Starting phenix.real_space_refine on Sun Jul 5 23:22:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ebs_27996/07_2026/8ebs_27996.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ebs_27996/07_2026/8ebs_27996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ebs_27996/07_2026/8ebs_27996.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ebs_27996/07_2026/8ebs_27996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ebs_27996/07_2026/8ebs_27996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ebs_27996/07_2026/8ebs_27996.map" model { file = "/net/cci-nas-00/data/ceres_data/8ebs_27996/07_2026/8ebs_27996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ebs_27996/07_2026/8ebs_27996.cif" } resolution = 4.0 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 Zn 5 6.06 5 P 105 5.49 5 S 167 5.16 5 C 19436 2.51 5 N 5384 2.21 5 O 5932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31035 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4931 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 24, 'TRANS': 586} Chain breaks: 1 Chain: "B" Number of atoms: 6120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6120 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 32, 'TRANS': 727} Chain: "C" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2895 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 342} Chain breaks: 4 Chain: "D" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3557 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain: "E" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2792 Classifications: {'peptide': 355} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 336} Chain breaks: 1 Chain: "F" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2057 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 8, 'TRANS': 252} Chain breaks: 1 Chain: "G" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 530 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "H" Number of atoms: 4264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4264 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 24, 'TRANS': 494} Chain breaks: 3 Chain: "I" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 504 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 6, 'TRANS': 54} Chain: "J" Number of atoms: 1201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1192 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3} Link IDs: {'PTRANS': 1, 'TRANS': 147} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 Conformer: "B" Number of residues, atoms: 149, 1192 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3} Link IDs: {'PTRANS': 1, 'TRANS': 147} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 bond proxies already assigned to first conformer: 1192 Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 602 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "L" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 489 Unusual residues: {'VM6': 1} Classifications: {'DNA': 22, 'undetermined': 1} Link IDs: {'rna3p': 21, None: 1} Not linked: pdbres="VM6 L 30 " pdbres=" DT L 31 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "M" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1078 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} 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: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5874 SG CYS B 116 51.367 30.526 73.414 1.00227.83 S ATOM 6183 SG CYS B 155 51.017 25.318 69.344 1.00215.53 S ATOM 6014 SG CYS B 134 47.771 30.137 68.007 1.00233.83 S ATOM 6472 SG CYS B 190 46.020 27.118 73.123 1.00212.40 S ATOM 19973 SG CYS E 345 27.407 53.693 151.335 1.00190.60 S ATOM 19995 SG CYS E 348 28.578 56.975 152.607 1.00180.36 S ATOM 20152 SG CYS E 368 28.046 56.539 148.810 1.00194.11 S ATOM 20173 SG CYS E 371 30.916 54.787 150.514 1.00188.68 S ATOM 20093 SG CYS E 360 28.763 42.651 147.881 1.00195.38 S ATOM 20111 SG CYS E 363 28.156 42.346 151.541 1.00197.98 S ATOM 20260 SG CYS E 382 30.730 44.837 150.249 1.00182.89 S ATOM 20277 SG CYS E 385 31.482 41.111 149.958 1.00193.57 S ATOM 19537 SG CYS E 291 71.596 37.668 150.062 1.00199.70 S ATOM 19559 SG CYS E 294 75.129 37.868 148.611 1.00199.73 S ATOM 19648 SG CYS E 305 72.375 39.863 147.016 1.00188.68 S ATOM 19671 SG CYS E 308 72.238 36.151 146.696 1.00185.52 S ATOM 22173 SG CYS F 268 52.954 28.763 142.366 1.00173.17 S ATOM 22192 SG CYS F 271 49.579 29.163 144.206 1.00180.54 S ATOM 22277 SG CYS F 282 51.566 26.121 144.780 1.00185.54 S ATOM 22297 SG CYS F 285 49.971 26.563 141.432 1.00183.63 S ATOM 22065 SG CYS F 255 57.438 26.213 153.751 1.00192.21 S ATOM 22082 SG CYS F 257 55.753 22.891 153.757 1.00198.54 S ATOM 22231 SG CYS F 276 59.607 23.128 153.738 1.00203.04 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS J 127 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS J 127 " occ=0.50 Time building chain proxies: 6.26, per 1000 atoms: 0.20 Number of scatterers: 31035 At special positions: 0 Unit cell: (139.944, 180.761, 203.252, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 5 29.99 Fe 4 26.01 Ca 2 19.99 S 167 16.00 P 105 15.00 O 5932 8.00 N 5384 7.00 C 19436 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " 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 368 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb=" ZN 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 291 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb=" ZN F 402 " pdb="ZN ZN F 402 " - pdb=" NE2 HIS F 258 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 255 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 257 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 276 " Number of angles added : 27 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6802 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 28 sheets defined 56.4% alpha, 10.5% beta 48 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 92 through 104 Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 149 through 162 removed outlier: 4.101A pdb=" N SER A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 189 removed outlier: 3.552A pdb=" N ILE A 185 " --> pdb=" O HIS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 276 through 287 removed outlier: 3.616A pdb=" N ILE A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.806A pdb=" N LEU A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 530 through 536 removed outlier: 3.781A pdb=" N TYR A 534 " --> pdb=" O ARG A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 554 Processing helix chain 'A' and resid 564 through 576 Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 609 through 612 Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.806A pdb=" N ALA A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 677 removed outlier: 4.351A pdb=" N ALA A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 removed outlier: 3.517A pdb=" N GLN A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 removed outlier: 3.638A pdb=" N ALA A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 34 Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 76 through 99 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.713A pdb=" N ALA B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 164 removed outlier: 3.664A pdb=" N PHE B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 209 through 214 removed outlier: 3.545A pdb=" N ASP B 214 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 223 removed outlier: 4.439A pdb=" N ASP B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 248 Processing helix chain 'B' and resid 252 through 277 Processing helix chain 'B' and resid 278 through 291 removed outlier: 3.637A pdb=" N ARG B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 298 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.830A pdb=" N LEU B 305 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 306 " --> pdb=" O ALA B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 306' Processing helix chain 'B' and resid 311 through 317 removed outlier: 3.592A pdb=" N LEU B 315 " --> pdb=" O PRO B 311 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 311 through 317' Processing helix chain 'B' and resid 320 through 325 removed outlier: 4.230A pdb=" N THR B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 344 Processing helix chain 'B' and resid 353 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.590A pdb=" N LEU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 390 through 393 removed outlier: 3.505A pdb=" N ASP B 393 " --> pdb=" O ASP B 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 390 through 393' Processing helix chain 'B' and resid 394 through 410 Processing helix chain 'B' and resid 440 through 451 removed outlier: 3.543A 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 Processing helix chain 'B' and resid 507 through 512 removed outlier: 4.161A pdb=" N GLU B 512 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 531 Processing helix chain 'B' and resid 541 through 556 Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.653A pdb=" N ASN B 560 " --> pdb=" O GLY B 556 " (cutoff:3.500A) 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 666 removed outlier: 4.079A pdb=" N ARG B 666 " --> pdb=" O GLN B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'B' and resid 702 through 706 Processing helix chain 'B' and resid 709 through 726 removed outlier: 3.797A pdb=" N GLN B 726 " --> pdb=" O ARG B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 734 removed outlier: 4.072A pdb=" N GLN B 733 " --> pdb=" O HIS B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 removed outlier: 3.703A pdb=" N GLU B 745 " --> pdb=" O LEU B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 756 Processing helix chain 'C' and resid 112 through 121 Processing helix chain 'C' and resid 121 through 133 Processing helix chain 'C' and resid 138 through 147 removed outlier: 4.285A pdb=" N ASN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG C 146 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 200 through 211 removed outlier: 3.663A pdb=" N LYS C 204 " --> pdb=" O TYR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 268 through 272 Processing helix chain 'C' and resid 297 through 320 removed outlier: 3.711A pdb=" N LEU C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 359 Processing helix chain 'C' and resid 379 through 384 removed outlier: 4.080A pdb=" N TYR C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 379 through 384' Processing helix chain 'C' and resid 398 through 413 removed outlier: 3.718A pdb=" N ALA C 413 " --> pdb=" O GLN C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 422 removed outlier: 3.570A pdb=" N LEU C 422 " --> pdb=" O THR C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 448 through 453 removed outlier: 3.656A pdb=" N MET C 452 " --> pdb=" O ALA C 448 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 448 through 453' Processing helix chain 'C' and resid 454 through 479 Processing helix chain 'C' and resid 483 through 516 removed outlier: 3.916A pdb=" N GLU C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Proline residue: C 507 - end of helix removed outlier: 3.622A pdb=" N GLN C 515 " --> pdb=" O LYS C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 548 removed outlier: 3.874A pdb=" N HIS C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 25 removed outlier: 3.631A pdb=" N PHE D 22 " --> pdb=" O ASN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 36 removed outlier: 3.546A pdb=" N GLY D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 47 Processing helix chain 'D' and resid 49 through 59 Processing helix chain 'D' and resid 60 through 62 No H-bonds generated for 'chain 'D' and resid 60 through 62' Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 79 through 94 Processing helix chain 'D' and resid 111 through 124 Processing helix chain 'D' and resid 132 through 136 removed outlier: 3.541A pdb=" N GLN D 135 " --> pdb=" O ASP D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 165 Processing helix chain 'D' and resid 172 through 183 Processing helix chain 'D' and resid 197 through 205 removed outlier: 3.509A 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: 3.513A pdb=" N ARG D 226 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 242 Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 284 through 291 removed outlier: 4.164A pdb=" N SER D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'D' and resid 347 through 357 Processing helix chain 'D' and resid 360 through 371 Processing helix chain 'D' and resid 373 through 378 removed outlier: 3.561A pdb=" N LYS D 378 " --> pdb=" O PRO D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 399 removed outlier: 3.502A pdb=" N ASP D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 429 Processing helix chain 'D' and resid 444 through 462 removed outlier: 4.065A pdb=" N SER D 449 " --> pdb=" O PRO D 445 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 14 removed outlier: 3.523A pdb=" N GLY E 13 " --> pdb=" O ARG E 10 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY E 14 " --> pdb=" O TRP E 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 10 through 14' Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 79 through 99 Processing helix chain 'E' and resid 123 through 135 removed outlier: 3.645A pdb=" N HIS E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 157 Processing helix chain 'E' and resid 182 through 192 Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'E' and resid 224 through 237 removed outlier: 3.638A pdb=" N SER E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 277 removed outlier: 3.512A pdb=" N ASP E 277 " --> pdb=" O MET E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 321 removed outlier: 4.046A pdb=" N SER E 321 " --> pdb=" O HIS E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 326 removed outlier: 3.657A pdb=" N LEU E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 378 removed outlier: 3.519A pdb=" N HIS E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 387 Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 33 through 52 removed outlier: 4.065A pdb=" N ASN F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 121 Processing helix chain 'F' and resid 132 through 151 Processing helix chain 'F' and resid 173 through 188 removed outlier: 3.580A pdb=" N ALA F 183 " --> pdb=" O ASN F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 211 Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 222 through 230 Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.674A pdb=" N GLN F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 27 Processing helix chain 'G' and resid 46 through 64 removed outlier: 3.511A pdb=" N VAL G 50 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 225 Processing helix chain 'H' and resid 226 through 237 Processing helix chain 'H' and resid 238 through 243 Processing helix chain 'H' and resid 245 through 249 Processing helix chain 'H' and resid 250 through 265 Processing helix chain 'H' and resid 278 through 290 Processing helix chain 'H' and resid 294 through 309 removed outlier: 3.596A pdb=" N LEU H 309 " --> pdb=" O ILE H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 554 through 562 removed outlier: 3.664A pdb=" N LYS H 560 " --> pdb=" O LEU H 556 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 586 removed outlier: 3.775A pdb=" N TYR H 585 " --> pdb=" O VAL H 581 " (cutoff:3.500A) Processing helix chain 'H' and resid 592 through 597 Processing helix chain 'H' and resid 599 through 608 Processing helix chain 'H' and resid 614 through 630 Processing helix chain 'H' and resid 677 through 681 Processing helix chain 'H' and resid 686 through 693 Processing helix chain 'H' and resid 711 through 721 Processing helix chain 'H' and resid 722 through 725 Processing helix chain 'H' and resid 763 through 767 Processing helix chain 'H' and resid 778 through 786 removed outlier: 3.927A pdb=" N VAL H 782 " --> pdb=" O ASN H 778 " (cutoff:3.500A) Processing helix chain 'H' and resid 817 through 865 Processing helix chain 'H' and resid 890 through 902 Processing helix chain 'H' and resid 903 through 913 removed outlier: 3.828A pdb=" N ARG H 908 " --> pdb=" O TRP H 904 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 281 removed outlier: 4.172A pdb=" N LEU I 279 " --> pdb=" O PRO I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 295 Processing helix chain 'I' and resid 298 through 309 removed outlier: 3.543A pdb=" N LEU I 302 " --> pdb=" O LEU I 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 317 Processing helix chain 'I' and resid 320 through 329 Processing helix chain 'J' and resid 28 through 40 removed outlier: 3.989A pdb=" N GLU J 32 " --> pdb=" O GLU J 28 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 60 Processing helix chain 'J' and resid 65 through 77 Processing helix chain 'J' and resid 86 through 114 Processing helix chain 'J' and resid 122 through 134 Processing helix chain 'J' and resid 138 through 149 Processing helix chain 'J' and resid 159 through 168 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 5.949A pdb=" N LYS A 59 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.611A pdb=" N GLU A 115 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272 removed outlier: 4.757A pdb=" N TYR A 175 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 168 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 391 removed outlier: 6.435A pdb=" N CYS A 390 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N THR A 409 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 362 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASP A 441 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A 364 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY A 436 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 467 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A 337 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLU A 490 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL A 339 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 579 through 580 removed outlier: 6.386A pdb=" N ILE A 559 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE A 626 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N PHE A 561 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N SER A 627 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N SER A 664 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N LYS A 688 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N CYS A 507 " --> pdb=" O LYS A 688 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ILE A 690 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU A 509 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AA7, first strand: chain 'B' and resid 173 through 174 removed outlier: 6.688A pdb=" N LEU B 105 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL B 206 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 107 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N SER B 208 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B 70 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N TYR B 207 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR B 72 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 249 through 251 removed outlier: 5.975A pdb=" N ASN B 430 " --> pdb=" O PHE B 421 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 421 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 490 through 494 removed outlier: 5.794A pdb=" N CYS B 491 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE B 679 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET B 493 " --> pdb=" O PHE B 679 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL B 536 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 535 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N SER B 598 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA B 537 " --> pdb=" O SER B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 177 through 179 Processing sheet with id=AB2, first strand: chain 'D' and resid 66 through 67 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 435 removed outlier: 3.913A pdb=" N GLN G 36 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 121 removed outlier: 4.673A pdb=" N ALA E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS E 110 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS E 116 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL E 108 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU E 120 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE E 104 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N HIS E 60 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU E 168 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR E 62 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE E 170 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL E 64 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG E 165 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N SER E 197 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 167 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE E 199 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE E 169 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 303 through 304 removed outlier: 3.546A pdb=" N LEU E 312 " --> pdb=" O VAL E 303 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR E 311 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY E 253 " --> pdb=" O THR E 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 257 through 258 Processing sheet with id=AB9, first strand: chain 'E' and resid 270 through 271 removed outlier: 4.336A pdb=" N THR E 285 " --> pdb=" O SER E 270 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 332 through 335 Processing sheet with id=AC2, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.445A pdb=" N VAL F 59 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LYS F 56 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASN F 9 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ALA F 58 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU F 11 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE F 60 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE F 13 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER F 62 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL F 15 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU F 8 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ARG F 160 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU F 10 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU F 162 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL F 12 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE F 164 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL F 14 " --> pdb=" O ILE F 164 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N LEU F 190 " --> pdb=" O MET F 157 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N SER F 159 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ASP F 192 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE F 161 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N CYS F 194 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL F 163 " --> pdb=" O CYS F 194 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU F 215 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA F 193 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 253 through 254 removed outlier: 4.162A pdb=" N ALA F 253 " --> pdb=" O ILE F 262 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 551 through 552 Processing sheet with id=AC5, first strand: chain 'H' and resid 669 through 670 Processing sheet with id=AC6, first strand: chain 'H' and resid 695 through 697 Processing sheet with id=AC7, first strand: chain 'H' and resid 705 through 707 removed outlier: 3.832A pdb=" N LYS H 705 " --> pdb=" O LEU H 732 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 759 through 760 removed outlier: 6.549A pdb=" N VAL H 759 " --> pdb=" O ILE H 794 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLY H 796 " --> pdb=" O VAL H 759 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL H 791 " --> pdb=" O TYR H 811 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR H 811 " --> pdb=" O VAL H 791 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA H 793 " --> pdb=" O ASP H 809 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL H 807 " --> pdb=" O THR H 795 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE H 797 " --> pdb=" O HIS H 805 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N HIS H 805 " --> pdb=" O PHE H 797 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 47 through 49 Processing sheet with id=AD1, first strand: chain 'J' and resid 120 through 121 removed outlier: 3.895A pdb=" N VAL J 157 " --> pdb=" O ILE J 121 " (cutoff:3.500A) 1482 hydrogen bonds defined for protein. 4297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 7.69 Time building geometry restraints manager: 4.67 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: 13553 1.43 - 1.64: 18075 1.64 - 1.85: 253 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 31893 Sorted by residual: bond pdb=" C8 VM6 L 30 " pdb=" C9 VM6 L 30 " ideal model delta sigma weight residual 1.504 1.368 0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" OP1 VM6 L 30 " pdb=" P VM6 L 30 " ideal model delta sigma weight residual 1.527 1.658 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" OP2 VM6 L 30 " pdb=" P VM6 L 30 " ideal model delta sigma weight residual 1.528 1.657 -0.129 2.00e-02 2.50e+03 4.15e+01 bond pdb=" C7 VM6 L 30 " pdb=" C8 VM6 L 30 " ideal model delta sigma weight residual 1.502 1.391 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C5 VM6 L 30 " pdb=" C6 VM6 L 30 " ideal model delta sigma weight residual 1.448 1.353 0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 31888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 43451 2.87 - 5.74: 119 5.74 - 8.61: 6 8.61 - 11.48: 0 11.48 - 14.35: 1 Bond angle restraints: 43577 Sorted by residual: angle pdb=" O4' DA L 32 " pdb=" C4' DA L 32 " pdb=" C3' DA L 32 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.63e+01 angle pdb=" C7 VM6 L 30 " pdb=" C8 VM6 L 30 " pdb=" C9 VM6 L 30 " ideal model delta sigma weight residual 112.55 126.90 -14.35 3.00e+00 1.11e-01 2.29e+01 angle pdb=" N3 DT L 23 " pdb=" C4 DT L 23 " pdb=" O4 DT L 23 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT L 17 " pdb=" C4 DT L 17 " pdb=" O4 DT L 17 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT M 41 " pdb=" C4 DT M 41 " pdb=" O4 DT M 41 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 ... (remaining 43572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.90: 18232 28.90 - 57.81: 763 57.81 - 86.71: 72 86.71 - 115.61: 5 115.61 - 144.52: 2 Dihedral angle restraints: 19074 sinusoidal: 8571 harmonic: 10503 Sorted by residual: dihedral pdb=" CA THR D 380 " pdb=" C THR D 380 " pdb=" N PRO D 381 " pdb=" CA PRO D 381 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C4' DG M 37 " pdb=" C3' DG M 37 " pdb=" O3' DG M 37 " pdb=" P DC M 38 " ideal model delta sinusoidal sigma weight residual 220.00 75.48 144.52 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CA GLU I 309 " pdb=" C GLU I 309 " pdb=" N ASN I 310 " pdb=" CA ASN I 310 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 19071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3173 0.028 - 0.057: 1043 0.057 - 0.085: 345 0.085 - 0.114: 254 0.114 - 0.142: 36 Chirality restraints: 4851 Sorted by residual: chirality pdb=" C3' DA M 34 " pdb=" C4' DA M 34 " pdb=" O3' DA M 34 " pdb=" C2' DA M 34 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ILE H 237 " pdb=" N ILE H 237 " pdb=" C ILE H 237 " pdb=" CB ILE H 237 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA PRO A 447 " pdb=" N PRO A 447 " pdb=" C PRO A 447 " pdb=" CB PRO A 447 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 4848 not shown) Planarity restraints: 5228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 VM6 L 30 " 0.006 2.00e-02 2.50e+03 1.67e-02 3.49e+00 pdb=" C20 VM6 L 30 " 0.003 2.00e-02 2.50e+03 pdb=" C8 VM6 L 30 " -0.020 2.00e-02 2.50e+03 pdb=" C9 VM6 L 30 " 0.027 2.00e-02 2.50e+03 pdb=" N1 VM6 L 30 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO A 583 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 74 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 75 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.021 5.00e-02 4.00e+02 ... (remaining 5225 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 466 2.65 - 3.21: 28929 3.21 - 3.77: 50942 3.77 - 4.34: 67840 4.34 - 4.90: 105960 Nonbonded interactions: 254137 Sorted by model distance: nonbonded pdb=" ND1 HIS F 258 " pdb="ZN ZN F 402 " model vdw 2.084 1.848 nonbonded pdb=" O LEU E 211 " pdb=" OG1 THR E 215 " model vdw 2.122 3.040 nonbonded pdb=" OH TYR D 35 " pdb=" O LEU D 93 " model vdw 2.153 3.040 nonbonded pdb=" O CYS F 255 " pdb=" N ARG F 259 " model vdw 2.169 3.120 nonbonded pdb=" O PRO B 171 " pdb=" OH TYR B 175 " model vdw 2.222 3.040 ... (remaining 254132 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 41.620 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 0.158 31919 Z= 0.228 Angle : 0.531 20.855 43616 Z= 0.352 Chirality : 0.038 0.142 4851 Planarity : 0.003 0.041 5228 Dihedral : 14.321 144.518 12272 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.12 % Rotamer: Outliers : 3.89 % Allowed : 4.81 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: 2.09 (0.15), residues: 3550 helix: 2.54 (0.13), residues: 1759 sheet: 0.26 (0.28), residues: 387 loop : 0.28 (0.18), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 192 TYR 0.016 0.001 TYR H 189 PHE 0.011 0.001 PHE D 403 TRP 0.009 0.001 TRP H 904 HIS 0.003 0.001 HIS G 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.23 (31893) covalent geometry : angle 0.50078 / 0.35 (43577) hydrogen bonds : bond 0.14910 / 9.67 ( 1603) hydrogen bonds : angle 5.57118 / 3.96 ( 4539) metal coordination : bond 0.03309 / 2.05 ( 24) metal coordination : angle 5.93046 / 3.11 ( 39) Misc. bond : bond 0.00078 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 479 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8985 (p) REVERT: A 105 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 276 MET cc_start: 0.7463 (mmt) cc_final: 0.6742 (mmt) REVERT: A 287 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9032 (mm) REVERT: A 326 LYS cc_start: 0.8423 (mmtt) cc_final: 0.7890 (mptt) REVERT: A 373 GLN cc_start: 0.8705 (mt0) cc_final: 0.8435 (mt0) REVERT: A 380 MET cc_start: 0.8816 (ttm) cc_final: 0.7578 (ttm) REVERT: A 412 MET cc_start: 0.8171 (mmm) cc_final: 0.7853 (mmt) REVERT: A 463 LYS cc_start: 0.8575 (pttt) cc_final: 0.8296 (pttp) REVERT: A 470 LEU cc_start: 0.8993 (mt) cc_final: 0.8776 (tt) REVERT: A 490 GLU cc_start: 0.8422 (tt0) cc_final: 0.7868 (tm-30) REVERT: A 518 PHE cc_start: 0.8792 (m-80) cc_final: 0.8472 (m-80) REVERT: A 519 TYR cc_start: 0.8553 (t80) cc_final: 0.6582 (t80) REVERT: A 525 ILE cc_start: 0.8856 (mt) cc_final: 0.8576 (pt) REVERT: A 569 LYS cc_start: 0.9266 (mttt) cc_final: 0.8812 (mmtp) REVERT: A 609 LYS cc_start: 0.9143 (tttt) cc_final: 0.8909 (ttpp) REVERT: A 660 TYR cc_start: 0.8118 (m-80) cc_final: 0.7755 (m-10) REVERT: A 682 ASP cc_start: 0.8632 (m-30) cc_final: 0.8401 (m-30) REVERT: A 685 TYR cc_start: 0.8573 (m-80) cc_final: 0.8338 (m-80) REVERT: A 708 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8553 (tp30) REVERT: B 42 MET cc_start: 0.7791 (tpt) cc_final: 0.7499 (tpp) REVERT: B 211 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7875 (t80) REVERT: B 384 HIS cc_start: 0.9422 (OUTLIER) cc_final: 0.9067 (p-80) REVERT: B 493 MET cc_start: 0.8738 (ptp) cc_final: 0.8491 (ptp) REVERT: B 677 MET cc_start: 0.9105 (mtt) cc_final: 0.8747 (mtm) REVERT: C 117 MET cc_start: 0.7153 (mtt) cc_final: 0.6676 (ptm) REVERT: C 219 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.8934 (tp30) REVERT: C 307 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.9107 (m-80) REVERT: C 310 HIS cc_start: 0.9123 (OUTLIER) cc_final: 0.8910 (p-80) REVERT: C 452 MET cc_start: 0.5913 (mtp) cc_final: 0.3825 (mtp) REVERT: D 34 LEU cc_start: 0.9235 (mt) cc_final: 0.8876 (mt) REVERT: D 57 MET cc_start: 0.9063 (mmm) cc_final: 0.8538 (mmp) REVERT: D 185 MET cc_start: 0.8362 (mtp) cc_final: 0.7481 (mtm) REVERT: D 201 PHE cc_start: 0.8756 (m-80) cc_final: 0.8386 (m-10) REVERT: D 205 LEU cc_start: 0.8842 (mt) cc_final: 0.8581 (tt) REVERT: D 318 TYR cc_start: 0.8163 (m-10) cc_final: 0.7879 (m-80) REVERT: D 335 LEU cc_start: 0.9319 (mt) cc_final: 0.8956 (mt) REVERT: D 390 GLN cc_start: 0.8814 (tp40) cc_final: 0.8613 (tp40) REVERT: D 392 ARG cc_start: 0.8945 (mtt180) cc_final: 0.8501 (ttm110) REVERT: E 52 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8549 (mm110) REVERT: F 42 MET cc_start: 0.9218 (mtm) cc_final: 0.8481 (mtt) REVERT: F 143 TYR cc_start: 0.9227 (t80) cc_final: 0.8925 (t80) REVERT: F 147 MET cc_start: 0.9007 (mmp) cc_final: 0.8563 (mmp) REVERT: F 175 MET cc_start: 0.8987 (ttt) cc_final: 0.8664 (tmm) REVERT: G 33 PHE cc_start: 0.7102 (m-80) cc_final: 0.6852 (m-80) REVERT: G 59 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8300 (mm-30) REVERT: G 60 LEU cc_start: 0.9247 (tp) cc_final: 0.9003 (tp) REVERT: G 61 MET cc_start: 0.8294 (ptp) cc_final: 0.6284 (ptp) REVERT: H 568 TYR cc_start: 0.2362 (OUTLIER) cc_final: 0.1548 (m-80) REVERT: H 688 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8029 (t0) REVERT: H 726 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8159 (pm20) REVERT: H 845 LEU cc_start: 0.9381 (mt) cc_final: 0.9114 (mt) REVERT: H 859 GLU cc_start: 0.8923 (tt0) cc_final: 0.8367 (tp30) REVERT: H 862 LYS cc_start: 0.8960 (mttt) cc_final: 0.8687 (mptt) REVERT: H 895 GLU cc_start: 0.8401 (tp30) cc_final: 0.8003 (tp30) REVERT: H 909 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8184 (mm-30) REVERT: I 276 LEU cc_start: 0.7075 (mp) cc_final: 0.6720 (tt) REVERT: I 313 LEU cc_start: 0.7571 (tp) cc_final: 0.7201 (tp) REVERT: J 72 MET cc_start: 0.4528 (ptm) cc_final: 0.4299 (ptt) REVERT: J 104 GLU cc_start: 0.9076 (tt0) cc_final: 0.8821 (tm-30) REVERT: J 108 LYS cc_start: 0.9528 (mtpt) cc_final: 0.9257 (mmmt) outliers start: 123 outliers final: 48 residues processed: 585 average time/residue: 0.2308 time to fit residues: 208.0917 Evaluate side-chains 361 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 301 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 15 TYR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 688 ASP Chi-restraints excluded: chain H residue 708 LYS Chi-restraints excluded: chain H residue 787 ASP Chi-restraints excluded: chain H residue 790 CYS Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 834 ARG Chi-restraints excluded: chain J residue 116 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.0010 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS A 366 ASN A 537 ASN A 709 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS D 20 GLN D 117 ASN D 161 HIS E 256 GLN E 265 GLN E 365 ASN G 36 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 644 HIS ** H 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.071869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.051885 restraints weight = 222111.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.053287 restraints weight = 119597.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.054147 restraints weight = 78360.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.054802 restraints weight = 59732.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.055081 restraints weight = 50090.509| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31919 Z= 0.159 Angle : 0.668 23.318 43616 Z= 0.331 Chirality : 0.043 0.257 4851 Planarity : 0.005 0.054 5228 Dihedral : 16.566 142.056 5231 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 3.13 % Allowed : 9.96 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.15), residues: 3550 helix: 2.02 (0.12), residues: 1784 sheet: 0.31 (0.28), residues: 364 loop : 0.16 (0.18), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 164 TYR 0.020 0.001 TYR A 571 PHE 0.026 0.002 PHE I 324 TRP 0.024 0.002 TRP A 381 HIS 0.007 0.001 HIS I 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (31893) covalent geometry : angle 0.63996 / 0.33 (43577) hydrogen bonds : bond 0.04645 / 3.01 ( 1603) hydrogen bonds : angle 4.91408 / 3.46 ( 4539) metal coordination : bond 0.01137 / 0.68 ( 24) metal coordination : angle 6.41908 / 3.51 ( 39) Misc. bond : bond 0.00063 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 318 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8873 (p) REVERT: A 276 MET cc_start: 0.6864 (mmt) cc_final: 0.5982 (mmt) REVERT: A 279 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7429 (mt-10) REVERT: A 322 LYS cc_start: 0.8752 (tptp) cc_final: 0.8469 (tptp) REVERT: A 326 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7874 (mmtm) REVERT: A 373 GLN cc_start: 0.8690 (mt0) cc_final: 0.8370 (mm-40) REVERT: A 375 LYS cc_start: 0.9234 (tttt) cc_final: 0.8715 (tttp) REVERT: A 380 MET cc_start: 0.8897 (ttm) cc_final: 0.8609 (ttm) REVERT: A 412 MET cc_start: 0.8178 (mmm) cc_final: 0.7913 (mmm) REVERT: A 424 GLU cc_start: 0.8739 (tp30) cc_final: 0.8470 (tp30) REVERT: A 463 LYS cc_start: 0.8542 (pttt) cc_final: 0.8215 (pttm) REVERT: A 470 LEU cc_start: 0.8990 (mt) cc_final: 0.8715 (tt) REVERT: A 490 GLU cc_start: 0.8437 (tt0) cc_final: 0.7859 (tm-30) REVERT: A 518 PHE cc_start: 0.8887 (m-80) cc_final: 0.8663 (m-80) REVERT: A 519 TYR cc_start: 0.8270 (t80) cc_final: 0.7566 (t80) REVERT: A 530 ARG cc_start: 0.8755 (mtm180) cc_final: 0.8205 (mtm-85) REVERT: A 536 MET cc_start: 0.8879 (mmm) cc_final: 0.8552 (tpt) REVERT: A 609 LYS cc_start: 0.9073 (tttt) cc_final: 0.8826 (ttpp) REVERT: A 660 TYR cc_start: 0.8160 (m-80) cc_final: 0.7805 (m-10) REVERT: A 666 ASP cc_start: 0.7317 (t0) cc_final: 0.6826 (t0) REVERT: A 669 GLU cc_start: 0.8688 (tt0) cc_final: 0.8377 (tt0) REVERT: A 682 ASP cc_start: 0.8646 (m-30) cc_final: 0.8388 (m-30) REVERT: A 708 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8718 (tp30) REVERT: A 715 LYS cc_start: 0.9355 (ttpt) cc_final: 0.9147 (ttpt) REVERT: B 211 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7697 (t80) REVERT: B 384 HIS cc_start: 0.9454 (OUTLIER) cc_final: 0.9132 (p-80) REVERT: B 677 MET cc_start: 0.9062 (mtt) cc_final: 0.8750 (mtm) REVERT: C 307 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.9107 (m-80) REVERT: C 310 HIS cc_start: 0.9223 (OUTLIER) cc_final: 0.8980 (p-80) REVERT: C 313 MET cc_start: 0.8836 (mmt) cc_final: 0.8573 (mmm) REVERT: D 34 LEU cc_start: 0.9259 (mt) cc_final: 0.8885 (mt) REVERT: D 57 MET cc_start: 0.9064 (mmm) cc_final: 0.8552 (mmm) REVERT: D 185 MET cc_start: 0.7962 (mtp) cc_final: 0.7722 (mtm) REVERT: D 201 PHE cc_start: 0.8748 (m-80) cc_final: 0.8457 (m-80) REVERT: D 205 LEU cc_start: 0.8905 (mt) cc_final: 0.8509 (tt) REVERT: D 348 ARG cc_start: 0.8488 (ttt-90) cc_final: 0.8263 (ttt90) REVERT: D 392 ARG cc_start: 0.8972 (mtt180) cc_final: 0.8490 (ttm110) REVERT: D 401 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8755 (tt) REVERT: E 91 PHE cc_start: 0.9084 (t80) cc_final: 0.8626 (t80) REVERT: F 147 MET cc_start: 0.9075 (mmp) cc_final: 0.8726 (mmp) REVERT: F 157 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8480 (ptt) REVERT: F 175 MET cc_start: 0.9069 (ttt) cc_final: 0.8815 (tmm) REVERT: G 16 MET cc_start: 0.8693 (mmm) cc_final: 0.8396 (mmm) REVERT: H 189 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7878 (p90) REVERT: H 566 MET cc_start: 0.4311 (OUTLIER) cc_final: 0.3780 (mtt) REVERT: H 568 TYR cc_start: 0.1514 (OUTLIER) cc_final: 0.0718 (m-80) REVERT: H 726 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8122 (pm20) REVERT: H 767 MET cc_start: 0.8171 (ttp) cc_final: 0.7922 (tmm) REVERT: H 843 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8908 (ttp80) REVERT: H 859 GLU cc_start: 0.8786 (tt0) cc_final: 0.7669 (tp30) REVERT: H 862 LYS cc_start: 0.9015 (mttt) cc_final: 0.8707 (mptt) REVERT: H 863 ARG cc_start: 0.8577 (ptp90) cc_final: 0.7848 (ptt-90) REVERT: J 108 LYS cc_start: 0.9528 (mtpt) cc_final: 0.9266 (mmmt) outliers start: 99 outliers final: 51 residues processed: 400 average time/residue: 0.2013 time to fit residues: 125.9977 Evaluate side-chains 338 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 275 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 15 TYR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 566 MET Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 843 ARG Chi-restraints excluded: chain I residue 310 ASN Chi-restraints excluded: chain I residue 315 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 73 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 275 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 299 optimal weight: 30.0000 chunk 325 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 18 optimal weight: 0.2980 chunk 214 optimal weight: 0.8980 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 709 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 HIS ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 644 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.070934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.050762 restraints weight = 223368.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.051851 restraints weight = 121792.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.052744 restraints weight = 80958.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.053343 restraints weight = 61689.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.053612 restraints weight = 51700.625| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 31919 Z= 0.185 Angle : 0.655 23.439 43616 Z= 0.325 Chirality : 0.041 0.205 4851 Planarity : 0.004 0.047 5228 Dihedral : 16.497 142.548 5182 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.35 % Allowed : 10.37 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.14), residues: 3550 helix: 1.80 (0.12), residues: 1789 sheet: 0.23 (0.28), residues: 365 loop : 0.05 (0.18), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 671 TYR 0.038 0.002 TYR D 318 PHE 0.030 0.001 PHE G 19 TRP 0.036 0.002 TRP D 55 HIS 0.010 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (31893) covalent geometry : angle 0.62399 / 0.32 (43577) hydrogen bonds : bond 0.04561 / 2.94 ( 1603) hydrogen bonds : angle 4.85380 / 3.43 ( 4539) metal coordination : bond 0.01313 / 0.78 ( 24) metal coordination : angle 6.71150 / 3.72 ( 39) Misc. bond : bond 0.00048 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 279 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8949 (p) REVERT: A 322 LYS cc_start: 0.8793 (tptp) cc_final: 0.8488 (tptp) REVERT: A 326 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7904 (mptt) REVERT: A 373 GLN cc_start: 0.8696 (mt0) cc_final: 0.8381 (mm110) REVERT: A 380 MET cc_start: 0.8963 (ttm) cc_final: 0.8601 (ttm) REVERT: A 418 LYS cc_start: 0.7891 (tptt) cc_final: 0.7299 (tptt) REVERT: A 463 LYS cc_start: 0.8621 (pttt) cc_final: 0.8300 (pttm) REVERT: A 482 PHE cc_start: 0.7818 (t80) cc_final: 0.7547 (t80) REVERT: A 490 GLU cc_start: 0.8397 (tt0) cc_final: 0.7832 (tm-30) REVERT: A 518 PHE cc_start: 0.8902 (m-80) cc_final: 0.8671 (m-80) REVERT: A 519 TYR cc_start: 0.8346 (t80) cc_final: 0.7524 (t80) REVERT: A 530 ARG cc_start: 0.8802 (mtm180) cc_final: 0.8356 (mtm-85) REVERT: A 536 MET cc_start: 0.8849 (mmm) cc_final: 0.8479 (tpt) REVERT: A 589 ARG cc_start: 0.9077 (ttp-170) cc_final: 0.8789 (ttp-170) REVERT: A 609 LYS cc_start: 0.9084 (tttt) cc_final: 0.8742 (ttpp) REVERT: A 639 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7941 (ttm170) REVERT: A 666 ASP cc_start: 0.7497 (t0) cc_final: 0.7224 (t0) REVERT: A 670 MET cc_start: 0.8824 (mmm) cc_final: 0.8616 (mmm) REVERT: A 696 MET cc_start: 0.8240 (mtp) cc_final: 0.7881 (mmm) REVERT: A 715 LYS cc_start: 0.9397 (ttpt) cc_final: 0.9190 (ttpt) REVERT: B 211 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.7617 (t80) REVERT: B 220 LEU cc_start: 0.9315 (tt) cc_final: 0.8955 (tt) REVERT: B 384 HIS cc_start: 0.9490 (OUTLIER) cc_final: 0.9199 (p-80) REVERT: B 527 MET cc_start: 0.9577 (mmm) cc_final: 0.9172 (mmm) REVERT: B 545 MET cc_start: 0.9558 (OUTLIER) cc_final: 0.9019 (ttm) REVERT: B 677 MET cc_start: 0.9068 (mtt) cc_final: 0.8734 (mtm) REVERT: B 724 MET cc_start: 0.8962 (mmm) cc_final: 0.8678 (mmm) REVERT: C 307 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.9137 (m-80) REVERT: C 310 HIS cc_start: 0.9228 (OUTLIER) cc_final: 0.8980 (p-80) REVERT: C 313 MET cc_start: 0.8876 (mmt) cc_final: 0.8611 (mmm) REVERT: D 34 LEU cc_start: 0.9260 (mt) cc_final: 0.8874 (mt) REVERT: D 57 MET cc_start: 0.9059 (mmm) cc_final: 0.8515 (mmm) REVERT: D 161 HIS cc_start: 0.8659 (OUTLIER) cc_final: 0.8331 (m-70) REVERT: D 201 PHE cc_start: 0.8819 (m-80) cc_final: 0.8530 (m-80) REVERT: D 205 LEU cc_start: 0.8938 (mt) cc_final: 0.8555 (tt) REVERT: D 363 GLN cc_start: 0.8560 (mt0) cc_final: 0.8171 (mp10) REVERT: D 392 ARG cc_start: 0.8964 (mtt180) cc_final: 0.8550 (ttm110) REVERT: E 52 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8295 (mm110) REVERT: F 42 MET cc_start: 0.9156 (mtp) cc_final: 0.8864 (mmm) REVERT: F 147 MET cc_start: 0.9147 (mmp) cc_final: 0.8682 (mmp) REVERT: F 157 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8455 (ptt) REVERT: F 175 MET cc_start: 0.9074 (ttt) cc_final: 0.8840 (ttp) REVERT: G 16 MET cc_start: 0.8704 (mmm) cc_final: 0.8434 (mmm) REVERT: H 566 MET cc_start: 0.4857 (OUTLIER) cc_final: 0.4429 (mtt) REVERT: H 568 TYR cc_start: 0.1445 (OUTLIER) cc_final: 0.0696 (m-80) REVERT: H 726 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8086 (pm20) REVERT: H 859 GLU cc_start: 0.8795 (tt0) cc_final: 0.8451 (tp30) REVERT: H 862 LYS cc_start: 0.9051 (mttt) cc_final: 0.8730 (mptt) REVERT: J 72 MET cc_start: 0.2498 (ptt) cc_final: 0.2285 (ptt) REVERT: J 106 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8568 (mm) outliers start: 106 outliers final: 69 residues processed: 364 average time/residue: 0.1983 time to fit residues: 114.5234 Evaluate side-chains 336 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 254 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 15 TYR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 566 MET Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 843 ARG Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 282 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 247 optimal weight: 0.0010 chunk 259 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN G 64 ASN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 644 HIS ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.071506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.053196 restraints weight = 223225.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.054149 restraints weight = 127705.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.054504 restraints weight = 84072.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.054746 restraints weight = 69352.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.055123 restraints weight = 53409.711| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31919 Z= 0.141 Angle : 0.640 23.271 43616 Z= 0.314 Chirality : 0.041 0.236 4851 Planarity : 0.004 0.044 5228 Dihedral : 16.527 141.516 5179 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.45 % Allowed : 11.16 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.14), residues: 3550 helix: 1.82 (0.12), residues: 1784 sheet: 0.18 (0.29), residues: 351 loop : 0.02 (0.17), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 17 TYR 0.022 0.001 TYR A 519 PHE 0.027 0.001 PHE E 374 TRP 0.013 0.001 TRP D 55 HIS 0.006 0.001 HIS I 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (31893) covalent geometry : angle 0.61255 / 0.31 (43577) hydrogen bonds : bond 0.03988 / 2.59 ( 1603) hydrogen bonds : angle 4.69950 / 3.33 ( 4539) metal coordination : bond 0.01166 / 0.71 ( 24) metal coordination : angle 6.28076 / 3.51 ( 39) Misc. bond : bond 0.00021 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 273 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8897 (p) REVERT: A 276 MET cc_start: 0.6878 (mmt) cc_final: 0.5795 (mmt) REVERT: A 279 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7534 (mt-10) REVERT: A 326 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7852 (mmtm) REVERT: A 373 GLN cc_start: 0.8714 (mt0) cc_final: 0.8408 (mm110) REVERT: A 380 MET cc_start: 0.8972 (ttm) cc_final: 0.8559 (ttm) REVERT: A 482 PHE cc_start: 0.7760 (t80) cc_final: 0.7542 (t80) REVERT: A 490 GLU cc_start: 0.8426 (tt0) cc_final: 0.7790 (tm-30) REVERT: A 518 PHE cc_start: 0.8962 (m-80) cc_final: 0.8671 (m-80) REVERT: A 519 TYR cc_start: 0.8368 (t80) cc_final: 0.7481 (t80) REVERT: A 530 ARG cc_start: 0.8843 (mtm180) cc_final: 0.8280 (mtm-85) REVERT: A 536 MET cc_start: 0.8941 (mmm) cc_final: 0.8603 (tpt) REVERT: A 589 ARG cc_start: 0.9120 (ttp-170) cc_final: 0.8826 (ttp-170) REVERT: A 609 LYS cc_start: 0.9050 (tttt) cc_final: 0.8772 (ttpp) REVERT: A 639 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7983 (ttm170) REVERT: A 666 ASP cc_start: 0.7400 (t0) cc_final: 0.7168 (t70) REVERT: A 669 GLU cc_start: 0.8750 (tt0) cc_final: 0.8173 (tt0) REVERT: A 670 MET cc_start: 0.8710 (mmm) cc_final: 0.8479 (mmm) REVERT: A 682 ASP cc_start: 0.8724 (m-30) cc_final: 0.8387 (m-30) REVERT: B 211 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.7650 (t80) REVERT: B 220 LEU cc_start: 0.9318 (tt) cc_final: 0.8983 (tt) REVERT: B 384 HIS cc_start: 0.9502 (OUTLIER) cc_final: 0.9217 (p-80) REVERT: B 527 MET cc_start: 0.9592 (mmm) cc_final: 0.9219 (mmm) REVERT: B 545 MET cc_start: 0.9554 (OUTLIER) cc_final: 0.8990 (ttm) REVERT: B 677 MET cc_start: 0.8977 (mtt) cc_final: 0.8582 (mtm) REVERT: B 724 MET cc_start: 0.9013 (mmm) cc_final: 0.8747 (mmm) REVERT: C 307 PHE cc_start: 0.9455 (OUTLIER) cc_final: 0.9158 (m-80) REVERT: C 310 HIS cc_start: 0.9269 (OUTLIER) cc_final: 0.9035 (p-80) REVERT: C 313 MET cc_start: 0.8787 (mmt) cc_final: 0.8526 (mmm) REVERT: C 441 MET cc_start: 0.8775 (mmp) cc_final: 0.8378 (mmp) REVERT: D 34 LEU cc_start: 0.9291 (mt) cc_final: 0.8917 (mt) REVERT: D 57 MET cc_start: 0.9064 (mmm) cc_final: 0.8573 (mmm) REVERT: D 161 HIS cc_start: 0.8754 (OUTLIER) cc_final: 0.8363 (m-70) REVERT: D 201 PHE cc_start: 0.8807 (m-80) cc_final: 0.8501 (m-80) REVERT: D 205 LEU cc_start: 0.8976 (mt) cc_final: 0.8568 (tt) REVERT: D 363 GLN cc_start: 0.8621 (mt0) cc_final: 0.8184 (mp10) REVERT: D 392 ARG cc_start: 0.8968 (mtt180) cc_final: 0.8548 (ttm110) REVERT: D 401 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8722 (tt) REVERT: E 52 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8303 (mm110) REVERT: E 58 MET cc_start: 0.9054 (tpp) cc_final: 0.8808 (tpt) REVERT: F 42 MET cc_start: 0.9182 (mtp) cc_final: 0.8968 (mmm) REVERT: F 147 MET cc_start: 0.9241 (mmp) cc_final: 0.8872 (mmm) REVERT: F 157 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8402 (ptt) REVERT: F 175 MET cc_start: 0.9094 (ttt) cc_final: 0.8865 (ttp) REVERT: G 16 MET cc_start: 0.8794 (mmm) cc_final: 0.8406 (mmm) REVERT: H 189 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7979 (p90) REVERT: H 568 TYR cc_start: 0.2218 (OUTLIER) cc_final: 0.0968 (m-80) REVERT: H 726 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8067 (mp0) REVERT: H 859 GLU cc_start: 0.8746 (tt0) cc_final: 0.8415 (tp30) REVERT: H 862 LYS cc_start: 0.9053 (mttt) cc_final: 0.8717 (mptt) REVERT: I 287 GLN cc_start: 0.9628 (tp-100) cc_final: 0.9353 (mt0) REVERT: I 288 MET cc_start: 0.7557 (mtt) cc_final: 0.7234 (ppp) REVERT: J 57 MET cc_start: 0.2734 (ttt) cc_final: 0.2459 (ppp) REVERT: J 106 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8423 (mm) outliers start: 109 outliers final: 73 residues processed: 363 average time/residue: 0.1926 time to fit residues: 112.3466 Evaluate side-chains 340 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 253 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 15 TYR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 834 ARG Chi-restraints excluded: chain H residue 843 ARG Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain I residue 310 ASN Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 18 optimal weight: 8.9990 chunk 282 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 290 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 chunk 362 optimal weight: 30.0000 chunk 272 optimal weight: 20.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN A 595 ASN ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 HIS C 496 ASN E 257 HIS F 65 GLN G 36 GLN ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.069126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.050000 restraints weight = 225075.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.051374 restraints weight = 135499.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.051413 restraints weight = 88060.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.051849 restraints weight = 71162.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.051901 restraints weight = 57958.336| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 31919 Z= 0.298 Angle : 0.754 25.109 43616 Z= 0.375 Chirality : 0.043 0.291 4851 Planarity : 0.004 0.049 5228 Dihedral : 16.682 141.587 5179 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.89 % Allowed : 11.80 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: 0.96 (0.14), residues: 3550 helix: 1.45 (0.12), residues: 1791 sheet: -0.17 (0.27), residues: 371 loop : -0.09 (0.18), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 280 TYR 0.024 0.002 TYR A 519 PHE 0.023 0.002 PHE G 19 TRP 0.014 0.002 TRP A 77 HIS 0.011 0.002 HIS H 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.30 (31893) covalent geometry : angle 0.71694 / 0.37 (43577) hydrogen bonds : bond 0.05289 / 3.37 ( 1603) hydrogen bonds : angle 5.02573 / 3.59 ( 4539) metal coordination : bond 0.02075 / 1.22 ( 24) metal coordination : angle 7.84910 / 4.38 ( 39) Misc. bond : bond 0.00051 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 254 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.9042 (p) REVERT: A 326 LYS cc_start: 0.8347 (mmtt) cc_final: 0.8054 (mmtp) REVERT: A 375 LYS cc_start: 0.9151 (tttt) cc_final: 0.8874 (ttmm) REVERT: A 380 MET cc_start: 0.9032 (ttm) cc_final: 0.8792 (ttm) REVERT: A 450 MET cc_start: 0.7769 (mmm) cc_final: 0.7435 (tpt) REVERT: A 482 PHE cc_start: 0.7837 (t80) cc_final: 0.7551 (t80) REVERT: A 490 GLU cc_start: 0.8341 (tt0) cc_final: 0.7869 (tm-30) REVERT: A 518 PHE cc_start: 0.8907 (m-80) cc_final: 0.8645 (m-80) REVERT: A 519 TYR cc_start: 0.8344 (t80) cc_final: 0.7458 (t80) REVERT: A 530 ARG cc_start: 0.8907 (mtm180) cc_final: 0.8618 (mtm-85) REVERT: A 609 LYS cc_start: 0.9086 (tttt) cc_final: 0.8830 (ttpp) REVERT: A 666 ASP cc_start: 0.7595 (t0) cc_final: 0.7136 (t0) REVERT: A 669 GLU cc_start: 0.8849 (tt0) cc_final: 0.8384 (tt0) REVERT: A 682 ASP cc_start: 0.8814 (m-30) cc_final: 0.8484 (m-30) REVERT: B 211 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.7939 (t80) REVERT: B 220 LEU cc_start: 0.9343 (tt) cc_final: 0.9090 (tt) REVERT: B 384 HIS cc_start: 0.9509 (OUTLIER) cc_final: 0.9242 (p-80) REVERT: B 493 MET cc_start: 0.8840 (ptp) cc_final: 0.8626 (ptp) REVERT: B 527 MET cc_start: 0.9620 (mmm) cc_final: 0.9249 (mmm) REVERT: B 545 MET cc_start: 0.9585 (OUTLIER) cc_final: 0.8996 (ttm) REVERT: B 599 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8541 (m) REVERT: B 620 MET cc_start: 0.8905 (mmm) cc_final: 0.8678 (mmm) REVERT: B 677 MET cc_start: 0.9073 (mtt) cc_final: 0.8647 (mtm) REVERT: B 724 MET cc_start: 0.9044 (mmm) cc_final: 0.8816 (mmm) REVERT: C 307 PHE cc_start: 0.9497 (OUTLIER) cc_final: 0.9122 (m-10) REVERT: C 310 HIS cc_start: 0.9275 (OUTLIER) cc_final: 0.9064 (p-80) REVERT: C 313 MET cc_start: 0.8826 (mmt) cc_final: 0.8549 (mmm) REVERT: C 441 MET cc_start: 0.8886 (mmp) cc_final: 0.8531 (mmp) REVERT: D 34 LEU cc_start: 0.9230 (mt) cc_final: 0.8866 (mt) REVERT: D 57 MET cc_start: 0.9071 (mmm) cc_final: 0.8511 (mmm) REVERT: D 161 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.8456 (m-70) REVERT: D 205 LEU cc_start: 0.9001 (mt) cc_final: 0.8715 (tt) REVERT: D 363 GLN cc_start: 0.8530 (mt0) cc_final: 0.8201 (mp10) REVERT: D 392 ARG cc_start: 0.8936 (mtt180) cc_final: 0.8542 (ttm110) REVERT: D 422 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8357 (mm) REVERT: E 52 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8316 (mm110) REVERT: F 42 MET cc_start: 0.9137 (mtp) cc_final: 0.8796 (mmm) REVERT: F 51 MET cc_start: 0.9332 (mmm) cc_final: 0.8994 (mmm) REVERT: F 147 MET cc_start: 0.9124 (mmp) cc_final: 0.8747 (mmp) REVERT: F 157 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8460 (ptm) REVERT: F 178 MET cc_start: 0.8975 (mmm) cc_final: 0.8691 (mmp) REVERT: G 16 MET cc_start: 0.8789 (mmm) cc_final: 0.8363 (mmm) REVERT: H 568 TYR cc_start: 0.2224 (OUTLIER) cc_final: 0.0971 (m-80) REVERT: H 726 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7998 (mp0) REVERT: H 859 GLU cc_start: 0.8825 (tt0) cc_final: 0.8069 (tp30) REVERT: H 862 LYS cc_start: 0.9181 (mttt) cc_final: 0.8862 (mptt) REVERT: H 863 ARG cc_start: 0.8649 (ptp90) cc_final: 0.8033 (ptt-90) REVERT: I 287 GLN cc_start: 0.9608 (tp-100) cc_final: 0.9293 (mt0) REVERT: J 57 MET cc_start: 0.3071 (ttt) cc_final: 0.2813 (ppp) outliers start: 123 outliers final: 91 residues processed: 358 average time/residue: 0.1882 time to fit residues: 108.1628 Evaluate side-chains 345 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 242 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 448 HIS Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 15 TYR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 593 THR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 643 ASN Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 680 CYS Chi-restraints excluded: chain H residue 718 ARG Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain I residue 310 ASN Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 155 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 189 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 GLN A 595 ASN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN H 209 HIS ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.070440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.050085 restraints weight = 223612.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.051437 restraints weight = 121547.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.052350 restraints weight = 81146.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.052879 restraints weight = 61525.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.053041 restraints weight = 51888.820| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31919 Z= 0.164 Angle : 0.674 26.844 43616 Z= 0.326 Chirality : 0.042 0.366 4851 Planarity : 0.004 0.043 5228 Dihedral : 16.709 139.405 5175 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.48 % Allowed : 12.78 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.14), residues: 3550 helix: 1.66 (0.12), residues: 1786 sheet: -0.10 (0.28), residues: 361 loop : -0.05 (0.18), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 834 TYR 0.022 0.001 TYR A 519 PHE 0.026 0.002 PHE I 324 TRP 0.013 0.001 TRP H 603 HIS 0.007 0.001 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (31893) covalent geometry : angle 0.63511 / 0.33 (43577) hydrogen bonds : bond 0.04217 / 2.73 ( 1603) hydrogen bonds : angle 4.79091 / 3.42 ( 4539) metal coordination : bond 0.01408 / 0.84 ( 24) metal coordination : angle 7.61647 / 4.21 ( 39) Misc. bond : bond 0.00021 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 259 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 VAL cc_start: 0.9261 (OUTLIER) cc_final: 0.8995 (p) REVERT: A 322 LYS cc_start: 0.8795 (tptp) cc_final: 0.8408 (tptp) REVERT: A 326 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7832 (mptt) REVERT: A 373 GLN cc_start: 0.8627 (mt0) cc_final: 0.8260 (mm110) REVERT: A 380 MET cc_start: 0.8981 (ttm) cc_final: 0.8724 (ttm) REVERT: A 450 MET cc_start: 0.7547 (mmm) cc_final: 0.7193 (tpt) REVERT: A 470 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9013 (mt) REVERT: A 482 PHE cc_start: 0.7661 (t80) cc_final: 0.7439 (t80) REVERT: A 490 GLU cc_start: 0.8378 (tt0) cc_final: 0.7850 (tm-30) REVERT: A 518 PHE cc_start: 0.8809 (m-80) cc_final: 0.8569 (m-80) REVERT: A 530 ARG cc_start: 0.8747 (mtm180) cc_final: 0.8476 (mtm-85) REVERT: A 536 MET cc_start: 0.8763 (mmm) cc_final: 0.8416 (tpt) REVERT: A 540 LYS cc_start: 0.9409 (ttmt) cc_final: 0.9080 (ttpp) REVERT: A 569 LYS cc_start: 0.9074 (mmtp) cc_final: 0.8849 (mmtm) REVERT: A 609 LYS cc_start: 0.9109 (tttt) cc_final: 0.8804 (ttpp) REVERT: A 668 GLN cc_start: 0.8863 (tt0) cc_final: 0.8480 (tp-100) REVERT: A 669 GLU cc_start: 0.8663 (tt0) cc_final: 0.7880 (tp30) REVERT: B 211 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7704 (t80) REVERT: B 220 LEU cc_start: 0.9315 (tt) cc_final: 0.9060 (tt) REVERT: B 384 HIS cc_start: 0.9478 (OUTLIER) cc_final: 0.9229 (p-80) REVERT: B 493 MET cc_start: 0.8843 (ptp) cc_final: 0.8618 (ptp) REVERT: B 527 MET cc_start: 0.9626 (mmm) cc_final: 0.9256 (mmm) REVERT: B 545 MET cc_start: 0.9590 (OUTLIER) cc_final: 0.8959 (ttm) REVERT: B 677 MET cc_start: 0.9098 (mtt) cc_final: 0.8668 (mtm) REVERT: B 724 MET cc_start: 0.8989 (mmm) cc_final: 0.8775 (mmm) REVERT: C 307 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.9073 (m-10) REVERT: C 313 MET cc_start: 0.8801 (mmt) cc_final: 0.8564 (mmm) REVERT: C 441 MET cc_start: 0.8778 (mmp) cc_final: 0.8469 (mmp) REVERT: D 34 LEU cc_start: 0.9213 (mt) cc_final: 0.8823 (mt) REVERT: D 57 MET cc_start: 0.8939 (mmm) cc_final: 0.8483 (mmm) REVERT: D 161 HIS cc_start: 0.8654 (OUTLIER) cc_final: 0.8308 (m-70) REVERT: D 201 PHE cc_start: 0.8699 (m-80) cc_final: 0.8463 (m-80) REVERT: D 205 LEU cc_start: 0.8886 (mt) cc_final: 0.8554 (tt) REVERT: D 363 GLN cc_start: 0.8506 (mt0) cc_final: 0.8225 (mp10) REVERT: D 392 ARG cc_start: 0.8850 (mtt180) cc_final: 0.8513 (ttm110) REVERT: E 52 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8086 (mm110) REVERT: E 137 MET cc_start: 0.8129 (tpt) cc_final: 0.7775 (tpt) REVERT: F 42 MET cc_start: 0.9132 (mtp) cc_final: 0.8788 (mmm) REVERT: F 51 MET cc_start: 0.9272 (mmm) cc_final: 0.8482 (mmm) REVERT: F 147 MET cc_start: 0.9100 (mmp) cc_final: 0.8816 (mmm) REVERT: F 157 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8385 (ptt) REVERT: G 16 MET cc_start: 0.8706 (mmm) cc_final: 0.8209 (mmm) REVERT: H 568 TYR cc_start: 0.1606 (OUTLIER) cc_final: 0.0745 (m-80) REVERT: H 718 ARG cc_start: 0.2724 (OUTLIER) cc_final: 0.2376 (ptp-110) REVERT: H 726 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8020 (pm20) REVERT: H 859 GLU cc_start: 0.8785 (tt0) cc_final: 0.8448 (tp30) REVERT: H 862 LYS cc_start: 0.9094 (mttt) cc_final: 0.8751 (mptt) REVERT: I 287 GLN cc_start: 0.9618 (tp-100) cc_final: 0.9366 (mt0) outliers start: 110 outliers final: 78 residues processed: 349 average time/residue: 0.1979 time to fit residues: 111.2371 Evaluate side-chains 334 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 245 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 448 HIS Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 209 HIS Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 593 THR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 643 ASN Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 680 CYS Chi-restraints excluded: chain H residue 718 ARG Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 64 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 307 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 595 ASN A 625 GLN ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.069915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.049373 restraints weight = 224643.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.050762 restraints weight = 121050.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.051590 restraints weight = 79571.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.052202 restraints weight = 61359.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.052577 restraints weight = 51970.906| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31919 Z= 0.200 Angle : 0.703 26.963 43616 Z= 0.342 Chirality : 0.043 0.491 4851 Planarity : 0.004 0.044 5228 Dihedral : 16.694 139.448 5168 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.42 % Allowed : 13.38 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: 0.98 (0.14), residues: 3550 helix: 1.51 (0.12), residues: 1793 sheet: -0.37 (0.27), residues: 388 loop : -0.08 (0.18), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 280 TYR 0.024 0.001 TYR A 95 PHE 0.037 0.002 PHE J 162 TRP 0.024 0.002 TRP H 602 HIS 0.007 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.20 (31893) covalent geometry : angle 0.66359 / 0.34 (43577) hydrogen bonds : bond 0.04452 / 2.87 ( 1603) hydrogen bonds : angle 4.87745 / 3.49 ( 4539) metal coordination : bond 0.01545 / 0.92 ( 24) metal coordination : angle 7.74551 / 4.33 ( 39) Misc. bond : bond 0.00029 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 251 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.8802 (tptp) cc_final: 0.8403 (tptp) REVERT: A 326 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7818 (mptt) REVERT: A 373 GLN cc_start: 0.8655 (mt0) cc_final: 0.8249 (mm110) REVERT: A 375 LYS cc_start: 0.9151 (tttt) cc_final: 0.8854 (ttmm) REVERT: A 380 MET cc_start: 0.9029 (ttm) cc_final: 0.8385 (ttm) REVERT: A 450 MET cc_start: 0.7541 (mmm) cc_final: 0.7048 (tpt) REVERT: A 470 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9039 (mt) REVERT: A 482 PHE cc_start: 0.7660 (t80) cc_final: 0.7439 (t80) REVERT: A 490 GLU cc_start: 0.8370 (tt0) cc_final: 0.7862 (tm-30) REVERT: A 518 PHE cc_start: 0.8827 (m-80) cc_final: 0.8529 (m-80) REVERT: A 530 ARG cc_start: 0.8801 (mtm180) cc_final: 0.8525 (mtm-85) REVERT: A 536 MET cc_start: 0.8833 (mmm) cc_final: 0.8468 (tpt) REVERT: A 540 LYS cc_start: 0.9410 (ttmt) cc_final: 0.9085 (ttpp) REVERT: A 569 LYS cc_start: 0.9129 (mmtp) cc_final: 0.8846 (mmtp) REVERT: A 589 ARG cc_start: 0.8899 (ttm170) cc_final: 0.8685 (ttp-170) REVERT: A 609 LYS cc_start: 0.9087 (tttt) cc_final: 0.8793 (ttpp) REVERT: A 613 THR cc_start: 0.6170 (OUTLIER) cc_final: 0.5651 (t) REVERT: A 668 GLN cc_start: 0.8916 (tt0) cc_final: 0.8512 (tp40) REVERT: A 669 GLU cc_start: 0.8693 (tt0) cc_final: 0.8025 (tp30) REVERT: A 678 ARG cc_start: 0.8340 (ptp90) cc_final: 0.7891 (mtm-85) REVERT: A 682 ASP cc_start: 0.8712 (m-30) cc_final: 0.8410 (m-30) REVERT: B 211 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.7718 (t80) REVERT: B 220 LEU cc_start: 0.9320 (tt) cc_final: 0.9047 (tt) REVERT: B 384 HIS cc_start: 0.9465 (OUTLIER) cc_final: 0.9220 (p-80) REVERT: B 493 MET cc_start: 0.8867 (ptp) cc_final: 0.8638 (ptp) REVERT: B 527 MET cc_start: 0.9639 (mmm) cc_final: 0.9274 (mmm) REVERT: B 545 MET cc_start: 0.9594 (OUTLIER) cc_final: 0.8942 (ttm) REVERT: B 677 MET cc_start: 0.9116 (mtt) cc_final: 0.8678 (mtm) REVERT: B 724 MET cc_start: 0.9016 (mmm) cc_final: 0.8798 (mmm) REVERT: C 215 MET cc_start: 0.6259 (ppp) cc_final: 0.5703 (tmm) REVERT: C 307 PHE cc_start: 0.9479 (OUTLIER) cc_final: 0.9164 (m-10) REVERT: C 313 MET cc_start: 0.8840 (mmt) cc_final: 0.8603 (mmm) REVERT: D 34 LEU cc_start: 0.9171 (mt) cc_final: 0.8780 (mt) REVERT: D 57 MET cc_start: 0.8948 (mmm) cc_final: 0.8514 (mmm) REVERT: D 161 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.8249 (m-70) REVERT: D 205 LEU cc_start: 0.8870 (mt) cc_final: 0.8556 (tt) REVERT: D 363 GLN cc_start: 0.8502 (mt0) cc_final: 0.8255 (mp10) REVERT: D 392 ARG cc_start: 0.8860 (mtt180) cc_final: 0.8525 (ttm110) REVERT: E 52 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8075 (mm110) REVERT: E 137 MET cc_start: 0.8223 (tpt) cc_final: 0.7979 (tpt) REVERT: F 42 MET cc_start: 0.9138 (mtp) cc_final: 0.8802 (mmm) REVERT: F 51 MET cc_start: 0.9271 (mmm) cc_final: 0.8504 (mmm) REVERT: F 147 MET cc_start: 0.9100 (mmp) cc_final: 0.8821 (mmm) REVERT: F 157 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8392 (ptt) REVERT: G 16 MET cc_start: 0.8732 (mmm) cc_final: 0.8320 (mmm) REVERT: H 568 TYR cc_start: 0.1490 (OUTLIER) cc_final: 0.0739 (m-80) REVERT: H 718 ARG cc_start: 0.2730 (OUTLIER) cc_final: 0.2412 (ptp-110) REVERT: H 726 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7984 (pm20) REVERT: H 859 GLU cc_start: 0.8808 (tt0) cc_final: 0.8254 (tp30) REVERT: H 862 LYS cc_start: 0.9108 (mttt) cc_final: 0.8769 (mptt) REVERT: H 863 ARG cc_start: 0.8641 (ptp90) cc_final: 0.8306 (ptt-90) outliers start: 108 outliers final: 85 residues processed: 339 average time/residue: 0.1940 time to fit residues: 105.9243 Evaluate side-chains 338 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 242 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 448 HIS Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 593 THR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 643 ASN Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 680 CYS Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 718 ARG Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain I residue 310 ASN Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 247 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 203 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 318 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 595 ASN A 665 GLN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 HIS F 65 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 HIS ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.069923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.049652 restraints weight = 221671.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.050943 restraints weight = 120737.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.051769 restraints weight = 80487.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.052342 restraints weight = 61787.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.052757 restraints weight = 52350.925| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31919 Z= 0.187 Angle : 0.706 27.771 43616 Z= 0.341 Chirality : 0.043 0.552 4851 Planarity : 0.004 0.067 5228 Dihedral : 16.735 138.745 5168 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.35 % Allowed : 13.73 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: 0.98 (0.14), residues: 3550 helix: 1.52 (0.12), residues: 1793 sheet: -0.39 (0.27), residues: 388 loop : -0.09 (0.18), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG H 608 TYR 0.019 0.001 TYR H 189 PHE 0.033 0.002 PHE J 162 TRP 0.021 0.001 TRP H 603 HIS 0.009 0.001 HIS H 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 (31893) covalent geometry : angle 0.66569 / 0.34 (43577) hydrogen bonds : bond 0.04341 / 2.81 ( 1603) hydrogen bonds : angle 4.83069 / 3.45 ( 4539) metal coordination : bond 0.01497 / 0.89 ( 24) metal coordination : angle 7.89411 / 4.45 ( 39) Misc. bond : bond 0.00025 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 248 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 322 LYS cc_start: 0.8859 (tptp) cc_final: 0.8444 (tptp) REVERT: A 326 LYS cc_start: 0.8377 (mmtt) cc_final: 0.7862 (mptt) REVERT: A 373 GLN cc_start: 0.8685 (mt0) cc_final: 0.8272 (mm110) REVERT: A 380 MET cc_start: 0.9044 (ttm) cc_final: 0.8381 (ttm) REVERT: A 450 MET cc_start: 0.7666 (mmm) cc_final: 0.7139 (tpt) REVERT: A 470 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9043 (mt) REVERT: A 482 PHE cc_start: 0.7734 (t80) cc_final: 0.7493 (t80) REVERT: A 490 GLU cc_start: 0.8416 (tt0) cc_final: 0.7861 (tm-30) REVERT: A 518 PHE cc_start: 0.8866 (m-80) cc_final: 0.8547 (m-80) REVERT: A 530 ARG cc_start: 0.8856 (mtm180) cc_final: 0.8549 (mtm-85) REVERT: A 536 MET cc_start: 0.8911 (mmm) cc_final: 0.8555 (tpt) REVERT: A 540 LYS cc_start: 0.9441 (ttmt) cc_final: 0.9112 (ttpp) REVERT: A 569 LYS cc_start: 0.9163 (mmtp) cc_final: 0.8877 (mmtp) REVERT: A 589 ARG cc_start: 0.8967 (ttm170) cc_final: 0.8759 (ttp-170) REVERT: A 609 LYS cc_start: 0.9083 (tttt) cc_final: 0.8793 (ttpp) REVERT: A 613 THR cc_start: 0.6172 (OUTLIER) cc_final: 0.5681 (t) REVERT: A 668 GLN cc_start: 0.8934 (tt0) cc_final: 0.8654 (tp-100) REVERT: A 669 GLU cc_start: 0.8814 (tt0) cc_final: 0.8089 (tp30) REVERT: A 675 LYS cc_start: 0.9543 (ttmt) cc_final: 0.9253 (ttmm) REVERT: A 682 ASP cc_start: 0.8744 (m-30) cc_final: 0.8420 (m-30) REVERT: B 211 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7730 (t80) REVERT: B 384 HIS cc_start: 0.9468 (OUTLIER) cc_final: 0.9235 (p-80) REVERT: B 493 MET cc_start: 0.8868 (ptp) cc_final: 0.8643 (ptp) REVERT: B 527 MET cc_start: 0.9645 (mmm) cc_final: 0.9294 (mmm) REVERT: B 545 MET cc_start: 0.9594 (OUTLIER) cc_final: 0.8941 (ttm) REVERT: B 724 MET cc_start: 0.9017 (mmm) cc_final: 0.8810 (mmm) REVERT: C 307 PHE cc_start: 0.9490 (OUTLIER) cc_final: 0.9182 (m-10) REVERT: C 313 MET cc_start: 0.8835 (mmt) cc_final: 0.8580 (mmm) REVERT: D 34 LEU cc_start: 0.9205 (mt) cc_final: 0.8811 (mt) REVERT: D 57 MET cc_start: 0.8973 (mmm) cc_final: 0.8518 (mmm) REVERT: D 161 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.8378 (m-70) REVERT: D 205 LEU cc_start: 0.8944 (mt) cc_final: 0.8604 (tt) REVERT: D 363 GLN cc_start: 0.8572 (mt0) cc_final: 0.8274 (mp10) REVERT: D 392 ARG cc_start: 0.8930 (mtt180) cc_final: 0.8567 (ttm110) REVERT: E 52 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8251 (mm110) REVERT: E 137 MET cc_start: 0.8324 (tpt) cc_final: 0.8020 (tpt) REVERT: F 42 MET cc_start: 0.9199 (mtp) cc_final: 0.8845 (mmm) REVERT: F 51 MET cc_start: 0.9326 (mmm) cc_final: 0.8542 (mmm) REVERT: F 147 MET cc_start: 0.9186 (mmp) cc_final: 0.8867 (mmm) REVERT: F 157 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8362 (ptt) REVERT: F 175 MET cc_start: 0.9004 (ttm) cc_final: 0.8406 (mtp) REVERT: G 16 MET cc_start: 0.8844 (mmm) cc_final: 0.8320 (mmm) REVERT: H 568 TYR cc_start: 0.1583 (OUTLIER) cc_final: 0.0817 (m-80) REVERT: H 718 ARG cc_start: 0.2749 (OUTLIER) cc_final: 0.2376 (ptp-110) REVERT: H 726 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7970 (pm20) REVERT: H 859 GLU cc_start: 0.8829 (tt0) cc_final: 0.8273 (tp30) REVERT: H 862 LYS cc_start: 0.9112 (mttt) cc_final: 0.8770 (mptt) REVERT: H 863 ARG cc_start: 0.8666 (ptp90) cc_final: 0.8331 (ptt-90) REVERT: I 287 GLN cc_start: 0.9592 (tp-100) cc_final: 0.9343 (mt0) outliers start: 106 outliers final: 85 residues processed: 336 average time/residue: 0.1945 time to fit residues: 105.7248 Evaluate side-chains 335 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 239 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 448 HIS Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 593 THR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 643 ASN Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 680 CYS Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 718 ARG Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 229 optimal weight: 7.9990 chunk 293 optimal weight: 40.0000 chunk 22 optimal weight: 1.9990 chunk 318 optimal weight: 6.9990 chunk 312 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 340 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 240 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 595 ASN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 HIS ** 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 = 0.3802 r_free = 0.3802 target = 0.070560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.050406 restraints weight = 220360.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.051754 restraints weight = 119499.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.052646 restraints weight = 79171.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.053176 restraints weight = 60206.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.053441 restraints weight = 50641.713| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31919 Z= 0.147 Angle : 0.699 27.228 43616 Z= 0.335 Chirality : 0.042 0.505 4851 Planarity : 0.004 0.050 5228 Dihedral : 16.721 138.280 5166 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.04 % Allowed : 14.23 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.14), residues: 3550 helix: 1.61 (0.12), residues: 1796 sheet: -0.35 (0.27), residues: 386 loop : -0.10 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 671 TYR 0.021 0.001 TYR A 95 PHE 0.032 0.001 PHE J 162 TRP 0.027 0.002 TRP H 603 HIS 0.005 0.001 HIS G 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (31893) covalent geometry : angle 0.66298 / 0.33 (43577) hydrogen bonds : bond 0.03988 / 2.60 ( 1603) hydrogen bonds : angle 4.73080 / 3.38 ( 4539) metal coordination : bond 0.01191 / 0.72 ( 24) metal coordination : angle 7.40298 / 4.17 ( 39) Misc. bond : bond 0.00015 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 249 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8122 (mmtm) REVERT: A 373 GLN cc_start: 0.8713 (mt0) cc_final: 0.8225 (mm110) REVERT: A 380 MET cc_start: 0.9040 (ttm) cc_final: 0.8386 (ttm) REVERT: A 450 MET cc_start: 0.7557 (mmm) cc_final: 0.7023 (tpt) REVERT: A 490 GLU cc_start: 0.8467 (tt0) cc_final: 0.7878 (tm-30) REVERT: A 518 PHE cc_start: 0.8858 (m-80) cc_final: 0.8585 (m-80) REVERT: A 519 TYR cc_start: 0.7923 (t80) cc_final: 0.7589 (t80) REVERT: A 530 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8532 (mtm-85) REVERT: A 536 MET cc_start: 0.8863 (mmm) cc_final: 0.8423 (tpt) REVERT: A 569 LYS cc_start: 0.9156 (mmtp) cc_final: 0.8953 (mmtm) REVERT: A 609 LYS cc_start: 0.9078 (tttt) cc_final: 0.8786 (ttpp) REVERT: A 613 THR cc_start: 0.6149 (OUTLIER) cc_final: 0.5669 (t) REVERT: A 668 GLN cc_start: 0.8911 (tt0) cc_final: 0.8595 (tp40) REVERT: A 669 GLU cc_start: 0.8735 (tt0) cc_final: 0.8135 (tp30) REVERT: A 675 LYS cc_start: 0.9538 (ttmt) cc_final: 0.9008 (ttmm) REVERT: A 682 ASP cc_start: 0.8712 (m-30) cc_final: 0.8344 (t0) REVERT: A 717 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9383 (mp) REVERT: B 211 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7626 (t80) REVERT: B 384 HIS cc_start: 0.9485 (OUTLIER) cc_final: 0.9254 (p-80) REVERT: B 527 MET cc_start: 0.9645 (mmm) cc_final: 0.9289 (mmm) REVERT: B 545 MET cc_start: 0.9589 (OUTLIER) cc_final: 0.9312 (ttp) REVERT: B 724 MET cc_start: 0.9045 (mmm) cc_final: 0.8819 (mmm) REVERT: C 307 PHE cc_start: 0.9488 (OUTLIER) cc_final: 0.9169 (m-10) REVERT: C 313 MET cc_start: 0.8816 (mmt) cc_final: 0.8564 (mmm) REVERT: D 34 LEU cc_start: 0.9197 (mt) cc_final: 0.8786 (mt) REVERT: D 57 MET cc_start: 0.8944 (mmm) cc_final: 0.8474 (mmm) REVERT: D 161 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8336 (m-70) REVERT: D 201 PHE cc_start: 0.8792 (m-80) cc_final: 0.8510 (m-80) REVERT: D 205 LEU cc_start: 0.8901 (mt) cc_final: 0.8546 (tt) REVERT: D 363 GLN cc_start: 0.8555 (mt0) cc_final: 0.8265 (mp10) REVERT: D 392 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8532 (ttm110) REVERT: D 441 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7274 (tpt) REVERT: E 52 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8187 (mm110) REVERT: E 137 MET cc_start: 0.8292 (tpt) cc_final: 0.8056 (tpt) REVERT: F 42 MET cc_start: 0.9186 (mtp) cc_final: 0.8836 (mmm) REVERT: F 51 MET cc_start: 0.9313 (mmm) cc_final: 0.8598 (mmm) REVERT: F 147 MET cc_start: 0.9199 (mmp) cc_final: 0.8879 (mmm) REVERT: F 157 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8321 (ptt) REVERT: F 175 MET cc_start: 0.8953 (ttm) cc_final: 0.8408 (mtp) REVERT: G 16 MET cc_start: 0.8860 (mmm) cc_final: 0.8597 (mmm) REVERT: H 568 TYR cc_start: 0.1763 (OUTLIER) cc_final: 0.0958 (m-80) REVERT: H 726 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7978 (pm20) REVERT: H 859 GLU cc_start: 0.8771 (tt0) cc_final: 0.8449 (tp30) REVERT: H 862 LYS cc_start: 0.9059 (mttt) cc_final: 0.8720 (mptt) REVERT: I 287 GLN cc_start: 0.9601 (tp-100) cc_final: 0.9360 (mt0) REVERT: I 327 MET cc_start: 0.3396 (mtt) cc_final: 0.3194 (mtt) outliers start: 96 outliers final: 77 residues processed: 326 average time/residue: 0.1881 time to fit residues: 99.3767 Evaluate side-chains 330 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 242 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 448 HIS Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 593 THR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 643 ASN Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 208 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 210 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 264 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 595 ASN ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.069229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.049004 restraints weight = 223698.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.050286 restraints weight = 121706.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.051101 restraints weight = 80839.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.051699 restraints weight = 62179.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.051955 restraints weight = 52934.504| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 31919 Z= 0.239 Angle : 0.759 27.754 43616 Z= 0.371 Chirality : 0.044 0.756 4851 Planarity : 0.004 0.100 5228 Dihedral : 16.801 138.314 5166 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.91 % Allowed : 14.67 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: 0.81 (0.14), residues: 3550 helix: 1.39 (0.12), residues: 1802 sheet: -0.41 (0.27), residues: 389 loop : -0.23 (0.18), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 400 TYR 0.021 0.002 TYR A 163 PHE 0.028 0.002 PHE J 162 TRP 0.079 0.002 TRP B 552 HIS 0.006 0.001 HIS H 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.24 (31893) covalent geometry : angle 0.72089 / 0.37 (43577) hydrogen bonds : bond 0.04713 / 3.04 ( 1603) hydrogen bonds : angle 4.95508 / 3.55 ( 4539) metal coordination : bond 0.01737 / 1.03 ( 24) metal coordination : angle 7.97992 / 4.44 ( 39) Misc. bond : bond 0.00033 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 241 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.8393 (mmtt) cc_final: 0.8167 (mmtm) REVERT: A 373 GLN cc_start: 0.8659 (mt0) cc_final: 0.8278 (mm110) REVERT: A 380 MET cc_start: 0.9066 (ttm) cc_final: 0.8380 (ttm) REVERT: A 450 MET cc_start: 0.7612 (mmm) cc_final: 0.7126 (tpt) REVERT: A 490 GLU cc_start: 0.8345 (tt0) cc_final: 0.7865 (tm-30) REVERT: A 518 PHE cc_start: 0.8856 (m-80) cc_final: 0.8577 (m-80) REVERT: A 519 TYR cc_start: 0.7896 (t80) cc_final: 0.7509 (t80) REVERT: A 530 ARG cc_start: 0.8877 (mtm180) cc_final: 0.8599 (mtm-85) REVERT: A 536 MET cc_start: 0.8866 (mmm) cc_final: 0.8445 (tpt) REVERT: A 609 LYS cc_start: 0.9064 (tttt) cc_final: 0.8778 (ttpp) REVERT: A 613 THR cc_start: 0.6073 (OUTLIER) cc_final: 0.5633 (t) REVERT: A 668 GLN cc_start: 0.9035 (tt0) cc_final: 0.8625 (tp40) REVERT: A 669 GLU cc_start: 0.8776 (tt0) cc_final: 0.8164 (tp30) REVERT: A 675 LYS cc_start: 0.9581 (ttmt) cc_final: 0.9365 (ttpt) REVERT: A 678 ARG cc_start: 0.8462 (ptp90) cc_final: 0.8020 (ptp90) REVERT: A 682 ASP cc_start: 0.8743 (m-30) cc_final: 0.8405 (m-30) REVERT: A 696 MET cc_start: 0.8648 (mmm) cc_final: 0.8328 (mmm) REVERT: A 717 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9379 (mp) REVERT: B 211 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7592 (t80) REVERT: B 384 HIS cc_start: 0.9483 (OUTLIER) cc_final: 0.9257 (p-80) REVERT: B 527 MET cc_start: 0.9653 (mmm) cc_final: 0.9303 (mmm) REVERT: B 677 MET cc_start: 0.9274 (mtm) cc_final: 0.8873 (mtm) REVERT: B 724 MET cc_start: 0.9033 (mmm) cc_final: 0.8831 (mmm) REVERT: C 307 PHE cc_start: 0.9495 (OUTLIER) cc_final: 0.9184 (m-10) REVERT: C 313 MET cc_start: 0.8849 (mmt) cc_final: 0.8577 (mmm) REVERT: D 34 LEU cc_start: 0.9192 (mt) cc_final: 0.8807 (mt) REVERT: D 57 MET cc_start: 0.8972 (mmm) cc_final: 0.8550 (mmm) REVERT: D 161 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.8377 (m-70) REVERT: D 205 LEU cc_start: 0.8910 (mt) cc_final: 0.8610 (tt) REVERT: D 363 GLN cc_start: 0.8521 (mt0) cc_final: 0.8178 (mp10) REVERT: D 392 ARG cc_start: 0.8886 (mtt180) cc_final: 0.8540 (ttm110) REVERT: D 441 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7289 (tpt) REVERT: E 52 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8185 (mm110) REVERT: F 42 MET cc_start: 0.9166 (mtp) cc_final: 0.8834 (mmm) REVERT: F 51 MET cc_start: 0.9315 (mmm) cc_final: 0.8621 (mmm) REVERT: F 147 MET cc_start: 0.9131 (mmp) cc_final: 0.8777 (mmp) REVERT: F 157 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8381 (ptm) REVERT: F 175 MET cc_start: 0.8939 (ttm) cc_final: 0.8449 (mtp) REVERT: G 16 MET cc_start: 0.8993 (mmm) cc_final: 0.8490 (mmm) REVERT: H 568 TYR cc_start: 0.1683 (OUTLIER) cc_final: 0.0938 (m-80) REVERT: H 726 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7978 (pm20) REVERT: H 859 GLU cc_start: 0.8801 (tt0) cc_final: 0.8492 (tp30) REVERT: H 862 LYS cc_start: 0.9108 (mttt) cc_final: 0.8774 (mptt) REVERT: I 287 GLN cc_start: 0.9597 (tp-100) cc_final: 0.9373 (mt0) outliers start: 92 outliers final: 80 residues processed: 316 average time/residue: 0.1887 time to fit residues: 96.7240 Evaluate side-chains 325 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 235 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 63 TYR Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 201 HIS Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain D residue 448 HIS Chi-restraints excluded: chain E residue 11 TRP Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 157 MET Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 189 TYR Chi-restraints excluded: chain H residue 251 THR Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 543 VAL Chi-restraints excluded: chain H residue 568 TYR Chi-restraints excluded: chain H residue 593 THR Chi-restraints excluded: chain H residue 598 VAL Chi-restraints excluded: chain H residue 636 THR Chi-restraints excluded: chain H residue 643 ASN Chi-restraints excluded: chain H residue 649 LEU Chi-restraints excluded: chain H residue 660 TYR Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 792 GLN Chi-restraints excluded: chain H residue 799 PHE Chi-restraints excluded: chain H residue 845 LEU Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 108 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 331 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 595 ASN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 773 GLN ** 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 = 0.3785 r_free = 0.3785 target = 0.069759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.049852 restraints weight = 223569.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.051204 restraints weight = 120364.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.051999 restraints weight = 79198.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.052644 restraints weight = 60562.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.052944 restraints weight = 51179.718| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31919 Z= 0.184 Angle : 0.727 29.004 43616 Z= 0.350 Chirality : 0.043 0.570 4851 Planarity : 0.004 0.082 5228 Dihedral : 16.835 137.439 5166 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.00 % Allowed : 14.52 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: 0.84 (0.14), residues: 3550 helix: 1.44 (0.12), residues: 1804 sheet: -0.42 (0.27), residues: 391 loop : -0.24 (0.18), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 400 TYR 0.018 0.001 TYR A 163 PHE 0.035 0.002 PHE A 482 TRP 0.056 0.002 TRP B 552 HIS 0.005 0.001 HIS H 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (31893) covalent geometry : angle 0.68685 / 0.35 (43577) hydrogen bonds : bond 0.04338 / 2.81 ( 1603) hydrogen bonds : angle 4.87106 / 3.48 ( 4539) metal coordination : bond 0.01455 / 0.87 ( 24) metal coordination : angle 8.03661 / 4.45 ( 39) Misc. bond : bond 0.00023 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7725.17 seconds wall clock time: 133 minutes 18.10 seconds (7998.10 seconds total)