) Processing helix chain 'Q' and resid 585 through 597 removed outlier: 3.830A pdb=" N ARG Q 589 " --> pdb=" O LEU Q 585 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN Q 590 " --> pdb=" O THR Q 586 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA Q 596 " --> pdb=" O GLU Q 592 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER Q 597 " --> pdb=" O ILE Q 593 " (cutoff:3.500A) Processing helix chain 'Q' and resid 614 through 639 Processing helix chain 'Q' and resid 688 through 692 removed outlier: 4.086A pdb=" N ARG Q 692 " --> pdb=" O ARG Q 689 " (cutoff:3.500A) Processing helix chain 'Q' and resid 695 through 702 Processing helix chain 'Q' and resid 729 through 737 Processing helix chain 'Q' and resid 741 through 751 Processing helix chain 'Q' and resid 784 through 794 Processing helix chain 'Q' and resid 806 through 816 removed outlier: 3.609A pdb=" N GLU Q 811 " --> pdb=" O HIS Q 807 " (cutoff:3.500A) Processing helix chain 'Q' and resid 848 through 854 removed outlier: 3.783A pdb=" N LEU Q 853 " --> pdb=" O ASP Q 850 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS Q 854 " --> pdb=" O PHE Q 851 " (cutoff:3.500A) Processing helix chain 'Q' and resid 864 through 869 removed outlier: 3.595A pdb=" N HIS Q 868 " --> pdb=" O ARG Q 864 " (cutoff:3.500A) Processing helix chain 'Q' and resid 873 through 877 Processing helix chain 'Q' and resid 881 through 888 Processing helix chain 'Q' and resid 892 through 901 Processing helix chain 'R' and resid 105 through 107 No H-bonds generated for 'chain 'R' and resid 105 through 107' Processing helix chain 'R' and resid 143 through 148 Processing helix chain 'R' and resid 152 through 160 Processing helix chain 'R' and resid 180 through 192 Processing helix chain 'R' and resid 202 through 214 removed outlier: 4.074A pdb=" N GLY R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 240 Processing helix chain 'R' and resid 247 through 256 Processing helix chain 'R' and resid 262 through 265 No H-bonds generated for 'chain 'R' and resid 262 through 265' Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'R' and resid 279 through 289 Processing helix chain 'S' and resid 192 through 195 Processing helix chain 'S' and resid 198 through 214 Processing helix chain 'S' and resid 226 through 256 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 61 removed outlier: 6.456A pdb=" N LYS A 59 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ARG D 337 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.655A pdb=" N CYS A 108 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS A 117 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 171 removed outlier: 4.608A pdb=" N TYR A 175 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 392 removed outlier: 6.193A pdb=" N VAL A 405 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE A 392 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE A 407 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N CYS A 361 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N SER A 408 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 363 " --> pdb=" O SER A 408 " (cutoff:3.500A) 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 removed outlier: 7.050A pdb=" N GLY A 336 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR A 467 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE A 338 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL A 339 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU A 490 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 690 removed outlier: 3.619A pdb=" N TRP A 511 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA A 657 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ALA A 508 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE A 659 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL A 510 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER A 661 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N CYS A 512 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.314A 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: 3.503A pdb=" N LEU B 8 " --> pdb=" O VAL B 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 41 removed outlier: 4.528A pdb=" N VAL B 454 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS B 69 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N VAL B 232 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE B 71 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP B 234 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.626A 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: 7.287A pdb=" N VAL B 249 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU B 433 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU B 251 " --> pdb=" O PRO B 431 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B 432 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ILE B 418 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU B 352 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 479 through 481 Processing sheet with id=AB1, first strand: chain 'B' and resid 490 through 495 removed outlier: 8.207A pdb=" N GLY B 675 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N MET B 493 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET B 677 " --> pdb=" O MET B 493 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE B 495 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N PHE B 679 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 96 through 100 removed outlier: 3.597A pdb=" N ILE D 109 " --> pdb=" O HIS D 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 248 through 251 removed outlier: 3.787A pdb=" N TYR D 249 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR D 281 " --> pdb=" O TYR D 249 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ARG D 279 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU D 270 " --> pdb=" O THR D 284 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 402 through 409 removed outlier: 3.709A pdb=" N VAL D 442 " --> pdb=" O PHE D 433 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE D 433 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 184 through 186 removed outlier: 7.372A pdb=" N LEU D 184 " --> pdb=" O THR D 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 118 removed outlier: 6.627A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER E 164 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N TYR E 62 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLU E 166 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL E 64 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU E 168 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASP E 66 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE E 170 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG E 195 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ILE E 169 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER E 197 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE E 171 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE E 199 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY E 200 " --> pdb=" O HIS E 220 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 289 through 291 removed outlier: 3.862A pdb=" N ALA E 296 " --> pdb=" O CYS E 291 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 332 through 335 removed outlier: 3.625A pdb=" N GLN E 332 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL E 359 " --> pdb=" O GLN E 332 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE E 334 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN E 365 " --> pdb=" O CYS E 360 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 303 through 305 removed outlier: 4.207A pdb=" N VAL E 303 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS E 305 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E 310 " --> pdb=" O CYS E 305 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 343 through 345 removed outlier: 7.179A pdb=" N ARG E 343 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY E 350 " --> pdb=" O CYS E 345 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 67 through 69 removed outlier: 6.185A pdb=" N GLU F 156 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU F 10 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS F 158 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL F 12 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG F 160 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL F 14 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU F 162 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASP F 16 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE F 164 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU F 190 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL F 163 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP F 192 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LYS F 165 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N CYS F 194 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 253 through 255 removed outlier: 5.275A pdb=" N ALA F 253 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 262 " --> pdb=" O ALA F 253 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS F 255 " --> pdb=" O ASN F 260 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN F 260 " --> pdb=" O CYS F 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 273 through 275 removed outlier: 4.156A pdb=" N SER F 273 " --> pdb=" O CYS F 268 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR F 266 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLY F 265 " --> pdb=" O MET E 252 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET E 252 " --> pdb=" O GLY F 265 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL F 267 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE E 250 " --> pdb=" O VAL F 267 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 5 through 11 removed outlier: 3.507A pdb=" N HIS G 42 " --> pdb=" O ASP G 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP G 39 " --> pdb=" O HIS G 42 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE G 44 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP G 37 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 103 through 105 removed outlier: 4.334A pdb=" N LYS K 110 " --> pdb=" O CYS K 105 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 138 through 140 removed outlier: 6.921A pdb=" N MET K 178 " --> pdb=" O LYS K 167 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS K 167 " --> pdb=" O MET K 178 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 248 through 252 removed outlier: 4.967A pdb=" N THR K 260 " --> pdb=" O PRO K 248 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 526 through 531 removed outlier: 3.503A pdb=" N ASN N 519 " --> pdb=" O TYR N 470 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR N 470 " --> pdb=" O ASN N 519 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA N 521 " --> pdb=" O VAL N 468 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL N 468 " --> pdb=" O ALA N 521 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG N 575 " --> pdb=" O VAL N 591 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL N 591 " --> pdb=" O ARG N 575 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LYS N 577 " --> pdb=" O ALA N 589 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA N 589 " --> pdb=" O LYS N 577 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU N 579 " --> pdb=" O ILE N 587 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE N 587 " --> pdb=" O GLU N 579 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR N 581 " --> pdb=" O SER N 585 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N SER N 585 " --> pdb=" O TYR N 581 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 477 through 480 Processing sheet with id=AD2, first strand: chain 'N' and resid 490 through 492 Processing sheet with id=AD3, first strand: chain 'O' and resid 58 through 60 removed outlier: 4.351A pdb=" N PHE O 64 " --> pdb=" O ILE O 71 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 74 through 80 removed outlier: 3.770A pdb=" N THR O 124 " --> pdb=" O ILE O 80 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS O 145 " --> pdb=" O ALA O 129 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N HIS O 131 " --> pdb=" O ALA O 143 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ALA O 143 " --> pdb=" O HIS O 131 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG O 133 " --> pdb=" O LEU O 141 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU O 141 " --> pdb=" O ARG O 133 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE O 135 " --> pdb=" O LYS O 139 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LYS O 139 " --> pdb=" O PHE O 135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 83 through 85 Processing sheet with id=AD6, first strand: chain 'P' and resid 50 through 54 removed outlier: 5.640A pdb=" N SER P 44 " --> pdb=" O LEU P 31 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU P 31 " --> pdb=" O SER P 44 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ARG P 72 " --> pdb=" O CYS P 81 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N CYS P 81 " --> pdb=" O ARG P 72 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 190 through 192 removed outlier: 6.214A pdb=" N LEU Q 32 " --> pdb=" O TYR Q 191 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL Q 33 " --> pdb=" O ILE Q 161 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA Q 163 " --> pdb=" O VAL Q 33 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LEU Q 58 " --> pdb=" O THR Q 129 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE Q 131 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU Q 60 " --> pdb=" O ILE Q 131 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL Q 133 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU Q 62 " --> pdb=" O VAL Q 133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 86 through 88 Processing sheet with id=AD9, first strand: chain 'Q' and resid 211 through 217 removed outlier: 6.156A pdb=" N VAL Q 605 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE Q 214 " --> pdb=" O VAL Q 605 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE Q 607 " --> pdb=" O ILE Q 214 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL Q 216 " --> pdb=" O PHE Q 607 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE Q 609 " --> pdb=" O VAL Q 216 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU Q 608 " --> pdb=" O LEU Q 580 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE Q 553 " --> pdb=" O VAL Q 407 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 552 through 556 current: chain 'S' and resid 358 through 360 Processing sheet with id=AE1, first strand: chain 'Q' and resid 705 through 709 removed outlier: 4.416A pdb=" N VAL Q 686 " --> pdb=" O GLU Q 707 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL Q 709 " --> pdb=" O VAL Q 686 " (cutoff:3.500A) removed outlier: 13.172A pdb=" N ASP Q 715 " --> pdb=" O SER Q 683 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL Q 685 " --> pdb=" O ASP Q 715 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ASP Q 687 " --> pdb=" O ILE Q 717 " (cutoff:3.500A) removed outlier: 14.602A pdb=" N THR Q 719 " --> pdb=" O ASP Q 687 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU Q 760 " --> pdb=" O LYS Q 727 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU Q 757 " --> pdb=" O ARG Q 799 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE Q 761 " --> pdb=" O CYS Q 803 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 101 through 104 Processing sheet with id=AE3, first strand: chain 'R' and resid 130 through 132 removed outlier: 3.547A pdb=" N TYR R 130 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR R 136 " --> pdb=" O LEU R 132 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU R 166 " --> pdb=" O CYS R 137 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU R 139 " --> pdb=" O LEU R 166 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL R 168 " --> pdb=" O LEU R 139 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU R 141 " --> pdb=" O VAL R 168 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU R 170 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR R 195 " --> pdb=" O LEU R 169 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL R 171 " --> pdb=" O THR R 195 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE R 197 " --> pdb=" O VAL R 171 " (cutoff:3.500A) 1348 hydrogen bonds defined for protein. 3783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 7.61 Time building geometry restraints manager: 3.83 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: 15046 1.43 - 1.64: 20561 1.64 - 1.86: 299 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 35918 Sorted by residual: bond pdb=" CA PRO O 121 " pdb=" C PRO O 121 " ideal model delta sigma weight residual 1.517 1.502 0.015 6.70e-03 2.23e+04 5.15e+00 bond pdb=" C LYS Q 260 " pdb=" N PRO Q 261 " ideal model delta sigma weight residual 1.337 1.356 -0.019 9.80e-03 1.04e+04 3.95e+00 bond pdb=" C VAL C 453 " pdb=" N PRO C 454 " ideal model delta sigma weight residual 1.331 1.349 -0.018 1.21e-02 6.83e+03 2.14e+00 bond pdb=" C PRO B 354 " pdb=" N PRO B 355 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.55e+00 bond pdb=" CA PRO S 197 " pdb=" C PRO S 197 " ideal model delta sigma weight residual 1.514 1.508 0.006 5.50e-03 3.31e+04 1.12e+00 ... (remaining 35913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 48408 1.70 - 3.40: 459 3.40 - 5.10: 53 5.10 - 6.80: 8 6.80 - 8.50: 3 Bond angle restraints: 48931 Sorted by residual: angle pdb=" N GLY E 253 " pdb=" CA GLY E 253 " pdb=" C GLY E 253 " ideal model delta sigma weight residual 112.33 116.61 -4.28 1.10e+00 8.26e-01 1.51e+01 angle pdb=" C HIS B 612 " pdb=" N HIS B 613 " pdb=" CA HIS B 613 " ideal model delta sigma weight residual 121.54 127.93 -6.39 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C MET E 252 " pdb=" N GLY E 253 " pdb=" CA GLY E 253 " ideal model delta sigma weight residual 120.44 123.42 -2.98 1.09e+00 8.42e-01 7.50e+00 angle pdb=" C ASP B 423 " pdb=" N ARG B 424 " pdb=" CA ARG B 424 " ideal model delta sigma weight residual 121.54 126.64 -5.10 1.91e+00 2.74e-01 7.14e+00 angle pdb=" N ASN A 621 " pdb=" CA ASN A 621 " pdb=" C ASN A 621 " ideal model delta sigma weight residual 114.56 111.33 3.23 1.27e+00 6.20e-01 6.47e+00 ... (remaining 48926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 19853 17.61 - 35.22: 1206 35.22 - 52.82: 398 52.82 - 70.43: 110 70.43 - 88.04: 14 Dihedral angle restraints: 21581 sinusoidal: 9122 harmonic: 12459 Sorted by residual: dihedral pdb=" N ARG D 392 " pdb=" CA ARG D 392 " pdb=" CB ARG D 392 " pdb=" CG ARG D 392 " ideal model delta sinusoidal sigma weight residual -60.00 -119.08 59.08 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU E 328 " pdb=" CB LEU E 328 " pdb=" CG LEU E 328 " pdb=" CD1 LEU E 328 " ideal model delta sinusoidal sigma weight residual 60.00 118.95 -58.95 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N GLN A 710 " pdb=" CA GLN A 710 " pdb=" CB GLN A 710 " pdb=" CG GLN A 710 " ideal model delta sinusoidal sigma weight residual -60.00 -118.55 58.55 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 21578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 4186 0.036 - 0.073: 955 0.073 - 0.109: 359 0.109 - 0.146: 67 0.146 - 0.182: 2 Chirality restraints: 5569 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 2.34 0.18 2.00e-01 2.50e+01 8.29e-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 -2.47 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA VAL O 120 " pdb=" N VAL O 120 " pdb=" C VAL O 120 " pdb=" CB VAL O 120 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 5566 not shown) Planarity restraints: 6010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO A 583 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 353 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO B 354 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 354 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 354 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 613 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C HIS B 613 " -0.026 2.00e-02 2.50e+03 pdb=" O HIS B 613 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR B 614 " 0.009 2.00e-02 2.50e+03 ... (remaining 6007 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4430 2.76 - 3.29: 34704 3.29 - 3.83: 59217 3.83 - 4.36: 66857 4.36 - 4.90: 113998 Nonbonded interactions: 279206 Sorted by model distance: nonbonded pdb=" OH TYR E 322 " pdb=" O ALA F 254 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR B 209 " pdb=" O ASP B 234 " model vdw 2.240 3.040 nonbonded pdb=" OE2 GLU B 546 " pdb=" NZ LYS S 240 " model vdw 2.251 3.120 nonbonded pdb=" O GLY A 582 " pdb=" NH2 ARG A 589 " model vdw 2.266 3.120 nonbonded pdb=" O CYS B 243 " pdb=" OG SER B 246 " model vdw 2.269 3.040 ... (remaining 279201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 41.860 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 0.095 35949 Z= 0.094 Angle : 0.451 9.011 48976 Z= 0.231 Chirality : 0.037 0.182 5569 Planarity : 0.003 0.056 6010 Dihedral : 13.383 88.041 13483 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.90 % Allowed : 7.63 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % 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: 1.31 (0.14), residues: 4175 helix: 2.32 (0.12), residues: 1960 sheet: 0.39 (0.24), residues: 575 loop : -0.76 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 342 TYR 0.011 0.001 TYR E 322 PHE 0.014 0.001 PHE F 32 TRP 0.009 0.001 TRP H 904 HIS 0.004 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00177 (35918) covalent geometry : angle 0.43588 (48931) hydrogen bonds : bond 0.12672 ( 1406) hydrogen bonds : angle 4.70205 ( 3899) metal coordination : bond 0.01756 ( 31) metal coordination : angle 3.83545 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 381 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8940 (tpp) cc_final: 0.8632 (tpp) REVERT: B 57 MET cc_start: 0.7999 (tmm) cc_final: 0.7782 (tmm) REVERT: B 84 ILE cc_start: 0.8430 (mm) cc_final: 0.8125 (mm) REVERT: B 207 TYR cc_start: 0.7885 (p90) cc_final: 0.7370 (p90) REVERT: B 490 LEU cc_start: 0.9135 (pt) cc_final: 0.8921 (pp) REVERT: C 452 MET cc_start: 0.4109 (ttt) cc_final: 0.3007 (mmm) REVERT: C 474 HIS cc_start: 0.8735 (m-70) cc_final: 0.8502 (t70) REVERT: D 61 PHE cc_start: 0.8091 (m-80) cc_final: 0.7412 (t80) REVERT: D 74 TRP cc_start: 0.8993 (m-10) cc_final: 0.8278 (m-10) REVERT: D 157 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8599 (tm-30) REVERT: E 57 MET cc_start: 0.7983 (mtp) cc_final: 0.7684 (mtp) REVERT: E 153 MET cc_start: 0.9256 (mmm) cc_final: 0.8947 (mmm) REVERT: F 37 CYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8519 (p) REVERT: F 175 MET cc_start: 0.8269 (ppp) cc_final: 0.7962 (ppp) REVERT: F 231 PHE cc_start: 0.8839 (m-10) cc_final: 0.7927 (m-10) REVERT: F 245 PRO cc_start: 0.8113 (Cg_endo) cc_final: 0.7806 (Cg_exo) REVERT: G 24 ASP cc_start: 0.8578 (t70) cc_final: 0.7937 (t0) REVERT: G 62 ASP cc_start: 0.8877 (p0) cc_final: 0.8673 (p0) REVERT: H 904 TRP cc_start: 0.7407 (OUTLIER) cc_final: 0.7181 (t-100) REVERT: K 28 ILE cc_start: 0.8950 (mt) cc_final: 0.8734 (mm) REVERT: K 134 ASP cc_start: 0.9192 (m-30) cc_final: 0.8916 (p0) REVERT: K 246 TYR cc_start: 0.8317 (m-80) cc_final: 0.8022 (m-10) REVERT: K 257 TYR cc_start: 0.8562 (m-80) cc_final: 0.8004 (m-80) REVERT: K 263 MET cc_start: 0.6529 (ttp) cc_final: 0.6075 (ptm) REVERT: K 273 MET cc_start: 0.5430 (mmm) cc_final: 0.5146 (mmm) REVERT: N 616 MET cc_start: 0.2256 (mtp) cc_final: 0.1785 (mmt) REVERT: Q 182 MET cc_start: 0.9283 (mtp) cc_final: 0.9071 (mtp) REVERT: Q 722 MET cc_start: 0.9084 (ttp) cc_final: 0.8388 (tmm) REVERT: Q 902 HIS cc_start: 0.9154 (t70) cc_final: 0.8898 (m170) REVERT: R 129 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7938 (t70) REVERT: R 204 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8177 (tt0) REVERT: R 208 TYR cc_start: 0.7387 (m-10) cc_final: 0.6834 (m-80) REVERT: S 192 ASP cc_start: 0.7833 (t0) cc_final: 0.7570 (t70) REVERT: S 214 ARG cc_start: 0.8215 (mtp180) cc_final: 0.7746 (mpp80) REVERT: S 242 TYR cc_start: 0.9164 (t80) cc_final: 0.8828 (t80) REVERT: S 244 ASN cc_start: 0.9413 (t0) cc_final: 0.9138 (t0) outliers start: 33 outliers final: 12 residues processed: 410 average time/residue: 0.2190 time to fit residues: 146.3004 Evaluate side-chains 259 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 244 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain Q residue 573 VAL Chi-restraints excluded: chain Q residue 799 ARG Chi-restraints excluded: chain R residue 129 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 5.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS A 625 GLN A 668 GLN A 711 GLN B 114 ASN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 HIS C 405 GLN C 524 HIS C 534 ASN D 352 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 ASN E 275 HIS E 317 HIS ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 236 HIS ** P 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 HIS ** Q 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.083761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.055637 restraints weight = 173175.158| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 4.13 r_work: 0.2983 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 35949 Z= 0.205 Angle : 0.599 10.470 48976 Z= 0.302 Chirality : 0.042 0.259 5569 Planarity : 0.004 0.060 6010 Dihedral : 13.030 85.290 5383 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.86 % Allowed : 11.10 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % 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: 0.90 (0.14), residues: 4175 helix: 1.86 (0.12), residues: 1996 sheet: 0.11 (0.22), residues: 610 loop : -0.84 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 473 TYR 0.017 0.002 TYR Q 581 PHE 0.028 0.002 PHE A 615 TRP 0.028 0.002 TRP A 511 HIS 0.010 0.001 HIS Q 869 Details of bonding type rmsd covalent geometry : bond 0.00457 (35918) covalent geometry : angle 0.58231 (48931) hydrogen bonds : bond 0.03619 ( 1406) hydrogen bonds : angle 3.98649 ( 3899) metal coordination : bond 0.00993 ( 31) metal coordination : angle 4.63419 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 266 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.9146 (mpp) cc_final: 0.8912 (mpp) REVERT: B 1 MET cc_start: 0.8930 (tpp) cc_final: 0.8564 (tpp) REVERT: B 57 MET cc_start: 0.8293 (tmm) cc_final: 0.8060 (tmm) REVERT: B 77 VAL cc_start: 0.8645 (t) cc_final: 0.8369 (t) REVERT: B 80 ILE cc_start: 0.8860 (mt) cc_final: 0.8605 (mt) REVERT: B 84 ILE cc_start: 0.9005 (mm) cc_final: 0.8691 (mm) REVERT: C 452 MET cc_start: 0.4301 (ttt) cc_final: 0.3278 (mmm) REVERT: C 474 HIS cc_start: 0.8747 (m-70) cc_final: 0.8505 (t70) REVERT: C 493 MET cc_start: 0.4153 (tmm) cc_final: 0.3419 (ptt) REVERT: D 61 PHE cc_start: 0.8309 (m-80) cc_final: 0.7471 (t80) REVERT: D 74 TRP cc_start: 0.9012 (m-10) cc_final: 0.8367 (m-10) REVERT: D 443 VAL cc_start: 0.9227 (m) cc_final: 0.9025 (p) REVERT: E 57 MET cc_start: 0.7829 (mtp) cc_final: 0.7258 (mtp) REVERT: E 153 MET cc_start: 0.9310 (mmm) cc_final: 0.9095 (mmm) REVERT: F 118 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7511 (mp) REVERT: F 175 MET cc_start: 0.8060 (ppp) cc_final: 0.7775 (ppp) REVERT: F 231 PHE cc_start: 0.8688 (m-10) cc_final: 0.7832 (m-10) REVERT: F 245 PRO cc_start: 0.8115 (Cg_endo) cc_final: 0.7716 (Cg_exo) REVERT: G 24 ASP cc_start: 0.8787 (t70) cc_final: 0.8398 (t0) REVERT: H 904 TRP cc_start: 0.7598 (OUTLIER) cc_final: 0.7014 (t-100) REVERT: K 28 ILE cc_start: 0.8978 (mt) cc_final: 0.8759 (mm) REVERT: K 216 GLN cc_start: 0.8368 (pt0) cc_final: 0.8028 (pm20) REVERT: K 246 TYR cc_start: 0.8366 (m-80) cc_final: 0.7922 (m-10) REVERT: K 257 TYR cc_start: 0.8667 (m-80) cc_final: 0.8330 (m-80) REVERT: N 592 MET cc_start: 0.3678 (mmt) cc_final: 0.3436 (mmp) REVERT: N 616 MET cc_start: 0.2482 (mtp) cc_final: 0.1994 (mmt) REVERT: O 102 MET cc_start: 0.1745 (tpt) cc_final: -0.1075 (mmm) REVERT: O 107 TRP cc_start: 0.8593 (m100) cc_final: 0.8373 (m100) REVERT: Q 182 MET cc_start: 0.9345 (mtp) cc_final: 0.9033 (mtp) REVERT: Q 722 MET cc_start: 0.9263 (ttp) cc_final: 0.8523 (tmm) REVERT: Q 902 HIS cc_start: 0.9163 (t70) cc_final: 0.8919 (m170) outliers start: 68 outliers final: 33 residues processed: 319 average time/residue: 0.2176 time to fit residues: 115.6398 Evaluate side-chains 252 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 194 CYS Chi-restraints excluded: chain F residue 256 PHE Chi-restraints excluded: chain H residue 899 ILE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain K residue 196 SER Chi-restraints excluded: chain N residue 471 LEU Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain P residue 115 LEU Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 573 VAL Chi-restraints excluded: chain Q residue 726 ARG Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 130 TYR Chi-restraints excluded: chain R residue 168 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 264 optimal weight: 20.0000 chunk 223 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 369 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 221 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS B 452 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN C 524 HIS ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 524 GLN Q 849 GLN ** Q 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 118 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.083796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.056568 restraints weight = 172590.096| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 4.43 r_work: 0.2980 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35949 Z= 0.119 Angle : 0.511 10.762 48976 Z= 0.253 Chirality : 0.039 0.177 5569 Planarity : 0.004 0.057 6010 Dihedral : 12.983 84.057 5372 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.08 % Allowed : 11.92 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % 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: 0.90 (0.14), residues: 4175 helix: 1.87 (0.12), residues: 1991 sheet: -0.05 (0.22), residues: 626 loop : -0.77 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 473 TYR 0.031 0.001 TYR R 130 PHE 0.022 0.001 PHE O 248 TRP 0.016 0.001 TRP A 511 HIS 0.015 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00264 (35918) covalent geometry : angle 0.49477 (48931) hydrogen bonds : bond 0.02984 ( 1406) hydrogen bonds : angle 3.78463 ( 3899) metal coordination : bond 0.00954 ( 31) metal coordination : angle 4.30766 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 241 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.6172 (p90) REVERT: B 1 MET cc_start: 0.8960 (tpp) cc_final: 0.8632 (tpp) REVERT: B 57 MET cc_start: 0.8336 (tmm) cc_final: 0.8084 (tmm) REVERT: B 77 VAL cc_start: 0.8750 (t) cc_final: 0.8516 (t) REVERT: B 84 ILE cc_start: 0.9171 (mm) cc_final: 0.8918 (mm) REVERT: B 724 MET cc_start: 0.9412 (mmp) cc_final: 0.9165 (mmm) REVERT: C 452 MET cc_start: 0.4524 (ttt) cc_final: 0.3336 (mmm) REVERT: C 474 HIS cc_start: 0.8749 (m-70) cc_final: 0.8509 (t70) REVERT: D 61 PHE cc_start: 0.8306 (m-80) cc_final: 0.7464 (t80) REVERT: D 74 TRP cc_start: 0.9019 (m-10) cc_final: 0.8367 (m-10) REVERT: D 185 MET cc_start: 0.9180 (mmt) cc_final: 0.8842 (mmm) REVERT: D 443 VAL cc_start: 0.9270 (m) cc_final: 0.9066 (p) REVERT: E 57 MET cc_start: 0.7889 (mtp) cc_final: 0.7382 (mtp) REVERT: F 51 MET cc_start: 0.8422 (mmm) cc_final: 0.7837 (mmm) REVERT: F 118 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7523 (tp) REVERT: F 175 MET cc_start: 0.8098 (ppp) cc_final: 0.7793 (ppp) REVERT: F 231 PHE cc_start: 0.8757 (m-10) cc_final: 0.7935 (m-80) REVERT: F 245 PRO cc_start: 0.8076 (Cg_endo) cc_final: 0.7744 (Cg_exo) REVERT: G 24 ASP cc_start: 0.8812 (t70) cc_final: 0.8448 (t0) REVERT: G 39 ASP cc_start: 0.8191 (t0) cc_final: 0.7833 (t0) REVERT: H 904 TRP cc_start: 0.7467 (OUTLIER) cc_final: 0.7151 (t60) REVERT: H 906 GLN cc_start: 0.8166 (mm110) cc_final: 0.7791 (mm110) REVERT: K 28 ILE cc_start: 0.8902 (mt) cc_final: 0.8662 (mm) REVERT: K 37 MET cc_start: 0.7840 (tmm) cc_final: 0.7376 (tmm) REVERT: K 246 TYR cc_start: 0.8278 (m-80) cc_final: 0.7877 (m-10) REVERT: K 257 TYR cc_start: 0.8730 (m-80) cc_final: 0.8206 (m-80) REVERT: K 263 MET cc_start: 0.6655 (ttp) cc_final: 0.6203 (ptm) REVERT: N 471 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8185 (mm) REVERT: N 616 MET cc_start: 0.2355 (mtp) cc_final: 0.1846 (mmt) REVERT: O 102 MET cc_start: 0.1705 (tpt) cc_final: -0.1020 (mmm) REVERT: Q 76 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9342 (pp) REVERT: Q 182 MET cc_start: 0.9318 (mtp) cc_final: 0.9004 (mtp) REVERT: Q 722 MET cc_start: 0.9250 (ttp) cc_final: 0.8523 (tmm) REVERT: Q 902 HIS cc_start: 0.9162 (t70) cc_final: 0.8914 (m170) REVERT: R 208 TYR cc_start: 0.8171 (m-80) cc_final: 0.7570 (m-80) REVERT: S 243 LEU cc_start: 0.9224 (tt) cc_final: 0.9013 (tt) outliers start: 76 outliers final: 31 residues processed: 301 average time/residue: 0.2035 time to fit residues: 103.9412 Evaluate side-chains 254 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 194 CYS Chi-restraints excluded: chain F residue 256 PHE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain K residue 196 SER Chi-restraints excluded: chain N residue 471 LEU Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 573 VAL Chi-restraints excluded: chain Q residue 578 VAL Chi-restraints excluded: chain Q residue 726 ARG Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 130 TYR Chi-restraints excluded: chain R residue 168 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 129 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 chunk 30 optimal weight: 0.0000 chunk 288 optimal weight: 5.9990 chunk 176 optimal weight: 0.0040 chunk 265 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 343 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 405 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.083594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.056628 restraints weight = 172944.391| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.39 r_work: 0.2976 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35949 Z= 0.108 Angle : 0.506 11.854 48976 Z= 0.248 Chirality : 0.039 0.177 5569 Planarity : 0.003 0.058 6010 Dihedral : 12.987 84.878 5371 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.91 % Allowed : 12.55 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % 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: 0.86 (0.14), residues: 4175 helix: 1.85 (0.12), residues: 1984 sheet: -0.11 (0.22), residues: 628 loop : -0.78 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 408 TYR 0.023 0.001 TYR R 130 PHE 0.016 0.001 PHE A 615 TRP 0.013 0.001 TRP A 511 HIS 0.013 0.001 HIS O 263 Details of bonding type rmsd covalent geometry : bond 0.00241 (35918) covalent geometry : angle 0.49120 (48931) hydrogen bonds : bond 0.02828 ( 1406) hydrogen bonds : angle 3.67043 ( 3899) metal coordination : bond 0.00808 ( 31) metal coordination : angle 4.09177 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 233 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6159 (p90) REVERT: B 1 MET cc_start: 0.8967 (tpp) cc_final: 0.8705 (tpp) REVERT: B 57 MET cc_start: 0.8353 (tmm) cc_final: 0.8093 (tmm) REVERT: B 84 ILE cc_start: 0.9275 (mm) cc_final: 0.9032 (mm) REVERT: B 480 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8407 (t) REVERT: B 724 MET cc_start: 0.9388 (mmp) cc_final: 0.9169 (mmm) REVERT: C 452 MET cc_start: 0.4539 (ttt) cc_final: 0.3351 (mmm) REVERT: C 474 HIS cc_start: 0.8752 (m-70) cc_final: 0.8509 (t70) REVERT: C 528 MET cc_start: 0.6698 (mmm) cc_final: 0.6440 (mmm) REVERT: D 57 MET cc_start: 0.9010 (mmm) cc_final: 0.8779 (mtp) REVERT: D 61 PHE cc_start: 0.8372 (m-80) cc_final: 0.7495 (t80) REVERT: D 74 TRP cc_start: 0.9025 (m-10) cc_final: 0.8386 (m-10) REVERT: D 185 MET cc_start: 0.9062 (mmt) cc_final: 0.8750 (mmm) REVERT: E 57 MET cc_start: 0.7926 (mtp) cc_final: 0.7402 (mtp) REVERT: E 153 MET cc_start: 0.9307 (mmm) cc_final: 0.9029 (mmm) REVERT: E 159 MET cc_start: 0.9287 (tpp) cc_final: 0.8609 (tpp) REVERT: F 51 MET cc_start: 0.8571 (mmm) cc_final: 0.7817 (mmm) REVERT: F 118 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7452 (mp) REVERT: F 175 MET cc_start: 0.8095 (ppp) cc_final: 0.7788 (ppp) REVERT: F 231 PHE cc_start: 0.8729 (m-10) cc_final: 0.7917 (m-80) REVERT: F 245 PRO cc_start: 0.8125 (Cg_endo) cc_final: 0.7808 (Cg_exo) REVERT: G 24 ASP cc_start: 0.8815 (t70) cc_final: 0.8471 (t0) REVERT: G 39 ASP cc_start: 0.8330 (t0) cc_final: 0.7920 (t0) REVERT: H 904 TRP cc_start: 0.7496 (OUTLIER) cc_final: 0.7220 (t60) REVERT: H 906 GLN cc_start: 0.8186 (mm110) cc_final: 0.7753 (mm110) REVERT: K 37 MET cc_start: 0.7844 (tmm) cc_final: 0.7351 (tmm) REVERT: K 214 MET cc_start: 0.8980 (tmm) cc_final: 0.8768 (tmm) REVERT: K 246 TYR cc_start: 0.8285 (m-80) cc_final: 0.7859 (m-10) REVERT: K 257 TYR cc_start: 0.8674 (m-80) cc_final: 0.8225 (m-80) REVERT: K 263 MET cc_start: 0.6662 (ttp) cc_final: 0.6128 (ptm) REVERT: N 471 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8190 (mm) REVERT: N 616 MET cc_start: 0.2323 (mtp) cc_final: 0.1832 (mmt) REVERT: O 102 MET cc_start: 0.1275 (tpt) cc_final: -0.1156 (mmm) REVERT: Q 182 MET cc_start: 0.9326 (mtp) cc_final: 0.9012 (mtp) REVERT: Q 722 MET cc_start: 0.9245 (ttp) cc_final: 0.8497 (tmm) REVERT: Q 748 MET cc_start: 0.8934 (ttt) cc_final: 0.8551 (tpt) REVERT: Q 902 HIS cc_start: 0.9168 (t70) cc_final: 0.8921 (m170) REVERT: R 208 TYR cc_start: 0.8234 (m-80) cc_final: 0.7707 (m-80) REVERT: S 243 LEU cc_start: 0.9197 (tt) cc_final: 0.8919 (tt) outliers start: 70 outliers final: 38 residues processed: 286 average time/residue: 0.2024 time to fit residues: 98.0986 Evaluate side-chains 267 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 194 CYS Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain N residue 471 LEU Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 573 VAL Chi-restraints excluded: chain Q residue 578 VAL Chi-restraints excluded: chain Q residue 610 TYR Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 130 TYR Chi-restraints excluded: chain R residue 168 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 3 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 373 optimal weight: 3.9990 chunk 385 optimal weight: 9.9990 chunk 324 optimal weight: 30.0000 chunk 400 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 333 optimal weight: 20.0000 chunk 415 optimal weight: 30.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN A 635 GLN A 665 GLN B 474 HIS ** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 HIS B 659 HIS ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 GLN ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 HIS ** K 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 254 HIS ** Q 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 215 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.080676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.053045 restraints weight = 172058.375| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 4.30 r_work: 0.2863 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 35949 Z= 0.220 Angle : 0.599 13.069 48976 Z= 0.299 Chirality : 0.042 0.180 5569 Planarity : 0.004 0.064 6010 Dihedral : 13.331 84.933 5371 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.46 % Allowed : 12.28 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % 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 (0.14), residues: 4175 helix: 1.67 (0.12), residues: 2014 sheet: -0.23 (0.22), residues: 634 loop : -0.81 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Q 726 TYR 0.017 0.001 TYR B 207 PHE 0.037 0.002 PHE S 211 TRP 0.033 0.002 TRP A 511 HIS 0.022 0.001 HIS O 263 Details of bonding type rmsd covalent geometry : bond 0.00495 (35918) covalent geometry : angle 0.58144 (48931) hydrogen bonds : bond 0.03541 ( 1406) hydrogen bonds : angle 3.81948 ( 3899) metal coordination : bond 0.01010 ( 31) metal coordination : angle 4.76610 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 229 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 717 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9365 (mm) REVERT: B 1 MET cc_start: 0.8803 (tpp) cc_final: 0.8255 (tpp) REVERT: C 452 MET cc_start: 0.4565 (ttt) cc_final: 0.3557 (tpt) REVERT: C 474 HIS cc_start: 0.8774 (m-70) cc_final: 0.8471 (t70) REVERT: D 61 PHE cc_start: 0.8558 (m-80) cc_final: 0.7418 (t80) REVERT: D 74 TRP cc_start: 0.9076 (m-10) cc_final: 0.8528 (m-10) REVERT: D 228 MET cc_start: 0.7740 (mmp) cc_final: 0.6677 (mmp) REVERT: E 57 MET cc_start: 0.7920 (mtp) cc_final: 0.7359 (mtp) REVERT: E 159 MET cc_start: 0.9326 (tpp) cc_final: 0.8834 (tpp) REVERT: E 322 TYR cc_start: 0.7884 (m-80) cc_final: 0.7139 (m-80) REVERT: F 118 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7720 (tp) REVERT: F 119 MET cc_start: 0.3720 (mtm) cc_final: 0.3510 (mtm) REVERT: F 175 MET cc_start: 0.7872 (ppp) cc_final: 0.7539 (ppp) REVERT: F 231 PHE cc_start: 0.8734 (m-10) cc_final: 0.7875 (m-80) REVERT: G 24 ASP cc_start: 0.8829 (t70) cc_final: 0.8452 (t0) REVERT: H 904 TRP cc_start: 0.7507 (OUTLIER) cc_final: 0.6406 (t-100) REVERT: H 906 GLN cc_start: 0.8373 (mm110) cc_final: 0.7943 (mm-40) REVERT: K 37 MET cc_start: 0.8021 (tmm) cc_final: 0.7582 (tmm) REVERT: K 75 PHE cc_start: 0.7278 (t80) cc_final: 0.6956 (t80) REVERT: K 113 MET cc_start: 0.4368 (mmp) cc_final: 0.1918 (ttt) REVERT: K 257 TYR cc_start: 0.8642 (m-80) cc_final: 0.8192 (m-80) REVERT: K 273 MET cc_start: 0.6391 (mmm) cc_final: 0.6165 (mmm) REVERT: N 471 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8325 (mm) REVERT: N 616 MET cc_start: 0.2711 (mtp) cc_final: 0.2196 (mmt) REVERT: O 102 MET cc_start: 0.1320 (tpt) cc_final: -0.1010 (ttm) REVERT: O 167 MET cc_start: 0.7985 (mtt) cc_final: 0.7750 (mpp) REVERT: Q 182 MET cc_start: 0.9351 (mtp) cc_final: 0.9023 (mtp) REVERT: Q 610 TYR cc_start: 0.8661 (OUTLIER) cc_final: 0.8157 (m-80) REVERT: Q 722 MET cc_start: 0.9337 (ttp) cc_final: 0.8648 (tmm) REVERT: Q 748 MET cc_start: 0.9133 (ttt) cc_final: 0.8721 (tpt) REVERT: Q 902 HIS cc_start: 0.9204 (t70) cc_final: 0.8959 (m170) REVERT: R 208 TYR cc_start: 0.8515 (m-80) cc_final: 0.8297 (m-80) REVERT: S 243 LEU cc_start: 0.9292 (tt) cc_final: 0.9053 (tt) outliers start: 90 outliers final: 49 residues processed: 300 average time/residue: 0.1986 time to fit residues: 100.7755 Evaluate side-chains 262 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 208 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 185 GLN Chi-restraints excluded: chain F residue 194 CYS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain K residue 196 SER Chi-restraints excluded: chain N residue 471 LEU Chi-restraints excluded: chain N residue 516 LEU Chi-restraints excluded: chain N residue 571 ILE Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 9 ARG Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 573 VAL Chi-restraints excluded: chain Q residue 578 VAL Chi-restraints excluded: chain Q residue 610 TYR Chi-restraints excluded: chain Q residue 799 ARG Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 130 TYR Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain S residue 196 LEU Chi-restraints excluded: chain S residue 205 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 57 optimal weight: 0.7980 chunk 320 optimal weight: 7.9990 chunk 336 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 354 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 299 optimal weight: 30.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN B 643 GLN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 HIS ** K 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.081393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.055545 restraints weight = 170924.205| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.70 r_work: 0.2908 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35949 Z= 0.123 Angle : 0.537 13.326 48976 Z= 0.263 Chirality : 0.040 0.177 5569 Planarity : 0.003 0.057 6010 Dihedral : 13.231 85.612 5367 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.97 % Allowed : 13.29 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % 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 (0.14), residues: 4175 helix: 1.72 (0.12), residues: 2001 sheet: -0.28 (0.22), residues: 631 loop : -0.83 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 726 TYR 0.018 0.001 TYR R 130 PHE 0.026 0.001 PHE S 211 TRP 0.014 0.001 TRP A 511 HIS 0.007 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00278 (35918) covalent geometry : angle 0.51736 (48931) hydrogen bonds : bond 0.02927 ( 1406) hydrogen bonds : angle 3.66281 ( 3899) metal coordination : bond 0.00811 ( 31) metal coordination : angle 4.72687 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 223 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7793 (p90) REVERT: A 717 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9311 (mm) REVERT: B 1 MET cc_start: 0.8861 (tpp) cc_final: 0.8358 (tpp) REVERT: B 57 MET cc_start: 0.8489 (tmm) cc_final: 0.8269 (tmm) REVERT: B 438 MET cc_start: 0.8918 (mtt) cc_final: 0.8245 (mpp) REVERT: C 452 MET cc_start: 0.4814 (ttt) cc_final: 0.3684 (tpt) REVERT: C 474 HIS cc_start: 0.8782 (m-70) cc_final: 0.8459 (t70) REVERT: D 61 PHE cc_start: 0.8590 (m-80) cc_final: 0.7426 (t80) REVERT: D 74 TRP cc_start: 0.9063 (m-10) cc_final: 0.8523 (m-10) REVERT: D 228 MET cc_start: 0.7763 (mmp) cc_final: 0.6661 (mmp) REVERT: E 57 MET cc_start: 0.8045 (mtp) cc_final: 0.7559 (mtp) REVERT: E 159 MET cc_start: 0.9301 (tpp) cc_final: 0.8711 (tpp) REVERT: E 322 TYR cc_start: 0.7931 (m-80) cc_final: 0.7212 (m-80) REVERT: F 118 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7442 (mp) REVERT: F 175 MET cc_start: 0.7904 (ppp) cc_final: 0.7591 (ppp) REVERT: F 231 PHE cc_start: 0.8739 (m-10) cc_final: 0.7906 (m-80) REVERT: G 24 ASP cc_start: 0.8897 (t70) cc_final: 0.8553 (t0) REVERT: H 903 SER cc_start: 0.7926 (m) cc_final: 0.7362 (p) REVERT: H 904 TRP cc_start: 0.7821 (OUTLIER) cc_final: 0.6737 (t-100) REVERT: K 75 PHE cc_start: 0.7082 (t80) cc_final: 0.6788 (t80) REVERT: K 257 TYR cc_start: 0.8606 (m-80) cc_final: 0.8033 (m-80) REVERT: N 471 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8354 (mm) REVERT: N 616 MET cc_start: 0.2768 (mtp) cc_final: 0.2314 (mmt) REVERT: O 102 MET cc_start: 0.1287 (tpt) cc_final: -0.0957 (ttm) REVERT: O 167 MET cc_start: 0.7997 (mtt) cc_final: 0.7796 (mtt) REVERT: Q 182 MET cc_start: 0.9324 (mtp) cc_final: 0.8997 (mtp) REVERT: Q 610 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: Q 722 MET cc_start: 0.9349 (ttp) cc_final: 0.8696 (tmm) REVERT: Q 748 MET cc_start: 0.9133 (ttt) cc_final: 0.8748 (tpt) REVERT: Q 902 HIS cc_start: 0.9218 (t70) cc_final: 0.8989 (m170) REVERT: R 208 TYR cc_start: 0.8502 (m-80) cc_final: 0.8272 (m-80) REVERT: S 243 LEU cc_start: 0.9278 (tt) cc_final: 0.9076 (tt) outliers start: 72 outliers final: 42 residues processed: 278 average time/residue: 0.2013 time to fit residues: 95.2541 Evaluate side-chains 261 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 185 GLN Chi-restraints excluded: chain F residue 194 CYS Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain K residue 196 SER Chi-restraints excluded: chain N residue 471 LEU Chi-restraints excluded: chain N residue 520 ILE Chi-restraints excluded: chain N residue 571 ILE Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 9 ARG Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 573 VAL Chi-restraints excluded: chain Q residue 578 VAL Chi-restraints excluded: chain Q residue 610 TYR Chi-restraints excluded: chain Q residue 799 ARG Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 130 TYR Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain S residue 196 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 50 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 380 optimal weight: 30.0000 chunk 28 optimal weight: 5.9990 chunk 336 optimal weight: 20.0000 chunk 227 optimal weight: 4.9990 chunk 303 optimal weight: 9.9990 chunk 353 optimal weight: 9.9990 chunk 400 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 330 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN B 203 ASN ** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 HIS ** K 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 254 HIS ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.080171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.051672 restraints weight = 171195.193| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 4.46 r_work: 0.2869 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 35949 Z= 0.200 Angle : 0.586 12.994 48976 Z= 0.288 Chirality : 0.041 0.174 5569 Planarity : 0.004 0.061 6010 Dihedral : 13.314 86.254 5367 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.13 % Allowed : 13.18 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % 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: 0.63 (0.14), residues: 4175 helix: 1.69 (0.12), residues: 2000 sheet: -0.32 (0.21), residues: 635 loop : -0.92 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 487 TYR 0.016 0.001 TYR R 130 PHE 0.027 0.001 PHE A 615 TRP 0.029 0.001 TRP A 511 HIS 0.006 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00453 (35918) covalent geometry : angle 0.56753 (48931) hydrogen bonds : bond 0.03312 ( 1406) hydrogen bonds : angle 3.76935 ( 3899) metal coordination : bond 0.00965 ( 31) metal coordination : angle 4.82598 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 212 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 717 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9312 (mm) REVERT: B 1 MET cc_start: 0.8746 (tpp) cc_final: 0.8489 (tpp) REVERT: B 109 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9173 (tp) REVERT: B 438 MET cc_start: 0.8929 (mtt) cc_final: 0.8183 (mpp) REVERT: C 452 MET cc_start: 0.4493 (ttt) cc_final: 0.3490 (mmm) REVERT: C 474 HIS cc_start: 0.8754 (m-70) cc_final: 0.8405 (t70) REVERT: D 61 PHE cc_start: 0.8701 (m-80) cc_final: 0.7425 (t80) REVERT: D 74 TRP cc_start: 0.9066 (m-10) cc_final: 0.8523 (m-10) REVERT: D 228 MET cc_start: 0.7721 (mmp) cc_final: 0.6636 (mmp) REVERT: E 57 MET cc_start: 0.8044 (mtp) cc_final: 0.7508 (mtp) REVERT: E 58 MET cc_start: 0.8048 (tpp) cc_final: 0.7832 (tpp) REVERT: E 159 MET cc_start: 0.9327 (tpp) cc_final: 0.8757 (tpp) REVERT: E 322 TYR cc_start: 0.7963 (m-80) cc_final: 0.7242 (m-80) REVERT: F 118 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7407 (mp) REVERT: F 175 MET cc_start: 0.7817 (ppp) cc_final: 0.7481 (ppp) REVERT: F 231 PHE cc_start: 0.8693 (m-10) cc_final: 0.7863 (m-80) REVERT: F 261 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8232 (mt) REVERT: G 24 ASP cc_start: 0.8906 (t70) cc_final: 0.8569 (t0) REVERT: G 37 ASP cc_start: 0.9085 (p0) cc_final: 0.8838 (p0) REVERT: G 50 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8144 (t) REVERT: G 54 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8504 (mp10) REVERT: H 903 SER cc_start: 0.8026 (m) cc_final: 0.7542 (p) REVERT: H 904 TRP cc_start: 0.7865 (OUTLIER) cc_final: 0.6543 (t-100) REVERT: K 75 PHE cc_start: 0.7204 (t80) cc_final: 0.6921 (t80) REVERT: K 113 MET cc_start: 0.4370 (mmp) cc_final: 0.2033 (ttt) REVERT: N 471 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8495 (mm) REVERT: N 524 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6367 (mt0) REVERT: N 616 MET cc_start: 0.2838 (mtp) cc_final: 0.2389 (mmt) REVERT: O 102 MET cc_start: 0.1360 (tpt) cc_final: -0.0772 (ttm) REVERT: Q 182 MET cc_start: 0.9354 (mtp) cc_final: 0.9064 (mtp) REVERT: Q 610 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: Q 722 MET cc_start: 0.9337 (ttp) cc_final: 0.8726 (tmm) REVERT: Q 748 MET cc_start: 0.9172 (ttt) cc_final: 0.8801 (tpt) REVERT: Q 902 HIS cc_start: 0.9196 (t70) cc_final: 0.8968 (m170) REVERT: R 208 TYR cc_start: 0.8657 (m-80) cc_final: 0.8289 (m-80) REVERT: R 230 ASP cc_start: 0.7941 (t0) cc_final: 0.7641 (m-30) REVERT: S 243 LEU cc_start: 0.9267 (tt) cc_final: 0.9058 (tt) outliers start: 78 outliers final: 51 residues processed: 273 average time/residue: 0.2010 time to fit residues: 93.5637 Evaluate side-chains 262 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain E residue 19 TRP Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 185 GLN Chi-restraints excluded: chain F residue 194 CYS Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain K residue 196 SER Chi-restraints excluded: chain N residue 471 LEU Chi-restraints excluded: chain N residue 524 GLN Chi-restraints excluded: chain N residue 571 ILE Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain P residue 9 ARG Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 573 VAL Chi-restraints excluded: chain Q residue 578 VAL Chi-restraints excluded: chain Q residue 610 TYR Chi-restraints excluded: chain Q residue 799 ARG Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 130 TYR Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain S residue 196 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 105 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 236 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 386 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 219 optimal weight: 30.0000 chunk 255 optimal weight: 50.0000 chunk 41 optimal weight: 4.9990 chunk 375 optimal weight: 9.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN D 424 HIS ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.080786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.052597 restraints weight = 171790.073| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.90 r_work: 0.2899 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35949 Z= 0.122 Angle : 0.547 12.761 48976 Z= 0.266 Chirality : 0.039 0.173 5569 Planarity : 0.003 0.057 6010 Dihedral : 13.261 86.402 5367 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.61 % Allowed : 13.86 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % 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: 0.65 (0.13), residues: 4175 helix: 1.68 (0.12), residues: 1999 sheet: -0.28 (0.22), residues: 634 loop : -0.90 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 400 TYR 0.016 0.001 TYR R 130 PHE 0.028 0.001 PHE O 248 TRP 0.016 0.001 TRP A 77 HIS 0.006 0.001 HIS F 248 Details of bonding type rmsd covalent geometry : bond 0.00277 (35918) covalent geometry : angle 0.52962 (48931) hydrogen bonds : bond 0.02904 ( 1406) hydrogen bonds : angle 3.65136 ( 3899) metal coordination : bond 0.00808 ( 31) metal coordination : angle 4.58973 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7741 (p90) REVERT: A 717 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9289 (mm) REVERT: B 438 MET cc_start: 0.8874 (mtt) cc_final: 0.8157 (mpp) REVERT: C 452 MET cc_start: 0.4481 (ttt) cc_final: 0.3589 (tpt) REVERT: C 474 HIS cc_start: 0.8766 (m-70) cc_final: 0.8412 (t70) REVERT: C 528 MET cc_start: 0.7198 (mmm) cc_final: 0.6886 (mpp) REVERT: D 61 PHE cc_start: 0.8696 (m-80) cc_final: 0.7435 (t80) REVERT: D 74 TRP cc_start: 0.9023 (m-10) cc_final: 0.8497 (m-10) REVERT: D 228 MET cc_start: 0.7780 (mmp) cc_final: 0.6729 (mmp) REVERT: E 57 MET cc_start: 0.8149 (mtp) cc_final: 0.7694 (mtp) REVERT: E 153 MET cc_start: 0.9331 (mmm) cc_final: 0.9063 (mmm) REVERT: E 159 MET cc_start: 0.9287 (tpp) cc_final: 0.8655 (tpp) REVERT: E 322 TYR cc_start: 0.8031 (m-80) cc_final: 0.7335 (m-80) REVERT: F 118 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7391 (mp) REVERT: F 175 MET cc_start: 0.7819 (ppp) cc_final: 0.7509 (ppp) REVERT: F 231 PHE cc_start: 0.8701 (m-10) cc_final: 0.7860 (m-80) REVERT: G 24 ASP cc_start: 0.8894 (t70) cc_final: 0.8530 (t0) REVERT: G 37 ASP cc_start: 0.9061 (p0) cc_final: 0.8792 (p0) REVERT: G 54 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8477 (mp10) REVERT: H 903 SER cc_start: 0.7975 (m) cc_final: 0.7518 (p) REVERT: H 904 TRP cc_start: 0.7740 (OUTLIER) cc_final: 0.6421 (t-100) REVERT: K 75 PHE cc_start: 0.7137 (t80) cc_final: 0.6859 (t80) REVERT: K 113 MET cc_start: 0.4390 (mmp) cc_final: 0.2028 (ttt) REVERT: N 471 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8509 (mm) REVERT: N 524 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6410 (mt0) REVERT: N 616 MET cc_start: 0.2818 (mtp) cc_final: 0.2379 (mmt) REVERT: O 102 MET cc_start: 0.1265 (tpt) cc_final: -0.0821 (ttm) REVERT: P 9 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.5722 (mtm110) REVERT: Q 182 MET cc_start: 0.9328 (mtp) cc_final: 0.9026 (mtp) REVERT: Q 610 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: Q 722 MET cc_start: 0.9324 (ttp) cc_final: 0.8691 (tmm) REVERT: Q 748 MET cc_start: 0.9154 (ttt) cc_final: 0.8813 (tpt) REVERT: Q 902 HIS cc_start: 0.9191 (t70) cc_final: 0.8966 (m170) REVERT: R 208 TYR cc_start: 0.8624 (m-80) cc_final: 0.8382 (m-80) REVERT: R 230 ASP cc_start: 0.8007 (t0) cc_final: 0.7708 (m-30) outliers start: 59 outliers final: 36 residues processed: 260 average time/residue: 0.1949 time to fit residues: 86.2488 Evaluate side-chains 247 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 203 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 254 PHE Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 194 CYS Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain K residue 196 SER Chi-restraints excluded: chain N residue 471 LEU Chi-restraints excluded: chain N residue 524 GLN Chi-restraints excluded: chain N residue 571 ILE Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 9 ARG Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 573 VAL Chi-restraints excluded: chain Q residue 578 VAL Chi-restraints excluded: chain Q residue 610 TYR Chi-restraints excluded: chain Q residue 799 ARG Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 130 TYR Chi-restraints excluded: chain S residue 196 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 148 optimal weight: 10.0000 chunk 379 optimal weight: 40.0000 chunk 229 optimal weight: 50.0000 chunk 27 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 410 optimal weight: 30.0000 chunk 362 optimal weight: 20.0000 chunk 252 optimal weight: 6.9990 chunk 306 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN B 97 GLN ** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 869 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 = 0.4033 r_free = 0.4033 target = 0.079252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.051245 restraints weight = 170971.328| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 4.21 r_work: 0.2811 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 35949 Z= 0.261 Angle : 0.636 13.937 48976 Z= 0.315 Chirality : 0.042 0.176 5569 Planarity : 0.004 0.062 6010 Dihedral : 13.443 88.407 5367 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.67 % Allowed : 13.84 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % 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: 0.50 (0.13), residues: 4175 helix: 1.57 (0.12), residues: 2010 sheet: -0.44 (0.22), residues: 609 loop : -0.97 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 676 TYR 0.017 0.001 TYR B 207 PHE 0.030 0.002 PHE A 615 TRP 0.030 0.002 TRP A 511 HIS 0.007 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00588 (35918) covalent geometry : angle 0.61894 (48931) hydrogen bonds : bond 0.03481 ( 1406) hydrogen bonds : angle 3.85911 ( 3899) metal coordination : bond 0.01059 ( 31) metal coordination : angle 4.92373 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 717 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9327 (mm) REVERT: B 1 MET cc_start: 0.8286 (tpp) cc_final: 0.7720 (ttt) REVERT: C 452 MET cc_start: 0.4614 (ttt) cc_final: 0.3595 (tpt) REVERT: C 474 HIS cc_start: 0.8742 (m-70) cc_final: 0.8354 (t70) REVERT: C 528 MET cc_start: 0.7272 (mmm) cc_final: 0.6940 (mpp) REVERT: D 61 PHE cc_start: 0.8781 (m-80) cc_final: 0.7638 (t80) REVERT: D 228 MET cc_start: 0.7751 (mmp) cc_final: 0.6682 (mmp) REVERT: E 57 MET cc_start: 0.8214 (mtp) cc_final: 0.7707 (mtp) REVERT: E 159 MET cc_start: 0.9348 (tpp) cc_final: 0.8818 (tpp) REVERT: E 322 TYR cc_start: 0.8024 (m-80) cc_final: 0.7377 (m-80) REVERT: F 118 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7686 (tp) REVERT: F 175 MET cc_start: 0.7878 (ppp) cc_final: 0.7581 (ppp) REVERT: F 231 PHE cc_start: 0.8728 (m-10) cc_final: 0.7926 (m-80) REVERT: G 24 ASP cc_start: 0.8912 (t70) cc_final: 0.8551 (t0) REVERT: G 37 ASP cc_start: 0.9158 (p0) cc_final: 0.8902 (p0) REVERT: G 50 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8222 (t) REVERT: G 54 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8564 (mp10) REVERT: H 904 TRP cc_start: 0.7789 (OUTLIER) cc_final: 0.6299 (t-100) REVERT: K 75 PHE cc_start: 0.7084 (t80) cc_final: 0.6814 (t80) REVERT: K 113 MET cc_start: 0.4725 (mmp) cc_final: 0.2543 (ttt) REVERT: N 471 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8554 (mm) REVERT: N 524 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6539 (mt0) REVERT: N 616 MET cc_start: 0.3016 (mtp) cc_final: 0.2570 (mmt) REVERT: O 102 MET cc_start: 0.1430 (tpt) cc_final: -0.0684 (ttm) REVERT: O 154 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8431 (mm-30) REVERT: Q 182 MET cc_start: 0.9345 (mtp) cc_final: 0.9071 (mtp) REVERT: Q 610 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: Q 722 MET cc_start: 0.9338 (ttp) cc_final: 0.8728 (tmm) REVERT: Q 748 MET cc_start: 0.9217 (ttt) cc_final: 0.8905 (tpt) REVERT: Q 902 HIS cc_start: 0.9175 (t70) cc_final: 0.8935 (m-70) REVERT: R 208 TYR cc_start: 0.8826 (m-80) cc_final: 0.8562 (m-80) REVERT: R 230 ASP cc_start: 0.7987 (t0) cc_final: 0.7654 (m-30) outliers start: 61 outliers final: 44 residues processed: 258 average time/residue: 0.2128 time to fit residues: 92.5975 Evaluate side-chains 252 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 19 TRP Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 194 CYS Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain K residue 196 SER Chi-restraints excluded: chain K residue 245 GLU Chi-restraints excluded: chain N residue 462 PHE Chi-restraints excluded: chain N residue 471 LEU Chi-restraints excluded: chain N residue 524 GLN Chi-restraints excluded: chain N residue 571 ILE Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain P residue 9 ARG Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 573 VAL Chi-restraints excluded: chain Q residue 578 VAL Chi-restraints excluded: chain Q residue 610 TYR Chi-restraints excluded: chain Q residue 799 ARG Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 130 TYR Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain S residue 196 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 318 optimal weight: 8.9990 chunk 244 optimal weight: 30.0000 chunk 364 optimal weight: 6.9990 chunk 277 optimal weight: 7.9990 chunk 292 optimal weight: 20.0000 chunk 393 optimal weight: 40.0000 chunk 259 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 300 optimal weight: 30.0000 chunk 191 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 GLN B 148 HIS ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 ASN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 HIS ** Q 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.078907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.050260 restraints weight = 168537.607| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.91 r_work: 0.2833 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 35949 Z= 0.236 Angle : 0.640 16.940 48976 Z= 0.312 Chirality : 0.042 0.240 5569 Planarity : 0.004 0.060 6010 Dihedral : 13.514 89.079 5367 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.61 % Allowed : 13.92 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % 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: 0.37 (0.13), residues: 4175 helix: 1.46 (0.12), residues: 2011 sheet: -0.49 (0.22), residues: 603 loop : -1.02 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 513 TYR 0.021 0.001 TYR N 478 PHE 0.029 0.001 PHE O 248 TRP 0.024 0.002 TRP A 77 HIS 0.007 0.001 HIS F 248 Details of bonding type rmsd covalent geometry : bond 0.00532 (35918) covalent geometry : angle 0.61991 (48931) hydrogen bonds : bond 0.03357 ( 1406) hydrogen bonds : angle 3.92043 ( 3899) metal coordination : bond 0.01037 ( 31) metal coordination : angle 5.23503 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8350 Ramachandran restraints generated. 4175 Oldfield, 0 Emsley, 4175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 717 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9292 (mm) REVERT: B 1 MET cc_start: 0.8264 (tpp) cc_final: 0.7817 (ttt) REVERT: B 109 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9171 (tp) REVERT: C 452 MET cc_start: 0.4798 (ttt) cc_final: 0.3737 (tpt) REVERT: C 474 HIS cc_start: 0.8832 (m-70) cc_final: 0.8365 (t-90) REVERT: C 528 MET cc_start: 0.7381 (mmm) cc_final: 0.7030 (mpp) REVERT: D 61 PHE cc_start: 0.8812 (m-80) cc_final: 0.7696 (t80) REVERT: D 228 MET cc_start: 0.7709 (mmp) cc_final: 0.6713 (mmp) REVERT: E 57 MET cc_start: 0.8229 (mtp) cc_final: 0.7714 (mtp) REVERT: E 159 MET cc_start: 0.9331 (tpp) cc_final: 0.8771 (tpp) REVERT: F 118 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7729 (tp) REVERT: F 175 MET cc_start: 0.7791 (ppp) cc_final: 0.7462 (ppp) REVERT: F 231 PHE cc_start: 0.8685 (m-10) cc_final: 0.7892 (m-80) REVERT: G 24 ASP cc_start: 0.8948 (t70) cc_final: 0.8563 (t0) REVERT: G 37 ASP cc_start: 0.9166 (p0) cc_final: 0.8896 (p0) REVERT: G 54 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8504 (mp10) REVERT: H 904 TRP cc_start: 0.7860 (OUTLIER) cc_final: 0.6251 (t-100) REVERT: K 113 MET cc_start: 0.4825 (mmp) cc_final: 0.2806 (ttt) REVERT: K 273 MET cc_start: 0.7096 (mmm) cc_final: 0.4700 (pmm) REVERT: N 471 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8572 (mm) REVERT: N 477 MET cc_start: 0.7630 (mmm) cc_final: 0.7325 (mmm) REVERT: N 524 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6532 (mt0) REVERT: N 616 MET cc_start: 0.3120 (mtp) cc_final: 0.2654 (mmt) REVERT: O 102 MET cc_start: 0.1231 (tpt) cc_final: -0.0876 (ttm) REVERT: O 154 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8417 (mm-30) REVERT: Q 182 MET cc_start: 0.9304 (mtp) cc_final: 0.9030 (mtp) REVERT: Q 610 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: Q 722 MET cc_start: 0.9310 (ttp) cc_final: 0.8752 (tmm) REVERT: Q 748 MET cc_start: 0.9231 (ttt) cc_final: 0.8756 (tpp) REVERT: Q 902 HIS cc_start: 0.9166 (t70) cc_final: 0.8929 (m-70) REVERT: R 208 TYR cc_start: 0.8934 (m-80) cc_final: 0.8675 (m-80) REVERT: R 230 ASP cc_start: 0.7857 (t0) cc_final: 0.7483 (m-30) REVERT: S 207 ASP cc_start: 0.9012 (m-30) cc_final: 0.8718 (m-30) outliers start: 59 outliers final: 44 residues processed: 255 average time/residue: 0.2094 time to fit residues: 90.1460 Evaluate side-chains 246 residues out of total 3775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain E residue 19 TRP Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 194 CYS Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain H residue 904 TRP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 175 TRP Chi-restraints excluded: chain K residue 196 SER Chi-restraints excluded: chain K residue 245 GLU Chi-restraints excluded: chain N residue 462 PHE Chi-restraints excluded: chain N residue 471 LEU Chi-restraints excluded: chain N residue 524 GLN Chi-restraints excluded: chain N residue 571 ILE Chi-restraints excluded: chain N residue 594 VAL Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 88 THR Chi-restraints excluded: chain P residue 9 ARG Chi-restraints excluded: chain P residue 16 MET Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 133 VAL Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 573 VAL Chi-restraints excluded: chain Q residue 578 VAL Chi-restraints excluded: chain Q residue 610 TYR Chi-restraints excluded: chain Q residue 799 ARG Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 130 TYR Chi-restraints excluded: chain S residue 243 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: chunk 395 optimal weight: 50.0000 chunk 295 optimal weight: 6.9990 chunk 333 optimal weight: 8.9990 chunk 334 optimal weight: 7.9990 chunk 76 optimal weight: 30.0000 chunk 150 optimal weight: 20.0000 chunk 397 optimal weight: 30.0000 chunk 365 optimal weight: 3.9990 chunk 287 optimal weight: 10.0000 chunk 353 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** K 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 228 GLN ** Q 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 HIS ** Q 869 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 = 0.4015 r_free = 0.4015 target = 0.078328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.049937 restraints weight = 166906.699| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 4.12 r_work: 0.2791 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 35949 Z= 0.257 Angle : 0.658 16.059 48976 Z= 0.325 Chirality : 0.043 0.169 5569 Planarity : 0.004 0.061 6010 Dihedral : 13.589 88.227 5367 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.48 % Allowed : 14.25 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.76 % 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: 0.32 (0.13), residues: 4175 helix: 1.42 (0.12), residues: 2004 sheet: -0.58 (0.22), residues: 610 loop : -1.01 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 730 TYR 0.017 0.001 TYR A 139 PHE 0.032 0.002 PHE O 248 TRP 0.029 0.002 TRP A 511 HIS 0.008 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00580 (35918) covalent geometry : angle 0.64019 (48931) hydrogen bonds : bond 0.03594 ( 1406) hydrogen bonds : angle 4.01563 ( 3899) metal coordination : bond 0.01085 ( 31) metal coordination : angle 5.08986 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13363.51 seconds wall clock time: 227 minutes 59.67 seconds (13679.67 seconds total)