Starting phenix.real_space_refine on Sat Jun 6 00:23:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28ke_56573/06_2026/28ke_56573.cif Found real_map, /net/cci-nas-00/data/ceres_data/28ke_56573/06_2026/28ke_56573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28ke_56573/06_2026/28ke_56573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28ke_56573/06_2026/28ke_56573.map" model { file = "/net/cci-nas-00/data/ceres_data/28ke_56573/06_2026/28ke_56573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28ke_56573/06_2026/28ke_56573.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 6 6.06 5 P 40 5.49 5 S 146 5.16 5 C 15236 2.51 5 N 4173 2.21 5 O 4502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24107 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5052 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 25, 'TRANS': 599} Chain breaks: 3 Chain: "B" Number of atoms: 5600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5600 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 29, 'TRANS': 664} Chain breaks: 2 Chain: "C" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1221 Classifications: {'peptide': 152} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 145} Chain: "D" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3490 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 1 Chain: "E" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2923 Classifications: {'peptide': 372} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 353} Chain breaks: 1 Chain: "F" Number of atoms: 2045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2045 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 1 Chain: "G" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 537 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "H" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 642 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "I" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 322 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain breaks: 1 Chain: "N" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 165} Chain: "L" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 415 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "M" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 405 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} 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: "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 5995 SG CYS B 116 56.185 38.932 65.812 1.00222.50 S ATOM 6304 SG CYS B 155 52.473 35.094 61.863 1.00229.46 S ATOM 6135 SG CYS B 134 55.234 41.048 60.256 1.00213.53 S ATOM 6593 SG CYS B 190 50.256 40.375 64.368 1.00214.73 S ATOM 17955 SG CYS E 345 40.215 62.257 160.274 1.00 92.06 S ATOM 17977 SG CYS E 348 42.153 65.371 161.188 1.00 77.62 S ATOM 18134 SG CYS E 368 40.400 65.175 157.803 1.00 87.77 S ATOM 18155 SG CYS E 371 43.429 63.050 158.424 1.00 77.72 S ATOM 18075 SG CYS E 360 39.001 51.213 154.672 1.00111.21 S ATOM 18093 SG CYS E 363 39.920 49.805 158.136 1.00116.26 S ATOM 18242 SG CYS E 382 42.039 52.555 156.586 1.00 83.11 S ATOM 18259 SG CYS E 385 42.199 48.972 155.525 1.00 85.80 S ATOM 17519 SG CYS E 291 79.075 37.795 149.286 1.00 84.09 S ATOM 17541 SG CYS E 294 82.637 36.615 149.043 1.00 97.03 S ATOM 17630 SG CYS E 305 81.375 39.048 146.446 1.00 89.45 S ATOM 17653 SG CYS E 308 80.078 35.559 146.363 1.00 97.68 S ATOM 20175 SG CYS F 268 59.201 37.535 139.361 1.00 65.93 S ATOM 20194 SG CYS F 271 57.048 39.695 141.628 1.00 70.18 S ATOM 20279 SG CYS F 282 56.013 36.250 141.119 1.00 96.59 S ATOM 20299 SG CYS F 285 55.595 38.535 138.250 1.00103.44 S ATOM 20067 SG CYS F 255 60.075 34.986 154.006 1.00 74.47 S ATOM 20084 SG CYS F 257 58.337 32.297 151.873 1.00 78.65 S ATOM 20233 SG CYS F 276 62.073 32.046 152.440 1.00 77.35 S ATOM 21865 SG CYS N 105 48.702 102.565 47.799 1.00196.17 S ATOM 21889 SG CYS N 108 48.720 103.387 44.068 1.00204.58 S ATOM 22037 SG CYS N 126 50.685 100.460 45.433 1.00196.02 S ATOM 22059 SG CYS N 129 51.888 103.910 46.220 1.00200.61 S Time building chain proxies: 5.88, per 1000 atoms: 0.24 Number of scatterers: 24107 At special positions: 0 Unit cell: (120.6, 154.1, 207.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 146 16.00 P 40 15.00 O 4502 8.00 N 4173 7.00 C 15236 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " 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 368 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " 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 276 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 255 " pdb=" ZN N 301 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 126 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 105 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 129 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 108 " Number of angles added : 33 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 25 sheets defined 53.0% alpha, 10.8% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 92 through 104 Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 149 through 162 removed outlier: 3.551A pdb=" N MET A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.805A pdb=" N ILE A 185 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 346 through 358 removed outlier: 3.836A pdb=" N GLY A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.935A pdb=" N LEU A 413 " --> pdb=" O THR A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 removed outlier: 3.925A pdb=" N THR A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 448 through 457 removed outlier: 3.530A pdb=" N ARG A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 515 through 525 removed outlier: 4.199A pdb=" N ALA A 524 " --> pdb=" O ARG A 520 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 536 removed outlier: 4.122A pdb=" N LEU A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 553 Processing helix chain 'A' and resid 564 through 576 Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 632 through 641 Processing helix chain 'A' and resid 667 through 676 removed outlier: 4.365A pdb=" N ALA A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 684 removed outlier: 3.569A pdb=" N VAL A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP A 682 " --> pdb=" O ARG A 678 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 774 through 780 removed outlier: 3.991A pdb=" N ARG A 779 " --> pdb=" O PRO A 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 35 Processing helix chain 'B' and resid 46 through 63 Processing helix chain 'B' and resid 76 through 99 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.536A pdb=" N ARG B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.983A pdb=" N LYS B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.830A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 277 Processing helix chain 'B' and resid 278 through 289 Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 325 through 344 Processing helix chain 'B' and resid 353 through 366 Processing helix chain 'B' and resid 369 through 387 removed outlier: 5.100A pdb=" N ALA B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 408 Processing helix chain 'B' and resid 440 through 450 removed outlier: 3.724A pdb=" N ILE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Proline residue: B 446 - end of helix Processing helix chain 'B' and resid 465 through 471 removed outlier: 3.709A pdb=" N LYS B 469 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 511 removed outlier: 3.501A pdb=" N ARG B 511 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 531 removed outlier: 3.787A pdb=" N ILE B 517 " --> pdb=" O ASP B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 555 Processing helix chain 'B' and resid 556 through 563 Processing helix chain 'B' and resid 573 through 590 Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 630 through 645 Processing helix chain 'B' and resid 647 through 665 removed outlier: 3.597A pdb=" N PHE B 651 " --> pdb=" O ARG B 647 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 685 Processing helix chain 'B' and resid 686 through 692 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 700 through 701 No H-bonds generated for 'chain 'B' and resid 700 through 701' Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.637A pdb=" N LEU B 706 " --> pdb=" O ASP B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 725 Processing helix chain 'C' and resid 398 through 413 Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 454 through 478 removed outlier: 3.576A pdb=" N CYS C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 516 removed outlier: 4.672A 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 522 through 548 Processing helix chain 'D' and resid 18 through 25 removed outlier: 3.517A pdb=" N PHE D 22 " --> pdb=" O ASN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 37 through 46 Processing helix chain 'D' and resid 49 through 59 removed outlier: 3.582A pdb=" N ASN D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 74 through 75 No H-bonds generated for 'chain 'D' and resid 74 through 75' Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 79 through 93 Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 144 through 165 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.757A pdb=" N LEU D 205 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 222 Processing helix chain 'D' and resid 223 through 227 removed outlier: 3.530A pdb=" N GLY D 227 " --> pdb=" O GLN D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 242 removed outlier: 3.515A pdb=" N PHE D 242 " --> pdb=" O PHE D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 321 through 331 removed outlier: 4.198A pdb=" N PHE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 358 Processing helix chain 'D' and resid 360 through 371 Processing helix chain 'D' and resid 373 through 379 removed outlier: 3.654A pdb=" N LYS D 378 " --> pdb=" O VAL D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 397 removed outlier: 3.551A pdb=" N THR D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 400 No H-bonds generated for 'chain 'D' and resid 398 through 400' Processing helix chain 'D' and resid 414 through 429 removed outlier: 3.601A pdb=" N PHE D 418 " --> pdb=" O SER D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 462 removed outlier: 3.924A pdb=" N ASP D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS D 452 " --> pdb=" O HIS D 448 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 removed outlier: 3.826A pdb=" N GLU E 12 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY E 13 " --> pdb=" O ARG E 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 9 through 13' Processing helix chain 'E' and resid 17 through 22 removed outlier: 3.677A pdb=" N LEU E 22 " --> pdb=" O TRP E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 43 Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 79 through 99 Processing helix chain 'E' and resid 123 through 134 removed outlier: 4.627A pdb=" N HIS E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 157 removed outlier: 3.713A pdb=" N SER E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR E 155 " --> pdb=" O ILE E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 193 removed outlier: 3.855A pdb=" N LEU E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 215 removed outlier: 3.774A pdb=" N THR E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 235 removed outlier: 3.681A pdb=" N HIS E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 314 through 319 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 368 through 378 Processing helix chain 'E' and resid 382 through 388 removed outlier: 3.520A pdb=" N LYS E 388 " --> pdb=" O GLY E 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'F' and resid 33 through 52 removed outlier: 4.110A pdb=" N ASN F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 121 removed outlier: 3.556A pdb=" N LYS F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 148 removed outlier: 3.536A pdb=" N SER F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 187 Processing helix chain 'F' and resid 200 through 211 Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 234 through 239 Processing helix chain 'F' and resid 282 through 289 Processing helix chain 'G' and resid 13 through 26 Processing helix chain 'G' and resid 50 through 64 removed outlier: 3.569A pdb=" N ASN G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 82 removed outlier: 4.213A pdb=" N ILE H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 111 removed outlier: 3.833A pdb=" N TYR H 95 " --> pdb=" O SER H 91 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN H 111 " --> pdb=" O PHE H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 129 removed outlier: 3.746A pdb=" N THR H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN H 129 " --> pdb=" O TYR H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 140 Processing helix chain 'I' and resid 890 through 902 removed outlier: 4.661A pdb=" N ALA I 894 " --> pdb=" O THR I 890 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU I 895 " --> pdb=" O SER I 891 " (cutoff:3.500A) Processing helix chain 'I' and resid 903 through 916 removed outlier: 4.017A pdb=" N ARG I 908 " --> pdb=" O TRP I 904 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU I 909 " --> pdb=" O PRO I 905 " (cutoff:3.500A) Processing helix chain 'I' and resid 935 through 939 removed outlier: 3.579A pdb=" N GLN I 939 " --> pdb=" O PRO I 936 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 120 removed outlier: 3.998A pdb=" N HIS N 120 " --> pdb=" O TYR N 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 149 removed outlier: 3.619A pdb=" N LEU N 149 " --> pdb=" O LYS N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 156 Processing helix chain 'N' and resid 183 through 194 Processing helix chain 'N' and resid 199 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 7.030A pdb=" N LYS A 59 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG D 337 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 removed outlier: 5.530A 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: 4.533A pdb=" N TYR A 175 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 391 removed outlier: 7.030A pdb=" N GLY A 436 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 336 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 467 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL A 337 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU A 490 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL A 339 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 579 through 580 removed outlier: 6.584A pdb=" N ILE A 558 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE A 607 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE A 559 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU A 623 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU A 662 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN A 625 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N SER A 664 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN A 506 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N SER A 661 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA A 508 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL A 663 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL A 510 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N CYS A 507 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ILE A 690 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU A 509 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.554A pdb=" N VAL B 206 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU B 70 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N TYR B 207 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR B 72 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 231 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AB1, first strand: chain 'B' and resid 490 through 494 removed outlier: 6.388A pdb=" N CYS B 491 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE B 679 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET B 493 " --> pdb=" O PHE B 679 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL B 618 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 535 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 66 through 67 removed outlier: 3.638A pdb=" N LEU D 66 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AB4, first strand: chain 'D' and resid 249 through 250 Processing sheet with id=AB5, first strand: chain 'D' and resid 431 through 433 removed outlier: 3.556A pdb=" N VAL D 432 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL D 442 " --> pdb=" O VAL D 432 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY D 406 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY G 7 " --> pdb=" O GLY D 406 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.285A pdb=" N VAL E 63 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N THR E 109 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL E 65 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE E 104 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU E 120 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL E 108 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LYS E 116 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS E 110 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.985A pdb=" N ARG E 165 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N SER E 197 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL E 167 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE E 199 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE E 169 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS E 220 " --> pdb=" O VAL E 198 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 303 through 304 removed outlier: 4.340A pdb=" N THR E 311 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 257 through 258 removed outlier: 3.579A pdb=" N VAL F 249 " --> pdb=" O HIS E 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 289 through 290 Processing sheet with id=AC2, first strand: chain 'E' and resid 332 through 335 Processing sheet with id=AC3, first strand: chain 'F' and resid 67 through 69 removed outlier: 8.213A pdb=" N LYS F 56 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASN F 9 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA F 58 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU F 11 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE F 60 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE F 13 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N SER F 62 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL F 15 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU F 8 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ARG F 160 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU F 10 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU F 162 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL F 12 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE F 164 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL F 14 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N LEU F 190 " --> pdb=" O MET F 157 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER F 159 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ASP F 192 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE F 161 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N CYS F 194 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL F 163 " --> pdb=" O CYS F 194 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N LEU F 215 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA F 193 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 253 through 254 Processing sheet with id=AC5, first strand: chain 'N' and resid 103 through 104 Processing sheet with id=AC6, first strand: chain 'N' and resid 138 through 140 Processing sheet with id=AC7, first strand: chain 'N' and resid 246 through 251 removed outlier: 4.499A pdb=" N THR N 260 " --> pdb=" O PRO N 248 " (cutoff:3.500A) 1112 hydrogen bonds defined for protein. 3210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 2.91 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: 10335 1.43 - 1.64: 14121 1.64 - 1.86: 214 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 24682 Sorted by residual: bond pdb=" CB LYS C 494 " pdb=" CG LYS C 494 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.99e+00 bond pdb=" CB GLU H 94 " pdb=" CG GLU H 94 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CG1 ILE B 418 " pdb=" CD1 ILE B 418 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.43e+00 bond pdb=" CA MET H 122 " pdb=" CB MET H 122 " ideal model delta sigma weight residual 1.528 1.546 -0.018 1.56e-02 4.11e+03 1.31e+00 bond pdb=" CB LYS C 511 " pdb=" CG LYS C 511 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.15e+00 ... (remaining 24677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 33273 2.58 - 5.17: 215 5.17 - 7.75: 30 7.75 - 10.34: 3 10.34 - 12.92: 2 Bond angle restraints: 33523 Sorted by residual: angle pdb=" CA MET H 122 " pdb=" CB MET H 122 " pdb=" CG MET H 122 " ideal model delta sigma weight residual 114.10 124.04 -9.94 2.00e+00 2.50e-01 2.47e+01 angle pdb=" CA LEU B 333 " pdb=" CB LEU B 333 " pdb=" CG LEU B 333 " ideal model delta sigma weight residual 116.30 129.22 -12.92 3.50e+00 8.16e-02 1.36e+01 angle pdb=" CA LEU B 383 " pdb=" CB LEU B 383 " pdb=" CG LEU B 383 " ideal model delta sigma weight residual 116.30 128.80 -12.50 3.50e+00 8.16e-02 1.28e+01 angle pdb=" N MET D 441 " pdb=" CA MET D 441 " pdb=" CB MET D 441 " ideal model delta sigma weight residual 111.66 106.63 5.03 1.67e+00 3.59e-01 9.08e+00 angle pdb=" C MET H 122 " pdb=" CA MET H 122 " pdb=" CB MET H 122 " ideal model delta sigma weight residual 110.79 115.67 -4.88 1.66e+00 3.63e-01 8.64e+00 ... (remaining 33518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 14144 33.95 - 67.90: 694 67.90 - 101.85: 42 101.85 - 135.80: 1 135.80 - 169.75: 3 Dihedral angle restraints: 14884 sinusoidal: 6394 harmonic: 8490 Sorted by residual: dihedral pdb=" C4' DG M 31 " pdb=" C3' DG M 31 " pdb=" O3' DG M 31 " pdb=" P DT M 32 " ideal model delta sinusoidal sigma weight residual -140.00 29.75 -169.75 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA PRO B 532 " pdb=" C PRO B 532 " pdb=" N ASP B 533 " pdb=" CA ASP B 533 " ideal model delta harmonic sigma weight residual 180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" C4' DT L 5 " pdb=" C3' DT L 5 " pdb=" O3' DT L 5 " pdb=" P DT L 6 " ideal model delta sinusoidal sigma weight residual 220.00 69.77 150.23 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 14881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3101 0.053 - 0.105: 552 0.105 - 0.158: 95 0.158 - 0.211: 4 0.211 - 0.264: 1 Chirality restraints: 3753 Sorted by residual: chirality pdb=" CB ILE B 418 " pdb=" CA ILE B 418 " pdb=" CG1 ILE B 418 " pdb=" CG2 ILE B 418 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO B 532 " pdb=" N PRO B 532 " pdb=" C PRO B 532 " pdb=" CB PRO B 532 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CB VAL C 490 " pdb=" CA VAL C 490 " pdb=" CG1 VAL C 490 " pdb=" CG2 VAL C 490 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.48e-01 ... (remaining 3750 not shown) Planarity restraints: 4137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 501 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C GLN C 501 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN C 501 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL C 502 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 133 " -0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C ILE H 133 " 0.061 2.00e-02 2.50e+03 pdb=" O ILE H 133 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN H 134 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 444 " -0.055 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO D 445 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO D 445 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 445 " -0.046 5.00e-02 4.00e+02 ... (remaining 4134 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 808 2.71 - 3.26: 23615 3.26 - 3.81: 38236 3.81 - 4.35: 45651 4.35 - 4.90: 77846 Nonbonded interactions: 186156 Sorted by model distance: nonbonded pdb=" O THR B 405 " pdb=" OG1 THR B 409 " model vdw 2.164 3.040 nonbonded pdb=" OD1 ASP H 114 " pdb=" ND2 ASN H 117 " model vdw 2.186 3.120 nonbonded pdb=" O LYS F 116 " pdb=" OG1 THR F 120 " model vdw 2.198 3.040 nonbonded pdb=" O PRO A 66 " pdb=" OG1 THR A 146 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR B 72 " pdb=" OD2 ASP B 234 " model vdw 2.209 3.040 ... (remaining 186151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 31.430 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24710 Z= 0.137 Angle : 0.589 12.921 33568 Z= 0.302 Chirality : 0.041 0.264 3753 Planarity : 0.004 0.085 4137 Dihedral : 18.297 169.749 9376 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.26 % Allowed : 24.76 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 0.56 (0.16), residues: 2855 helix: 2.06 (0.14), residues: 1385 sheet: -0.31 (0.28), residues: 363 loop : -1.67 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 514 TYR 0.021 0.001 TYR C 516 PHE 0.027 0.001 PHE H 107 TRP 0.014 0.001 TRP I 904 HIS 0.007 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (24682) covalent geometry : angle 0.57031 / 0.30 (33523) hydrogen bonds : bond 0.14986 / 9.73 ( 1154) hydrogen bonds : angle 5.30013 / 3.80 ( 3298) metal coordination : bond 0.00611 / 0.36 ( 28) metal coordination : angle 4.05628 / 2.16 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7489 (pt0) REVERT: A 412 MET cc_start: 0.8432 (tpp) cc_final: 0.7966 (tpp) REVERT: B 453 SER cc_start: 0.7698 (OUTLIER) cc_final: 0.7299 (p) REVERT: C 449 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6679 (tp) REVERT: C 452 MET cc_start: 0.6828 (tpp) cc_final: 0.6552 (tpp) REVERT: C 453 VAL cc_start: 0.6580 (t) cc_final: 0.6319 (p) REVERT: C 457 ILE cc_start: 0.5528 (mt) cc_final: 0.5237 (mt) REVERT: C 492 LYS cc_start: 0.9205 (mmtp) cc_final: 0.8836 (mttt) REVERT: C 533 TYR cc_start: 0.8630 (m-10) cc_final: 0.8428 (m-10) REVERT: C 535 LYS cc_start: 0.8618 (tptp) cc_final: 0.8290 (tttp) REVERT: C 537 HIS cc_start: 0.8763 (t-170) cc_final: 0.8545 (t-170) REVERT: D 254 MET cc_start: 0.7499 (mtm) cc_final: 0.7249 (mtt) REVERT: D 315 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8906 (mt) REVERT: E 62 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.6859 (t80) REVERT: E 265 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: E 339 TYR cc_start: 0.6480 (t80) cc_final: 0.6017 (t80) REVERT: F 42 MET cc_start: 0.8974 (mtp) cc_final: 0.8738 (mtp) REVERT: F 215 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8659 (tp) REVERT: I 912 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6037 (mt-10) REVERT: I 928 LYS cc_start: 0.6512 (mmtt) cc_final: 0.5815 (tppt) REVERT: N 113 MET cc_start: 0.6004 (tpp) cc_final: 0.5765 (tpp) REVERT: N 118 MET cc_start: 0.8781 (tpp) cc_final: 0.8482 (mmm) REVERT: N 263 MET cc_start: 0.6487 (mmm) cc_final: 0.6192 (ptt) outliers start: 58 outliers final: 43 residues processed: 232 average time/residue: 0.1656 time to fit residues: 61.1725 Evaluate side-chains 219 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 CYS Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 140 THR Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 154 GLN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN A 564 ASN A 598 HIS A 603 ASN A 625 GLN A 665 GLN B 21 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 ASN B 201 HIS B 210 HIS B 241 ASN B 279 GLN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 ASN B 629 GLN B 707 ASN C 509 GLN C 537 HIS D 20 GLN D 83 GLN D 312 ASN D 458 GLN D 460 HIS E 147 ASN F 63 HIS F 128 HIS F 145 HIS G 3 ASN H 129 ASN I 914 GLN N 120 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.091297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.063860 restraints weight = 72045.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.062498 restraints weight = 48728.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.063078 restraints weight = 41600.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.063240 restraints weight = 37030.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063369 restraints weight = 32618.355| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24710 Z= 0.146 Angle : 0.545 10.075 33568 Z= 0.278 Chirality : 0.040 0.223 3753 Planarity : 0.004 0.040 4137 Dihedral : 13.086 167.134 3668 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.70 % Allowed : 22.58 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 0.67 (0.16), residues: 2855 helix: 2.04 (0.14), residues: 1414 sheet: -0.27 (0.29), residues: 367 loop : -1.54 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 473 TYR 0.020 0.001 TYR A 534 PHE 0.012 0.001 PHE C 500 TRP 0.012 0.001 TRP I 904 HIS 0.005 0.001 HIS C 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (24682) covalent geometry : angle 0.52368 / 0.28 (33523) hydrogen bonds : bond 0.04205 / 2.76 ( 1154) hydrogen bonds : angle 4.26254 / 3.07 ( 3298) metal coordination : bond 0.00706 / 0.40 ( 28) metal coordination : angle 4.15689 / 2.25 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 174 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8764 (tpp) cc_final: 0.8388 (tpp) REVERT: A 496 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8848 (mp) REVERT: A 568 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8440 (tp) REVERT: A 584 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7444 (p) REVERT: B 42 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8233 (ttt) REVERT: C 407 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8277 (mm) REVERT: C 449 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6697 (tp) REVERT: C 453 VAL cc_start: 0.6670 (t) cc_final: 0.6419 (p) REVERT: C 465 TYR cc_start: 0.7851 (OUTLIER) cc_final: 0.7606 (m-10) REVERT: C 526 GLU cc_start: 0.7755 (mp0) cc_final: 0.7478 (mp0) REVERT: C 533 TYR cc_start: 0.8730 (m-10) cc_final: 0.8499 (m-10) REVERT: C 535 LYS cc_start: 0.8630 (tptp) cc_final: 0.8295 (tttp) REVERT: C 537 HIS cc_start: 0.8787 (t70) cc_final: 0.8529 (t-170) REVERT: D 46 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8281 (mtm180) REVERT: D 62 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8555 (mp) REVERT: D 254 MET cc_start: 0.7490 (mtm) cc_final: 0.7208 (mtm) REVERT: D 258 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7643 (tt) REVERT: E 62 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.6904 (t80) REVERT: F 42 MET cc_start: 0.9013 (mtp) cc_final: 0.8756 (mtp) REVERT: G 32 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7489 (tppp) REVERT: I 912 GLU cc_start: 0.6400 (mm-30) cc_final: 0.5932 (mt-10) REVERT: I 928 LYS cc_start: 0.6524 (mmtt) cc_final: 0.5817 (tppt) REVERT: N 118 MET cc_start: 0.8871 (tpp) cc_final: 0.8601 (mmm) REVERT: N 258 ARG cc_start: 0.7307 (ttp80) cc_final: 0.7009 (ttp80) REVERT: N 263 MET cc_start: 0.6877 (mmm) cc_final: 0.6435 (ptt) REVERT: N 269 THR cc_start: 0.7746 (p) cc_final: 0.7426 (p) outliers start: 95 outliers final: 42 residues processed: 259 average time/residue: 0.1607 time to fit residues: 66.9239 Evaluate side-chains 223 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 562 GLN Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 3 ASN Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain N residue 119 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 265 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 chunk 248 optimal weight: 0.9990 chunk 198 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 158 optimal weight: 0.4980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN ** G 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.092055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.064140 restraints weight = 71988.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.063366 restraints weight = 49288.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.063899 restraints weight = 38945.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.064184 restraints weight = 33424.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.064286 restraints weight = 30612.591| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24710 Z= 0.112 Angle : 0.512 9.381 33568 Z= 0.257 Chirality : 0.039 0.213 3753 Planarity : 0.003 0.036 4137 Dihedral : 12.707 167.215 3604 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.85 % Allowed : 22.23 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 0.75 (0.16), residues: 2855 helix: 2.09 (0.14), residues: 1415 sheet: -0.10 (0.29), residues: 356 loop : -1.52 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 473 TYR 0.019 0.001 TYR A 534 PHE 0.016 0.001 PHE H 107 TRP 0.012 0.001 TRP I 904 HIS 0.004 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (24682) covalent geometry : angle 0.49177 / 0.26 (33523) hydrogen bonds : bond 0.03679 / 2.43 ( 1154) hydrogen bonds : angle 4.02152 / 2.89 ( 3298) metal coordination : bond 0.00502 / 0.28 ( 28) metal coordination : angle 3.87958 / 2.05 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 181 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8813 (tpp) cc_final: 0.8584 (tpt) REVERT: A 568 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8378 (tp) REVERT: A 584 THR cc_start: 0.7686 (OUTLIER) cc_final: 0.7398 (p) REVERT: B 42 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8168 (ttt) REVERT: B 365 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7502 (p) REVERT: C 449 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6683 (tp) REVERT: C 457 ILE cc_start: 0.5767 (mt) cc_final: 0.5565 (mt) REVERT: C 470 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8062 (mm-30) REVERT: C 526 GLU cc_start: 0.7946 (mp0) cc_final: 0.7624 (mp0) REVERT: C 535 LYS cc_start: 0.8616 (tptp) cc_final: 0.8196 (tppt) REVERT: D 46 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8147 (mtm180) REVERT: D 62 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8499 (mp) REVERT: D 254 MET cc_start: 0.7458 (mtm) cc_final: 0.7050 (mtm) REVERT: D 315 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8860 (mt) REVERT: E 62 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.7011 (t80) REVERT: E 339 TYR cc_start: 0.6619 (t80) cc_final: 0.6147 (t80) REVERT: F 42 MET cc_start: 0.9017 (mtp) cc_final: 0.8716 (mtp) REVERT: G 32 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7767 (tppp) REVERT: I 912 GLU cc_start: 0.6372 (mm-30) cc_final: 0.5913 (mt-10) REVERT: I 928 LYS cc_start: 0.6541 (mmtt) cc_final: 0.5822 (tppt) REVERT: N 118 MET cc_start: 0.8842 (tpp) cc_final: 0.8523 (mmm) REVERT: N 258 ARG cc_start: 0.7381 (ttp80) cc_final: 0.7121 (ttp80) REVERT: N 263 MET cc_start: 0.6960 (mmm) cc_final: 0.6405 (ptt) REVERT: N 269 THR cc_start: 0.7626 (p) cc_final: 0.7390 (p) outliers start: 99 outliers final: 50 residues processed: 266 average time/residue: 0.1684 time to fit residues: 71.9277 Evaluate side-chains 231 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 3 optimal weight: 0.5980 chunk 203 optimal weight: 0.1980 chunk 192 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN B 363 GLN C 537 HIS G 3 ASN G 36 GLN I 906 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.091679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.064129 restraints weight = 71833.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.062755 restraints weight = 50193.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063323 restraints weight = 41051.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.063500 restraints weight = 36120.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.063674 restraints weight = 31993.685| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24710 Z= 0.126 Angle : 0.512 9.314 33568 Z= 0.258 Chirality : 0.039 0.170 3753 Planarity : 0.003 0.037 4137 Dihedral : 12.710 167.930 3602 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.62 % Allowed : 22.46 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 0.78 (0.16), residues: 2855 helix: 2.12 (0.14), residues: 1413 sheet: -0.13 (0.29), residues: 364 loop : -1.50 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 473 TYR 0.018 0.001 TYR A 534 PHE 0.014 0.001 PHE C 500 TRP 0.011 0.001 TRP I 904 HIS 0.004 0.001 HIS C 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (24682) covalent geometry : angle 0.49212 / 0.26 (33523) hydrogen bonds : bond 0.03631 / 2.40 ( 1154) hydrogen bonds : angle 3.94803 / 2.84 ( 3298) metal coordination : bond 0.00544 / 0.31 ( 28) metal coordination : angle 3.92030 / 2.10 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 181 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8866 (tpp) cc_final: 0.8625 (tpt) REVERT: A 568 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8343 (tp) REVERT: A 584 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.7462 (p) REVERT: B 42 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8186 (ttt) REVERT: C 470 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8128 (mm-30) REVERT: C 473 ARG cc_start: 0.7798 (ttm110) cc_final: 0.7548 (ttm110) REVERT: C 498 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7448 (mt-10) REVERT: C 526 GLU cc_start: 0.7956 (mp0) cc_final: 0.7536 (mp0) REVERT: C 535 LYS cc_start: 0.8717 (tptp) cc_final: 0.8378 (tppt) REVERT: D 46 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8255 (mtm180) REVERT: D 62 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8496 (mp) REVERT: D 258 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7567 (tt) REVERT: D 315 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8894 (mt) REVERT: E 62 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.6800 (t80) REVERT: E 339 TYR cc_start: 0.6652 (t80) cc_final: 0.6230 (t80) REVERT: F 42 MET cc_start: 0.9017 (mtp) cc_final: 0.8724 (mtp) REVERT: I 912 GLU cc_start: 0.6355 (mm-30) cc_final: 0.5899 (mt-10) REVERT: I 928 LYS cc_start: 0.6519 (mmtt) cc_final: 0.5793 (tppt) REVERT: N 118 MET cc_start: 0.8856 (tpp) cc_final: 0.8541 (mmm) REVERT: N 258 ARG cc_start: 0.7315 (ttp80) cc_final: 0.7035 (ttp80) REVERT: N 263 MET cc_start: 0.7010 (mmm) cc_final: 0.6406 (ptt) REVERT: N 269 THR cc_start: 0.7571 (p) cc_final: 0.7367 (p) REVERT: N 270 TYR cc_start: 0.6220 (p90) cc_final: 0.5289 (p90) outliers start: 93 outliers final: 61 residues processed: 263 average time/residue: 0.1704 time to fit residues: 71.8088 Evaluate side-chains 242 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 173 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 125 optimal weight: 0.7980 chunk 279 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 237 optimal weight: 0.4980 chunk 18 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.091736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.064336 restraints weight = 71652.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.063079 restraints weight = 48936.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.063578 restraints weight = 40777.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.063885 restraints weight = 34379.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.063980 restraints weight = 31500.916| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24710 Z= 0.129 Angle : 0.529 13.124 33568 Z= 0.262 Chirality : 0.039 0.171 3753 Planarity : 0.003 0.060 4137 Dihedral : 12.720 168.187 3600 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.54 % Allowed : 22.93 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 0.79 (0.16), residues: 2855 helix: 2.10 (0.14), residues: 1421 sheet: -0.17 (0.29), residues: 368 loop : -1.45 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 419 TYR 0.024 0.001 TYR N 246 PHE 0.009 0.001 PHE D 162 TRP 0.011 0.001 TRP I 904 HIS 0.004 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (24682) covalent geometry : angle 0.50945 / 0.26 (33523) hydrogen bonds : bond 0.03583 / 2.37 ( 1154) hydrogen bonds : angle 3.91017 / 2.82 ( 3298) metal coordination : bond 0.00565 / 0.32 ( 28) metal coordination : angle 3.91260 / 2.09 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 181 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8917 (tpp) cc_final: 0.8692 (tpt) REVERT: A 568 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8351 (tp) REVERT: A 584 THR cc_start: 0.7697 (OUTLIER) cc_final: 0.7457 (p) REVERT: B 42 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8172 (ttt) REVERT: C 441 MET cc_start: 0.8517 (mmt) cc_final: 0.7965 (mmt) REVERT: C 449 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6715 (tp) REVERT: C 470 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8149 (mm-30) REVERT: C 473 ARG cc_start: 0.7875 (ttm110) cc_final: 0.7587 (ttm110) REVERT: C 494 LYS cc_start: 0.8544 (pttp) cc_final: 0.8323 (ptmm) REVERT: C 526 GLU cc_start: 0.7998 (mp0) cc_final: 0.7547 (mp0) REVERT: D 46 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8257 (mtm180) REVERT: D 62 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8496 (mp) REVERT: D 315 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8898 (mt) REVERT: E 62 TYR cc_start: 0.9033 (OUTLIER) cc_final: 0.6830 (t80) REVERT: E 339 TYR cc_start: 0.6619 (t80) cc_final: 0.6177 (t80) REVERT: F 42 MET cc_start: 0.8982 (mtp) cc_final: 0.8690 (mtp) REVERT: G 32 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7892 (tppp) REVERT: I 912 GLU cc_start: 0.6352 (mm-30) cc_final: 0.5895 (mt-10) REVERT: I 928 LYS cc_start: 0.6516 (mmtt) cc_final: 0.5790 (tppt) REVERT: N 118 MET cc_start: 0.8858 (tpp) cc_final: 0.8555 (mmm) REVERT: N 256 MET cc_start: 0.4494 (OUTLIER) cc_final: 0.3218 (ptm) REVERT: N 258 ARG cc_start: 0.7464 (ttp80) cc_final: 0.7118 (ttp80) REVERT: N 263 MET cc_start: 0.7055 (mmm) cc_final: 0.6392 (ptt) REVERT: N 270 TYR cc_start: 0.6206 (p90) cc_final: 0.5601 (p90) outliers start: 91 outliers final: 68 residues processed: 261 average time/residue: 0.1708 time to fit residues: 71.4948 Evaluate side-chains 250 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 172 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 512 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 58 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 261 optimal weight: 30.0000 chunk 23 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 284 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS C 537 HIS D 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.089621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.062361 restraints weight = 72430.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.060919 restraints weight = 51566.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.061400 restraints weight = 42679.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.061714 restraints weight = 35689.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.061808 restraints weight = 32805.067| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 24710 Z= 0.247 Angle : 0.616 13.600 33568 Z= 0.311 Chirality : 0.042 0.208 3753 Planarity : 0.004 0.072 4137 Dihedral : 12.967 169.880 3600 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.25 % Favored : 94.71 % Rotamer: Outliers : 4.59 % Allowed : 22.30 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 0.51 (0.16), residues: 2855 helix: 1.88 (0.14), residues: 1424 sheet: -0.49 (0.28), residues: 373 loop : -1.55 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 419 TYR 0.025 0.002 TYR N 270 PHE 0.017 0.002 PHE N 219 TRP 0.014 0.001 TRP I 904 HIS 0.004 0.001 HIS A 774 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (24682) covalent geometry : angle 0.59259 / 0.31 (33523) hydrogen bonds : bond 0.04633 / 3.05 ( 1154) hydrogen bonds : angle 4.21637 / 3.02 ( 3298) metal coordination : bond 0.01018 / 0.60 ( 28) metal coordination : angle 4.65723 / 2.65 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 170 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8973 (tpp) cc_final: 0.8710 (tpt) REVERT: A 568 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8365 (tp) REVERT: B 42 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8251 (ttt) REVERT: C 449 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6744 (tp) REVERT: C 473 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7758 (ttm110) REVERT: C 527 GLU cc_start: 0.8702 (pt0) cc_final: 0.7844 (pt0) REVERT: C 535 LYS cc_start: 0.8779 (tppt) cc_final: 0.8403 (tptm) REVERT: D 46 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8412 (mtm180) REVERT: D 62 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8644 (mp) REVERT: D 315 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8904 (mt) REVERT: D 334 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8288 (mtm) REVERT: E 62 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.6890 (t80) REVERT: E 339 TYR cc_start: 0.6708 (t80) cc_final: 0.6312 (t80) REVERT: F 42 MET cc_start: 0.8972 (mtp) cc_final: 0.8718 (mtp) REVERT: G 32 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7927 (tppp) REVERT: I 911 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6888 (mt-10) REVERT: I 912 GLU cc_start: 0.6342 (mm-30) cc_final: 0.5873 (mt-10) REVERT: I 928 LYS cc_start: 0.6594 (mmtt) cc_final: 0.5853 (tppt) REVERT: N 118 MET cc_start: 0.8870 (tpp) cc_final: 0.8530 (mmm) REVERT: N 256 MET cc_start: 0.4530 (OUTLIER) cc_final: 0.3556 (ptm) REVERT: N 258 ARG cc_start: 0.7279 (ttp80) cc_final: 0.6681 (mmm-85) REVERT: N 263 MET cc_start: 0.7008 (mmm) cc_final: 0.6797 (ptt) outliers start: 118 outliers final: 81 residues processed: 271 average time/residue: 0.1748 time to fit residues: 74.8875 Evaluate side-chains 257 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 165 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 658 ARG Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 172 HIS Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 167 optimal weight: 0.7980 chunk 229 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 HIS D 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.090480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.063327 restraints weight = 72176.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.061877 restraints weight = 50833.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.062291 restraints weight = 42629.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.062643 restraints weight = 35438.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.062739 restraints weight = 32452.872| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24710 Z= 0.167 Angle : 0.567 10.989 33568 Z= 0.282 Chirality : 0.041 0.303 3753 Planarity : 0.004 0.048 4137 Dihedral : 12.908 168.153 3600 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.05 % Allowed : 23.01 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 0.60 (0.16), residues: 2855 helix: 1.98 (0.14), residues: 1417 sheet: -0.46 (0.28), residues: 365 loop : -1.50 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 272 TYR 0.019 0.001 TYR A 534 PHE 0.011 0.001 PHE N 219 TRP 0.014 0.001 TRP I 904 HIS 0.018 0.001 HIS C 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (24682) covalent geometry : angle 0.54456 / 0.28 (33523) hydrogen bonds : bond 0.04000 / 2.64 ( 1154) hydrogen bonds : angle 4.06246 / 2.91 ( 3298) metal coordination : bond 0.00757 / 0.43 ( 28) metal coordination : angle 4.35873 / 2.38 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 167 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8883 (tpp) cc_final: 0.8629 (tpt) REVERT: A 568 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8371 (tp) REVERT: C 449 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6695 (tp) REVERT: C 473 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7818 (ttm110) REVERT: C 494 LYS cc_start: 0.8287 (ptmm) cc_final: 0.8072 (pttp) REVERT: C 498 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7465 (mt-10) REVERT: C 527 GLU cc_start: 0.8680 (pt0) cc_final: 0.7803 (pt0) REVERT: C 535 LYS cc_start: 0.8785 (tppt) cc_final: 0.8554 (tppp) REVERT: D 46 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8388 (mtm180) REVERT: D 62 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8598 (mp) REVERT: D 315 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8881 (mt) REVERT: D 334 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8284 (mtm) REVERT: D 441 MET cc_start: 0.6074 (tpp) cc_final: 0.5345 (tpp) REVERT: E 62 TYR cc_start: 0.9059 (OUTLIER) cc_final: 0.6823 (t80) REVERT: E 339 TYR cc_start: 0.6642 (t80) cc_final: 0.6236 (t80) REVERT: F 42 MET cc_start: 0.8959 (mtp) cc_final: 0.8683 (mtp) REVERT: G 32 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7943 (tppp) REVERT: H 75 ARG cc_start: 0.7788 (mtt-85) cc_final: 0.7497 (mpp80) REVERT: I 911 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6874 (mt-10) REVERT: I 912 GLU cc_start: 0.6335 (mm-30) cc_final: 0.5871 (mt-10) REVERT: I 928 LYS cc_start: 0.6570 (mmtt) cc_final: 0.5832 (tppt) REVERT: N 118 MET cc_start: 0.8847 (tpp) cc_final: 0.8494 (mmm) REVERT: N 256 MET cc_start: 0.4204 (OUTLIER) cc_final: 0.3660 (ptm) REVERT: N 258 ARG cc_start: 0.7181 (ttp80) cc_final: 0.6562 (mmm-85) REVERT: N 263 MET cc_start: 0.7223 (mmm) cc_final: 0.6987 (ptt) REVERT: N 270 TYR cc_start: 0.5850 (p90) cc_final: 0.5104 (p90) outliers start: 104 outliers final: 84 residues processed: 256 average time/residue: 0.1677 time to fit residues: 68.9539 Evaluate side-chains 254 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 160 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 551 HIS Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 104 ILE Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 172 HIS Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 283 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 240 optimal weight: 0.2980 chunk 180 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN C 537 HIS G 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.091849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.064142 restraints weight = 71579.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.063605 restraints weight = 46211.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.064111 restraints weight = 36393.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.064403 restraints weight = 31268.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.064491 restraints weight = 28787.344| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24710 Z= 0.103 Angle : 0.524 10.873 33568 Z= 0.259 Chirality : 0.039 0.185 3753 Planarity : 0.003 0.036 4137 Dihedral : 12.776 166.722 3600 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.11 % Allowed : 24.21 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 0.77 (0.16), residues: 2855 helix: 2.12 (0.14), residues: 1421 sheet: -0.28 (0.29), residues: 365 loop : -1.48 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 227 TYR 0.018 0.001 TYR A 534 PHE 0.012 0.001 PHE B 720 TRP 0.012 0.001 TRP A 429 HIS 0.029 0.001 HIS C 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (24682) covalent geometry : angle 0.50399 / 0.26 (33523) hydrogen bonds : bond 0.03308 / 2.19 ( 1154) hydrogen bonds : angle 3.86813 / 2.78 ( 3298) metal coordination : bond 0.00451 / 0.24 ( 28) metal coordination : angle 3.96117 / 2.07 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 177 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8097 (mt) REVERT: A 412 MET cc_start: 0.8836 (tpp) cc_final: 0.8616 (tpt) REVERT: A 568 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8483 (tp) REVERT: C 441 MET cc_start: 0.8610 (mmt) cc_final: 0.8026 (mmm) REVERT: C 473 ARG cc_start: 0.8016 (ttm110) cc_final: 0.7771 (ttm110) REVERT: C 527 GLU cc_start: 0.8639 (pt0) cc_final: 0.7753 (pt0) REVERT: D 46 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8379 (mtm180) REVERT: D 315 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8886 (mt) REVERT: D 334 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8207 (mtm) REVERT: E 62 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.7181 (t80) REVERT: E 339 TYR cc_start: 0.6578 (t80) cc_final: 0.6211 (t80) REVERT: F 42 MET cc_start: 0.8954 (mtp) cc_final: 0.8666 (mtp) REVERT: F 50 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8342 (t80) REVERT: G 32 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7917 (tppp) REVERT: I 911 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6774 (mt-10) REVERT: I 912 GLU cc_start: 0.6384 (mm-30) cc_final: 0.5907 (mt-10) REVERT: I 928 LYS cc_start: 0.6544 (mmtt) cc_final: 0.5820 (tppt) REVERT: N 118 MET cc_start: 0.8833 (tpp) cc_final: 0.8480 (mmm) REVERT: N 256 MET cc_start: 0.3961 (OUTLIER) cc_final: 0.3533 (ptm) REVERT: N 258 ARG cc_start: 0.7253 (ttp80) cc_final: 0.6527 (mmm-85) REVERT: N 263 MET cc_start: 0.7221 (mmm) cc_final: 0.6967 (ptt) REVERT: N 270 TYR cc_start: 0.5796 (p90) cc_final: 0.5052 (p90) outliers start: 80 outliers final: 61 residues processed: 243 average time/residue: 0.1638 time to fit residues: 64.6249 Evaluate side-chains 239 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 149 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 34 optimal weight: 0.0070 chunk 124 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 chunk 260 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.090816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.063316 restraints weight = 72264.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.062453 restraints weight = 48708.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.062739 restraints weight = 40400.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.062989 restraints weight = 33985.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.063163 restraints weight = 31368.668| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24710 Z= 0.157 Angle : 0.561 11.973 33568 Z= 0.276 Chirality : 0.040 0.351 3753 Planarity : 0.003 0.037 4137 Dihedral : 12.825 167.936 3600 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.35 % Allowed : 24.33 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.17), residues: 2855 helix: 2.10 (0.14), residues: 1421 sheet: -0.38 (0.29), residues: 368 loop : -1.48 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 272 TYR 0.018 0.001 TYR A 534 PHE 0.020 0.001 PHE N 219 TRP 0.011 0.001 TRP I 904 HIS 0.007 0.001 HIS C 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (24682) covalent geometry : angle 0.53971 / 0.28 (33523) hydrogen bonds : bond 0.03711 / 2.45 ( 1154) hydrogen bonds : angle 3.94032 / 2.83 ( 3298) metal coordination : bond 0.00675 / 0.39 ( 28) metal coordination : angle 4.18394 / 2.27 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 167 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8192 (mt) REVERT: A 412 MET cc_start: 0.8749 (tpp) cc_final: 0.8507 (tpt) REVERT: A 568 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8429 (tp) REVERT: B 438 MET cc_start: 0.8393 (tpp) cc_final: 0.7929 (mmm) REVERT: C 441 MET cc_start: 0.8556 (mmt) cc_final: 0.8036 (mmm) REVERT: C 449 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6546 (tp) REVERT: C 473 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7814 (ttm110) REVERT: C 498 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7336 (mt-10) REVERT: C 527 GLU cc_start: 0.8658 (pt0) cc_final: 0.7777 (pt0) REVERT: C 535 LYS cc_start: 0.8781 (tppp) cc_final: 0.8554 (tptp) REVERT: D 46 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8395 (mtm180) REVERT: D 315 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8883 (mt) REVERT: D 334 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8251 (mtm) REVERT: D 422 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7670 (pp) REVERT: E 62 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.7054 (t80) REVERT: E 339 TYR cc_start: 0.6651 (t80) cc_final: 0.6233 (t80) REVERT: F 42 MET cc_start: 0.8948 (mtp) cc_final: 0.8674 (mtp) REVERT: G 32 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7918 (tppp) REVERT: I 911 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6774 (mt-10) REVERT: I 912 GLU cc_start: 0.6363 (mm-30) cc_final: 0.5884 (mt-10) REVERT: I 928 LYS cc_start: 0.6554 (mmtt) cc_final: 0.5828 (tppt) REVERT: N 118 MET cc_start: 0.8844 (tpp) cc_final: 0.8488 (mmm) REVERT: N 197 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8547 (tp-100) REVERT: N 256 MET cc_start: 0.3999 (OUTLIER) cc_final: 0.2982 (ptm) REVERT: N 258 ARG cc_start: 0.7267 (ttp80) cc_final: 0.6682 (ptm-80) REVERT: N 263 MET cc_start: 0.7196 (mmm) cc_final: 0.6922 (ptt) REVERT: N 270 TYR cc_start: 0.5828 (p90) cc_final: 0.4955 (p90) outliers start: 86 outliers final: 70 residues processed: 242 average time/residue: 0.1636 time to fit residues: 64.3406 Evaluate side-chains 245 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 164 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 537 HIS Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 49 optimal weight: 6.9990 chunk 163 optimal weight: 0.0470 chunk 10 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 537 HIS N 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.090710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.063504 restraints weight = 71974.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.062101 restraints weight = 50925.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.062557 restraints weight = 42179.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.062883 restraints weight = 35279.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.062988 restraints weight = 32369.110| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24710 Z= 0.167 Angle : 0.575 11.424 33568 Z= 0.283 Chirality : 0.041 0.338 3753 Planarity : 0.004 0.037 4137 Dihedral : 12.854 168.252 3600 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.46 % Allowed : 24.29 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.16), residues: 2855 helix: 2.05 (0.14), residues: 1421 sheet: -0.43 (0.29), residues: 368 loop : -1.48 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 231 TYR 0.018 0.001 TYR A 534 PHE 0.029 0.001 PHE H 107 TRP 0.011 0.001 TRP I 904 HIS 0.020 0.001 HIS C 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (24682) covalent geometry : angle 0.55395 / 0.28 (33523) hydrogen bonds : bond 0.03810 / 2.52 ( 1154) hydrogen bonds : angle 3.97988 / 2.86 ( 3298) metal coordination : bond 0.00725 / 0.41 ( 28) metal coordination : angle 4.23991 / 2.31 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 166 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8197 (mt) REVERT: A 412 MET cc_start: 0.8755 (tpp) cc_final: 0.8520 (tpt) REVERT: A 568 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8328 (tp) REVERT: B 438 MET cc_start: 0.8689 (tpp) cc_final: 0.8177 (mmm) REVERT: C 441 MET cc_start: 0.8516 (mmt) cc_final: 0.7954 (mmm) REVERT: C 449 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6577 (tp) REVERT: C 473 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7792 (ttm110) REVERT: C 494 LYS cc_start: 0.8653 (pttp) cc_final: 0.8441 (ptmm) REVERT: C 527 GLU cc_start: 0.8662 (pt0) cc_final: 0.7821 (pt0) REVERT: D 46 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8378 (mtm180) REVERT: D 315 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8877 (mt) REVERT: D 334 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8286 (mtm) REVERT: D 422 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7813 (pp) REVERT: E 62 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.6936 (t80) REVERT: E 339 TYR cc_start: 0.6668 (t80) cc_final: 0.6239 (t80) REVERT: F 42 MET cc_start: 0.8953 (mtp) cc_final: 0.8671 (mtp) REVERT: G 32 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7909 (tppp) REVERT: I 911 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6732 (mt-10) REVERT: I 912 GLU cc_start: 0.6319 (mm-30) cc_final: 0.5856 (mt-10) REVERT: I 928 LYS cc_start: 0.6543 (mmtt) cc_final: 0.5810 (tppt) REVERT: N 118 MET cc_start: 0.8829 (tpp) cc_final: 0.8447 (mmm) REVERT: N 197 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8525 (tp-100) REVERT: N 256 MET cc_start: 0.4034 (OUTLIER) cc_final: 0.3045 (ptm) REVERT: N 263 MET cc_start: 0.7192 (mmm) cc_final: 0.6925 (ptt) REVERT: N 270 TYR cc_start: 0.5825 (p90) cc_final: 0.4982 (p90) outliers start: 89 outliers final: 75 residues processed: 244 average time/residue: 0.1606 time to fit residues: 63.5311 Evaluate side-chains 248 residues out of total 2569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 162 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 563 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain C residue 424 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 516 TYR Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 276 CYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain I residue 911 GLU Chi-restraints excluded: chain I residue 916 LEU Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 140 THR Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain N residue 226 LEU Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain N residue 256 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 238 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 255 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 251 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.091425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.064229 restraints weight = 71803.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.062920 restraints weight = 48870.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.063377 restraints weight = 40920.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.063680 restraints weight = 34488.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.063778 restraints weight = 31709.480| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24710 Z= 0.125 Angle : 0.553 14.622 33568 Z= 0.270 Chirality : 0.040 0.342 3753 Planarity : 0.003 0.038 4137 Dihedral : 12.800 167.564 3600 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.27 % Allowed : 24.45 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % 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: 0.75 (0.16), residues: 2855 helix: 2.09 (0.14), residues: 1422 sheet: -0.34 (0.29), residues: 368 loop : -1.45 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 231 TYR 0.018 0.001 TYR A 534 PHE 0.031 0.001 PHE C 500 TRP 0.011 0.001 TRP A 429 HIS 0.004 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (24682) covalent geometry : angle 0.53265 / 0.27 (33523) hydrogen bonds : bond 0.03468 / 2.31 ( 1154) hydrogen bonds : angle 3.87765 / 2.79 ( 3298) metal coordination : bond 0.00561 / 0.31 ( 28) metal coordination : angle 4.04518 / 2.16 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3925.44 seconds wall clock time: 68 minutes 55.26 seconds (4135.26 seconds total)