Starting phenix.real_space_refine on Sun Jul 5 23:42:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s0a_19619/07_2026/8s0a_19619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s0a_19619/07_2026/8s0a_19619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8s0a_19619/07_2026/8s0a_19619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s0a_19619/07_2026/8s0a_19619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s0a_19619/07_2026/8s0a_19619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s0a_19619/07_2026/8s0a_19619.map" } resolution = 3.2 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= 0.003 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 55 5.49 5 Mg 5 5.21 5 S 180 5.16 5 C 19577 2.51 5 N 5591 2.21 5 O 6020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 31433 Number of models: 1 Model: "" Number of chains: 14 Chain: "X" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "Y" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "2" Number of atoms: 5516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5516 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 30, 'TRANS': 663} Chain breaks: 2 Chain: "3" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4794 Classifications: {'peptide': 609} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 588} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "4" Number of atoms: 4969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4969 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 28, 'TRANS': 594} Chain breaks: 1 Chain: "5" Number of atoms: 5307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5307 Classifications: {'peptide': 669} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 642} Chain breaks: 4 Chain: "6" Number of atoms: 5386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5386 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 21, 'TRANS': 646} Chain breaks: 5 Chain: "7" Number of atoms: 4410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4410 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 25, 'TRANS': 532} Chain breaks: 6 Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2118 SG CYS 2 329 87.499 95.370 27.603 1.00 85.18 S ATOM 2141 SG CYS 2 332 89.776 97.408 25.734 1.00 80.95 S ATOM 2292 SG CYS 2 352 85.856 98.360 25.563 1.00 82.63 S ATOM 2314 SG CYS 2 355 87.467 95.463 23.932 1.00 82.47 S ATOM 12495 SG CYS 4 306 43.925 73.892 18.055 1.00 87.46 S ATOM 12517 SG CYS 4 309 40.665 73.558 16.340 1.00 84.38 S ATOM 12663 SG CYS 4 328 43.420 70.854 15.695 1.00 85.77 S ATOM 12684 SG CYS 4 331 43.927 73.954 14.411 1.00 85.27 S ATOM 17328 SG CYS 5 172 97.111 74.807 26.056 1.00 87.27 S ATOM 17351 SG CYS 5 175 100.015 75.297 23.768 1.00 83.41 S ATOM 17522 SG CYS 5 197 97.221 78.081 23.985 1.00 80.89 S ATOM 22656 SG CYS 6 158 57.524 85.608 18.435 1.00 84.64 S ATOM 22678 SG CYS 6 161 55.931 86.555 15.253 1.00 82.39 S ATOM 22839 SG CYS 6 180 54.360 83.749 17.405 1.00 82.74 S ATOM 22878 SG CYS 6 185 57.525 83.261 15.498 1.00 78.50 S ATOM 28215 SG CYS 7 184 58.954 48.528 20.068 1.00 87.25 S ATOM 28238 SG CYS 7 187 59.663 45.281 18.626 1.00 82.96 S ATOM 28384 SG CYS 7 206 62.352 47.792 19.968 1.00 84.23 S ATOM 28421 SG CYS 7 211 60.791 48.294 16.705 1.00 79.55 S Time building chain proxies: 6.21, per 1000 atoms: 0.20 Number of scatterers: 31433 At special positions: 0 Unit cell: (143.64, 145.8, 156.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 180 16.00 P 55 15.00 Mg 5 11.99 O 6020 8.00 N 5591 7.00 C 19577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21003 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 332 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 352 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 329 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 355 " pdb=" ZN 4 901 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 306 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 328 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 309 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 331 " pdb=" ZN 5 803 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 172 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 175 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 197 " pdb=" ZN 6 903 " pdb="ZN ZN 6 903 " - pdb=" SG CYS 6 185 " pdb="ZN ZN 6 903 " - pdb=" SG CYS 6 158 " pdb="ZN ZN 6 903 " - pdb=" SG CYS 6 161 " pdb="ZN ZN 6 903 " - pdb=" SG CYS 6 180 " pdb=" ZN 7 803 " pdb="ZN ZN 7 803 " - pdb=" SG CYS 7 184 " pdb="ZN ZN 7 803 " - pdb=" SG CYS 7 211 " pdb="ZN ZN 7 803 " - pdb=" SG CYS 7 187 " pdb="ZN ZN 7 803 " - pdb=" SG CYS 7 206 " Number of angles added : 24 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7276 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 42 sheets defined 47.1% alpha, 17.5% beta 21 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain '2' and resid 181 through 188 removed outlier: 3.912A pdb=" N MET 2 188 " --> pdb=" O GLU 2 184 " (cutoff:3.500A) Processing helix chain '2' and resid 188 through 206 Processing helix chain '2' and resid 213 through 225 removed outlier: 3.571A pdb=" N GLU 2 217 " --> pdb=" O ASN 2 213 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU 2 225 " --> pdb=" O ASP 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 233 through 241 Processing helix chain '2' and resid 241 through 248 removed outlier: 3.731A pdb=" N ALA 2 245 " --> pdb=" O GLU 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 251 through 271 removed outlier: 3.628A pdb=" N LEU 2 255 " --> pdb=" O ALA 2 251 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 278 removed outlier: 3.711A pdb=" N ILE 2 277 " --> pdb=" O LYS 2 273 " (cutoff:3.500A) Processing helix chain '2' and resid 298 through 302 Processing helix chain '2' and resid 381 through 385 Processing helix chain '2' and resid 401 through 403 No H-bonds generated for 'chain '2' and resid 401 through 403' Processing helix chain '2' and resid 459 through 469 Processing helix chain '2' and resid 472 through 481 removed outlier: 3.603A pdb=" N ILE 2 481 " --> pdb=" O ILE 2 477 " (cutoff:3.500A) Processing helix chain '2' and resid 488 through 501 Processing helix chain '2' and resid 528 through 540 removed outlier: 4.095A pdb=" N PHE 2 532 " --> pdb=" O ALA 2 528 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU 2 533 " --> pdb=" O LYS 2 529 " (cutoff:3.500A) Processing helix chain '2' and resid 574 through 579 Processing helix chain '2' and resid 588 through 592 removed outlier: 4.086A pdb=" N MET 2 592 " --> pdb=" O PHE 2 589 " (cutoff:3.500A) Processing helix chain '2' and resid 593 through 606 Processing helix chain '2' and resid 643 through 647 Processing helix chain '2' and resid 650 through 657 removed outlier: 3.598A pdb=" N ARG 2 656 " --> pdb=" O PRO 2 652 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE 2 657 " --> pdb=" O ILE 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 668 through 686 Processing helix chain '2' and resid 716 through 731 Processing helix chain '2' and resid 739 through 758 removed outlier: 3.700A pdb=" N VAL 2 743 " --> pdb=" O ASP 2 739 " (cutoff:3.500A) Processing helix chain '2' and resid 763 through 781 removed outlier: 4.314A pdb=" N ILE 2 767 " --> pdb=" O THR 2 763 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 805 removed outlier: 3.707A pdb=" N THR 2 805 " --> pdb=" O SER 2 801 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 818 Processing helix chain '2' and resid 818 through 823 Processing helix chain '2' and resid 827 through 852 Processing helix chain '2' and resid 862 through 872 Processing helix chain '2' and resid 877 through 883 Processing helix chain '2' and resid 883 through 889 removed outlier: 3.773A pdb=" N ARG 2 887 " --> pdb=" O SER 2 883 " (cutoff:3.500A) Processing helix chain '3' and resid 11 through 24 removed outlier: 3.682A pdb=" N ASP 3 24 " --> pdb=" O LEU 3 20 " (cutoff:3.500A) Processing helix chain '3' and resid 25 through 29 removed outlier: 3.847A pdb=" N GLN 3 29 " --> pdb=" O GLU 3 26 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 42 Processing helix chain '3' and resid 51 through 58 Processing helix chain '3' and resid 58 through 68 Processing helix chain '3' and resid 69 through 93 removed outlier: 7.914A pdb=" N THR 3 90 " --> pdb=" O SER 3 86 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N TYR 3 91 " --> pdb=" O ILE 3 87 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA 3 92 " --> pdb=" O ASP 3 88 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS 3 93 " --> pdb=" O ALA 3 89 " (cutoff:3.500A) Processing helix chain '3' and resid 106 through 110 removed outlier: 3.894A pdb=" N LYS 3 109 " --> pdb=" O PHE 3 106 " (cutoff:3.500A) Processing helix chain '3' and resid 112 through 116 removed outlier: 3.653A pdb=" N LEU 3 116 " --> pdb=" O PRO 3 113 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 121 Processing helix chain '3' and resid 224 through 229 removed outlier: 4.649A pdb=" N ASP 3 227 " --> pdb=" O ASP 3 224 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS 3 228 " --> pdb=" O LEU 3 225 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA 3 229 " --> pdb=" O VAL 3 226 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 224 through 229' Processing helix chain '3' and resid 279 through 292 removed outlier: 4.117A pdb=" N LYS 3 283 " --> pdb=" O GLU 3 279 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 302 removed outlier: 4.442A pdb=" N ASP 3 297 " --> pdb=" O LYS 3 293 " (cutoff:3.500A) Processing helix chain '3' and resid 310 through 323 Processing helix chain '3' and resid 350 through 362 removed outlier: 3.723A pdb=" N LEU 3 354 " --> pdb=" O ALA 3 350 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 379 Processing helix chain '3' and resid 396 through 401 Processing helix chain '3' and resid 410 through 414 Processing helix chain '3' and resid 415 through 429 removed outlier: 3.963A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL 3 425 " --> pdb=" O ALA 3 421 " (cutoff:3.500A) Processing helix chain '3' and resid 464 through 470 Processing helix chain '3' and resid 472 through 479 Processing helix chain '3' and resid 490 through 507 Processing helix chain '3' and resid 555 through 560 removed outlier: 3.922A pdb=" N LYS 3 559 " --> pdb=" O LYS 3 556 " (cutoff:3.500A) Processing helix chain '3' and resid 564 through 578 Processing helix chain '3' and resid 583 through 600 removed outlier: 3.644A pdb=" N ALA 3 587 " --> pdb=" O THR 3 583 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR 3 588 " --> pdb=" O GLN 3 584 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR 3 589 " --> pdb=" O GLU 3 585 " (cutoff:3.500A) Processing helix chain '3' and resid 601 through 603 No H-bonds generated for 'chain '3' and resid 601 through 603' Processing helix chain '3' and resid 614 through 632 removed outlier: 4.224A pdb=" N LEU 3 618 " --> pdb=" O THR 3 614 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU 3 619 " --> pdb=" O ALA 3 615 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG 3 632 " --> pdb=" O HIS 3 628 " (cutoff:3.500A) Processing helix chain '3' and resid 638 through 653 removed outlier: 3.671A pdb=" N ALA 3 645 " --> pdb=" O ASP 3 641 " (cutoff:3.500A) Processing helix chain '4' and resid 158 through 173 removed outlier: 3.698A pdb=" N GLN 4 171 " --> pdb=" O GLN 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 191 through 204 removed outlier: 3.554A pdb=" N GLN 4 195 " --> pdb=" O PRO 4 191 " (cutoff:3.500A) Processing helix chain '4' and resid 212 through 219 Processing helix chain '4' and resid 219 through 229 removed outlier: 4.049A pdb=" N TYR 4 223 " --> pdb=" O ASP 4 219 " (cutoff:3.500A) Processing helix chain '4' and resid 229 through 249 Proline residue: 4 235 - end of helix Processing helix chain '4' and resid 270 through 274 Processing helix chain '4' and resid 275 through 279 Processing helix chain '4' and resid 377 through 379 No H-bonds generated for 'chain '4' and resid 377 through 379' Processing helix chain '4' and resid 431 through 436 removed outlier: 3.605A pdb=" N ALA 4 436 " --> pdb=" O LEU 4 432 " (cutoff:3.500A) Processing helix chain '4' and resid 442 through 455 removed outlier: 3.984A pdb=" N LYS 4 455 " --> pdb=" O GLU 4 451 " (cutoff:3.500A) Processing helix chain '4' and resid 457 through 466 Processing helix chain '4' and resid 473 through 486 Processing helix chain '4' and resid 515 through 527 Processing helix chain '4' and resid 536 through 538 No H-bonds generated for 'chain '4' and resid 536 through 538' Processing helix chain '4' and resid 561 through 566 Processing helix chain '4' and resid 575 through 579 Processing helix chain '4' and resid 580 through 594 removed outlier: 3.819A pdb=" N VAL 4 586 " --> pdb=" O SER 4 582 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU 4 587 " --> pdb=" O THR 4 583 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU 4 589 " --> pdb=" O SER 4 585 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU 4 592 " --> pdb=" O HIS 4 588 " (cutoff:3.500A) Processing helix chain '4' and resid 629 through 635 Processing helix chain '4' and resid 637 through 643 removed outlier: 3.702A pdb=" N ARG 4 643 " --> pdb=" O THR 4 639 " (cutoff:3.500A) Processing helix chain '4' and resid 655 through 669 Processing helix chain '4' and resid 683 through 696 Processing helix chain '4' and resid 703 through 722 Processing helix chain '4' and resid 730 through 748 removed outlier: 3.887A pdb=" N LEU 4 734 " --> pdb=" O TYR 4 730 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU 4 735 " --> pdb=" O PRO 4 731 " (cutoff:3.500A) Processing helix chain '4' and resid 754 through 769 removed outlier: 3.553A pdb=" N VAL 4 758 " --> pdb=" O GLU 4 754 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU 4 769 " --> pdb=" O HIS 4 765 " (cutoff:3.500A) Processing helix chain '5' and resid 27 through 42 Processing helix chain '5' and resid 53 through 66 Processing helix chain '5' and resid 74 through 81 Processing helix chain '5' and resid 81 through 91 removed outlier: 3.727A pdb=" N ALA 5 85 " --> pdb=" O ASP 5 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR 5 89 " --> pdb=" O ALA 5 85 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS 5 90 " --> pdb=" O ASP 5 86 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 111 removed outlier: 3.549A pdb=" N HIS 5 95 " --> pdb=" O GLN 5 91 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) Processing helix chain '5' and resid 136 through 140 Processing helix chain '5' and resid 141 through 145 Processing helix chain '5' and resid 216 through 219 removed outlier: 4.065A pdb=" N CYS 5 219 " --> pdb=" O PRO 5 216 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 216 through 219' Processing helix chain '5' and resid 252 through 254 No H-bonds generated for 'chain '5' and resid 252 through 254' Processing helix chain '5' and resid 317 through 327 removed outlier: 3.567A pdb=" N GLU 5 321 " --> pdb=" O GLN 5 317 " (cutoff:3.500A) Processing helix chain '5' and resid 330 through 339 Processing helix chain '5' and resid 346 through 359 Processing helix chain '5' and resid 387 through 398 Processing helix chain '5' and resid 432 through 437 removed outlier: 3.771A pdb=" N ALA 5 437 " --> pdb=" O ALA 5 433 " (cutoff:3.500A) Processing helix chain '5' and resid 446 through 450 removed outlier: 3.514A pdb=" N LYS 5 449 " --> pdb=" O GLU 5 446 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET 5 450 " --> pdb=" O PHE 5 447 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 446 through 450' Processing helix chain '5' and resid 451 through 464 removed outlier: 3.578A pdb=" N HIS 5 459 " --> pdb=" O ARG 5 455 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU 5 460 " --> pdb=" O VAL 5 456 " (cutoff:3.500A) Processing helix chain '5' and resid 507 through 514 removed outlier: 3.803A pdb=" N ARG 5 513 " --> pdb=" O THR 5 509 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE 5 514 " --> pdb=" O ILE 5 510 " (cutoff:3.500A) Processing helix chain '5' and resid 525 through 543 removed outlier: 3.983A pdb=" N VAL 5 530 " --> pdb=" O GLU 5 526 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET 5 531 " --> pdb=" O GLU 5 527 " (cutoff:3.500A) Processing helix chain '5' and resid 555 through 570 removed outlier: 3.774A pdb=" N CYS 5 570 " --> pdb=" O CYS 5 566 " (cutoff:3.500A) Processing helix chain '5' and resid 575 through 601 Processing helix chain '5' and resid 609 through 627 removed outlier: 3.573A pdb=" N LEU 5 613 " --> pdb=" O THR 5 609 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS 5 627 " --> pdb=" O LEU 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 633 through 654 removed outlier: 4.015A pdb=" N ASP 5 650 " --> pdb=" O VAL 5 646 " (cutoff:3.500A) Processing helix chain '5' and resid 668 through 683 Processing helix chain '5' and resid 691 through 701 Processing helix chain '5' and resid 704 through 719 removed outlier: 3.538A pdb=" N ILE 5 708 " --> pdb=" O PRO 5 704 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 37 Processing helix chain '6' and resid 44 through 51 removed outlier: 3.828A pdb=" N GLN 6 48 " --> pdb=" O ILE 6 44 " (cutoff:3.500A) Processing helix chain '6' and resid 52 through 55 removed outlier: 3.771A pdb=" N ARG 6 55 " --> pdb=" O GLU 6 52 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 52 through 55' Processing helix chain '6' and resid 64 through 70 removed outlier: 3.794A pdb=" N LEU 6 68 " --> pdb=" O SER 6 64 " (cutoff:3.500A) Processing helix chain '6' and resid 72 through 82 Processing helix chain '6' and resid 82 through 102 Proline residue: 6 88 - end of helix Processing helix chain '6' and resid 122 through 126 Processing helix chain '6' and resid 127 through 131 Processing helix chain '6' and resid 211 through 215 Processing helix chain '6' and resid 229 through 234 Processing helix chain '6' and resid 322 through 329 Processing helix chain '6' and resid 330 through 342 Processing helix chain '6' and resid 345 through 355 removed outlier: 4.229A pdb=" N CYS 6 351 " --> pdb=" O TYR 6 347 " (cutoff:3.500A) Processing helix chain '6' and resid 361 through 374 Processing helix chain '6' and resid 403 through 413 Processing helix chain '6' and resid 422 through 424 No H-bonds generated for 'chain '6' and resid 422 through 424' Processing helix chain '6' and resid 447 through 452 Processing helix chain '6' and resid 461 through 465 removed outlier: 3.597A pdb=" N MET 6 465 " --> pdb=" O PHE 6 462 " (cutoff:3.500A) Processing helix chain '6' and resid 466 through 480 Processing helix chain '6' and resid 523 through 530 removed outlier: 3.801A pdb=" N PHE 6 530 " --> pdb=" O ILE 6 526 " (cutoff:3.500A) Processing helix chain '6' and resid 541 through 558 Processing helix chain '6' and resid 568 through 580 Processing helix chain '6' and resid 587 through 604 removed outlier: 3.682A pdb=" N ASP 6 592 " --> pdb=" O LYS 6 588 " (cutoff:3.500A) Processing helix chain '6' and resid 617 through 636 removed outlier: 3.697A pdb=" N LEU 6 621 " --> pdb=" O THR 6 617 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 656 removed outlier: 3.642A pdb=" N VAL 6 645 " --> pdb=" O GLN 6 641 " (cutoff:3.500A) Processing helix chain '6' and resid 718 through 738 Processing helix chain '6' and resid 744 through 757 Processing helix chain '6' and resid 762 through 783 Processing helix chain '7' and resid 5 through 19 removed outlier: 4.024A pdb=" N GLU 7 9 " --> pdb=" O ASP 7 5 " (cutoff:3.500A) Processing helix chain '7' and resid 31 through 42 Processing helix chain '7' and resid 52 through 56 Processing helix chain '7' and resid 60 through 69 Processing helix chain '7' and resid 69 through 89 Proline residue: 7 86 - end of helix Processing helix chain '7' and resid 97 through 109 Processing helix chain '7' and resid 127 through 132 removed outlier: 3.619A pdb=" N MET 7 131 " --> pdb=" O PRO 7 127 " (cutoff:3.500A) Processing helix chain '7' and resid 148 through 152 removed outlier: 3.725A pdb=" N VAL 7 152 " --> pdb=" O ILE 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 153 through 157 Processing helix chain '7' and resid 208 through 215 Processing helix chain '7' and resid 260 through 262 No H-bonds generated for 'chain '7' and resid 260 through 262' Processing helix chain '7' and resid 347 through 350 Processing helix chain '7' and resid 351 through 360 Processing helix chain '7' and resid 386 through 398 removed outlier: 4.235A pdb=" N LEU 7 390 " --> pdb=" O ALA 7 386 " (cutoff:3.500A) Processing helix chain '7' and resid 406 through 414 removed outlier: 7.550A pdb=" N GLY 7 411 " --> pdb=" O GLY 7 408 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL 7 412 " --> pdb=" O SER 7 409 " (cutoff:3.500A) Processing helix chain '7' and resid 432 through 437 Processing helix chain '7' and resid 446 through 450 Processing helix chain '7' and resid 451 through 465 Processing helix chain '7' and resid 508 through 515 removed outlier: 3.849A pdb=" N LEU 7 512 " --> pdb=" O PRO 7 508 " (cutoff:3.500A) Processing helix chain '7' and resid 526 through 544 Processing helix chain '7' and resid 555 through 567 Processing helix chain '7' and resid 576 through 595 removed outlier: 3.997A pdb=" N TYR 7 580 " --> pdb=" O SER 7 576 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA 7 583 " --> pdb=" O ASP 7 579 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET 7 588 " --> pdb=" O ALA 7 584 " (cutoff:3.500A) Processing helix chain '7' and resid 602 through 620 removed outlier: 3.759A pdb=" N LEU 7 606 " --> pdb=" O SER 7 602 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 642 removed outlier: 3.709A pdb=" N VAL 7 630 " --> pdb=" O GLU 7 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 229 through 232 Processing sheet with id=AA2, first strand: chain '2' and resid 319 through 323 removed outlier: 9.463A pdb=" N ILE 2 439 " --> pdb=" O SER 2 393 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP 2 395 " --> pdb=" O ILE 2 439 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ALA 2 441 " --> pdb=" O ASP 2 395 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE 2 397 " --> pdb=" O ALA 2 441 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N HIS 2 443 " --> pdb=" O ILE 2 397 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N LEU 2 399 " --> pdb=" O HIS 2 443 " (cutoff:3.500A) removed outlier: 12.928A pdb=" N ALA 2 445 " --> pdb=" O LEU 2 399 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR 2 415 " --> pdb=" O ASN 2 442 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL 2 444 " --> pdb=" O GLU 2 413 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU 2 413 " --> pdb=" O VAL 2 444 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG 2 377 " --> pdb=" O THR 2 313 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N CYS 2 315 " --> pdb=" O ARG 2 375 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ARG 2 375 " --> pdb=" O CYS 2 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 327 through 328 Processing sheet with id=AA4, first strand: chain '2' and resid 543 through 547 removed outlier: 6.432A pdb=" N ILE 2 544 " --> pdb=" O LEU 2 585 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASP 2 587 " --> pdb=" O ILE 2 544 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR 2 546 " --> pdb=" O ASP 2 587 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 559 through 562 Processing sheet with id=AA6, first strand: chain '2' and resid 608 through 613 Processing sheet with id=AA7, first strand: chain '2' and resid 858 through 861 Processing sheet with id=AA8, first strand: chain '3' and resid 46 through 50 removed outlier: 6.234A pdb=" N LEU 3 47 " --> pdb=" O GLY 3 101 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLU 3 103 " --> pdb=" O LEU 3 47 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL 3 49 " --> pdb=" O GLU 3 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain '3' and resid 124 through 134 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 124 through 134 current: chain '3' and resid 153 through 158 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 153 through 158 current: chain '3' and resid 216 through 222 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 216 through 222 current: chain '3' and resid 255 through 267 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 255 through 267 current: chain '5' and resid 178 through 183 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 178 through 183 current: chain '5' and resid 244 through 250 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 244 through 250 current: chain '5' and resid 292 through 301 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '3' and resid 251 through 252 Processing sheet with id=AB2, first strand: chain '3' and resid 327 through 328 removed outlier: 3.880A pdb=" N ARG 3 327 " --> pdb=" O ILE 3 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 365 through 367 removed outlier: 6.449A pdb=" N ILE 3 366 " --> pdb=" O CYS 3 407 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL 3 406 " --> pdb=" O LEU 3 449 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA 3 451 " --> pdb=" O VAL 3 406 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE 3 408 " --> pdb=" O ALA 3 451 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE 3 341 " --> pdb=" O VAL 3 448 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY 3 345 " --> pdb=" O ALA 3 452 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN 3 340 " --> pdb=" O LEU 3 481 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N PHE 3 483 " --> pdb=" O ASN 3 340 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU 3 342 " --> pdb=" O PHE 3 483 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N MET 3 485 " --> pdb=" O LEU 3 342 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE 3 344 " --> pdb=" O MET 3 485 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 381 through 384 Processing sheet with id=AB5, first strand: chain '3' and resid 430 through 435 Processing sheet with id=AB6, first strand: chain '3' and resid 608 through 609 Processing sheet with id=AB7, first strand: chain '4' and resid 207 through 211 removed outlier: 6.564A pdb=" N LEU 4 208 " --> pdb=" O ARG 4 261 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE 4 263 " --> pdb=" O LEU 4 208 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL 4 210 " --> pdb=" O PHE 4 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '4' and resid 312 through 316 removed outlier: 7.764A pdb=" N PHE 4 346 " --> pdb=" O PRO 4 297 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N MET 4 299 " --> pdb=" O SER 4 344 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N SER 4 344 " --> pdb=" O MET 4 299 " (cutoff:3.500A) removed outlier: 10.445A pdb=" N GLU 4 301 " --> pdb=" O ASN 4 342 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ASN 4 342 " --> pdb=" O GLU 4 301 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE 4 303 " --> pdb=" O ILE 4 340 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N HIS 4 368 " --> pdb=" O GLU 4 356 " (cutoff:3.500A) removed outlier: 11.294A pdb=" N THR 4 369 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N ILE 4 416 " --> pdb=" O THR 4 369 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE 4 371 " --> pdb=" O ILE 4 416 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL 4 418 " --> pdb=" O ILE 4 371 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE 4 373 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N HIS 4 420 " --> pdb=" O PHE 4 373 " (cutoff:3.500A) removed outlier: 10.315A pdb=" N HIS 4 375 " --> pdb=" O HIS 4 420 " (cutoff:3.500A) removed outlier: 13.478A pdb=" N ARG 4 422 " --> pdb=" O HIS 4 375 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR 4 391 " --> pdb=" O ILE 4 419 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR 4 421 " --> pdb=" O ASN 4 389 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN 4 389 " --> pdb=" O TYR 4 421 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS 4 353 " --> pdb=" O ILE 4 290 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR 4 292 " --> pdb=" O MET 4 351 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET 4 351 " --> pdb=" O THR 4 292 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 321 through 324 removed outlier: 3.616A pdb=" N ILE 4 322 " --> pdb=" O ARG 6 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 400 through 402 removed outlier: 7.964A pdb=" N ASN 4 407 " --> pdb=" O VAL 4 401 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 530 through 534 removed outlier: 6.456A pdb=" N GLN 4 531 " --> pdb=" O CYS 4 572 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ASP 4 574 " --> pdb=" O GLN 4 531 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR 4 533 " --> pdb=" O ASP 4 574 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE 4 506 " --> pdb=" O ALA 4 615 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ALA 4 617 " --> pdb=" O ILE 4 506 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU 4 508 " --> pdb=" O ALA 4 617 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU 4 507 " --> pdb=" O PHE 4 648 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N MET 4 650 " --> pdb=" O LEU 4 507 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N CYS 4 509 " --> pdb=" O MET 4 650 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '4' and resid 545 through 548 Processing sheet with id=AC4, first strand: chain '4' and resid 595 through 600 Processing sheet with id=AC5, first strand: chain '4' and resid 701 through 702 removed outlier: 6.901A pdb=" N ARG 4 701 " --> pdb=" O VAL 4 753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain '5' and resid 69 through 73 Processing sheet with id=AC7, first strand: chain '5' and resid 363 through 364 removed outlier: 3.910A pdb=" N LYS 5 363 " --> pdb=" O ARG 5 371 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '5' and resid 401 through 404 removed outlier: 6.524A pdb=" N VAL 5 402 " --> pdb=" O CYS 5 443 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL 5 442 " --> pdb=" O LEU 5 485 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ALA 5 487 " --> pdb=" O VAL 5 442 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE 5 444 " --> pdb=" O ALA 5 487 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY 5 381 " --> pdb=" O ALA 5 488 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN 5 376 " --> pdb=" O MET 5 516 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N PHE 5 518 " --> pdb=" O ASN 5 376 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU 5 378 " --> pdb=" O PHE 5 518 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL 5 520 " --> pdb=" O LEU 5 378 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU 5 380 " --> pdb=" O VAL 5 520 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 417 through 420 Processing sheet with id=AD1, first strand: chain '5' and resid 466 through 471 Processing sheet with id=AD2, first strand: chain '5' and resid 688 through 690 removed outlier: 7.319A pdb=" N VAL 5 729 " --> pdb=" O ARG 5 724 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 60 through 63 Processing sheet with id=AD4, first strand: chain '6' and resid 148 through 151 removed outlier: 9.981A pdb=" N SER 6 223 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N PHE 6 298 " --> pdb=" O SER 6 223 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU 6 225 " --> pdb=" O PHE 6 298 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA 6 300 " --> pdb=" O GLU 6 225 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE 6 227 " --> pdb=" O ALA 6 300 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N CYS 6 302 " --> pdb=" O ILE 6 227 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR 6 245 " --> pdb=" O CYS 6 301 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL 6 303 " --> pdb=" O ASP 6 243 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASP 6 243 " --> pdb=" O VAL 6 303 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LYS 6 241 " --> pdb=" O PRO 6 305 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG 6 207 " --> pdb=" O VAL 6 142 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR 6 144 " --> pdb=" O LYS 6 205 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LYS 6 205 " --> pdb=" O THR 6 144 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '6' and resid 164 through 169 removed outlier: 6.559A pdb=" N GLY 6 154 " --> pdb=" O ASP 6 167 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '6' and resid 378 through 379 removed outlier: 3.723A pdb=" N LYS 6 378 " --> pdb=" O LEU 6 386 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '6' and resid 416 through 420 removed outlier: 6.296A pdb=" N VAL 6 417 " --> pdb=" O CYS 6 458 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASP 6 460 " --> pdb=" O VAL 6 417 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR 6 419 " --> pdb=" O ASP 6 460 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS 6 457 " --> pdb=" O LEU 6 500 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ALA 6 502 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE 6 459 " --> pdb=" O ALA 6 502 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL 6 392 " --> pdb=" O ALA 6 501 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ALA 6 503 " --> pdb=" O VAL 6 392 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE 6 394 " --> pdb=" O ALA 6 503 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '6' and resid 431 through 435 Processing sheet with id=AD9, first strand: chain '6' and resid 481 through 486 Processing sheet with id=AE1, first strand: chain '6' and resid 585 through 586 removed outlier: 7.384A pdb=" N LYS 6 585 " --> pdb=" O VAL 6 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain '7' and resid 47 through 51 Processing sheet with id=AE3, first strand: chain '7' and resid 190 through 194 removed outlier: 8.031A pdb=" N PHE 7 229 " --> pdb=" O PRO 7 175 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N MET 7 177 " --> pdb=" O SER 7 227 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N SER 7 227 " --> pdb=" O MET 7 177 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N VAL 7 179 " --> pdb=" O ARG 7 225 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ARG 7 225 " --> pdb=" O VAL 7 179 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR 7 181 " --> pdb=" O GLN 7 223 " (cutoff:3.500A) removed outlier: 9.722A pdb=" N THR 7 296 " --> pdb=" O SER 7 252 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR 7 254 " --> pdb=" O THR 7 296 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLU 7 258 " --> pdb=" O ALA 7 300 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ARG 7 302 " --> pdb=" O GLU 7 258 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR 7 274 " --> pdb=" O HIS 7 301 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE 7 303 " --> pdb=" O SER 7 272 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER 7 272 " --> pdb=" O ILE 7 303 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS 7 305 " --> pdb=" O HIS 7 270 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N HIS 7 270 " --> pdb=" O LYS 7 305 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL 7 167 " --> pdb=" O GLN 7 238 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN 7 238 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG 7 169 " --> pdb=" O LYS 7 236 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '7' and resid 401 through 404 removed outlier: 6.841A pdb=" N CYS 7 378 " --> pdb=" O TRP 7 519 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE 7 521 " --> pdb=" O CYS 7 378 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET 7 380 " --> pdb=" O ILE 7 521 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '7' and resid 416 through 420 Processing sheet with id=AE6, first strand: chain '7' and resid 466 through 471 1360 hydrogen bonds defined for protein. 3870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 7.13 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9632 1.34 - 1.45: 4128 1.45 - 1.57: 17889 1.57 - 1.69: 103 1.69 - 1.81: 286 Bond restraints: 32038 Sorted by residual: bond pdb=" C3' DG X 13 " pdb=" C2' DG X 13 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.49e+00 bond pdb=" C3' DG Y -12 " pdb=" C2' DG Y -12 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.44e+00 bond pdb=" C3' DC Y -11 " pdb=" C2' DC Y -11 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.49e+00 bond pdb=" C3' DC X 14 " pdb=" C2' DC X 14 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.27e+00 bond pdb=" C3' DA Y -20 " pdb=" C2' DA Y -20 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 4.94e+00 ... (remaining 32033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 42614 1.48 - 2.97: 690 2.97 - 4.45: 95 4.45 - 5.94: 26 5.94 - 7.42: 4 Bond angle restraints: 43429 Sorted by residual: angle pdb=" C GLU 4 472 " pdb=" CA GLU 4 472 " pdb=" CB GLU 4 472 " ideal model delta sigma weight residual 116.54 110.09 6.45 1.15e+00 7.56e-01 3.15e+01 angle pdb=" C ARG 5 251 " pdb=" CA ARG 5 251 " pdb=" CB ARG 5 251 " ideal model delta sigma weight residual 117.23 109.81 7.42 1.36e+00 5.41e-01 2.98e+01 angle pdb=" N VAL 7 385 " pdb=" CA VAL 7 385 " pdb=" C VAL 7 385 " ideal model delta sigma weight residual 112.29 107.85 4.44 9.40e-01 1.13e+00 2.23e+01 angle pdb=" C ASN 4 376 " pdb=" CA ASN 4 376 " pdb=" CB ASN 4 376 " ideal model delta sigma weight residual 116.34 110.20 6.14 1.40e+00 5.10e-01 1.92e+01 angle pdb=" N3 DT X 16 " pdb=" C4 DT X 16 " pdb=" O4 DT X 16 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 43424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.96: 18676 26.96 - 53.92: 827 53.92 - 80.89: 138 80.89 - 107.85: 24 107.85 - 134.81: 3 Dihedral angle restraints: 19668 sinusoidal: 8476 harmonic: 11192 Sorted by residual: dihedral pdb=" C5' ADP 7 801 " pdb=" O5' ADP 7 801 " pdb=" PA ADP 7 801 " pdb=" O2A ADP 7 801 " ideal model delta sinusoidal sigma weight residual 300.00 165.19 134.81 1 2.00e+01 2.50e-03 4.09e+01 dihedral pdb=" C5' ADP 3 901 " pdb=" O5' ADP 3 901 " pdb=" PA ADP 3 901 " pdb=" O2A ADP 3 901 " ideal model delta sinusoidal sigma weight residual 300.00 173.37 126.63 1 2.00e+01 2.50e-03 3.83e+01 dihedral pdb=" C5' ADP 6 901 " pdb=" O5' ADP 6 901 " pdb=" PA ADP 6 901 " pdb=" O2A ADP 6 901 " ideal model delta sinusoidal sigma weight residual -60.00 -172.34 112.34 1 2.00e+01 2.50e-03 3.31e+01 ... (remaining 19665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3437 0.033 - 0.065: 945 0.065 - 0.098: 327 0.098 - 0.130: 207 0.130 - 0.163: 5 Chirality restraints: 4921 Sorted by residual: chirality pdb=" CB ILE 2 872 " pdb=" CA ILE 2 872 " pdb=" CG1 ILE 2 872 " pdb=" CG2 ILE 2 872 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CB ILE 6 249 " pdb=" CA ILE 6 249 " pdb=" CG1 ILE 6 249 " pdb=" CG2 ILE 6 249 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA VAL 6 206 " pdb=" N VAL 6 206 " pdb=" C VAL 6 206 " pdb=" CB VAL 6 206 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 4918 not shown) Planarity restraints: 5447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS 6 148 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO 6 149 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO 6 149 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO 6 149 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN 5 645 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C GLN 5 645 " 0.026 2.00e-02 2.50e+03 pdb=" O GLN 5 645 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL 5 646 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN 6 641 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO 6 642 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO 6 642 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO 6 642 " 0.020 5.00e-02 4.00e+02 ... (remaining 5444 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 164 2.59 - 3.17: 24309 3.17 - 3.74: 45510 3.74 - 4.32: 60539 4.32 - 4.90: 104632 Nonbonded interactions: 235154 Sorted by model distance: nonbonded pdb=" O3B ADP 7 801 " pdb="MG MG 7 802 " model vdw 2.010 2.170 nonbonded pdb=" O3B ADP 5 801 " pdb="MG MG 5 802 " model vdw 2.038 2.170 nonbonded pdb=" O3B ADP 6 901 " pdb="MG MG 6 902 " model vdw 2.063 2.170 nonbonded pdb=" O3B ADP 3 901 " pdb="MG MG 3 902 " model vdw 2.073 2.170 nonbonded pdb=" OG SER 3 352 " pdb="MG MG 3 902 " model vdw 2.079 2.170 ... (remaining 235149 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 Found NCS groups: ncs_group { reference = (chain 'X' and resid 3 through 22) selection = (chain 'Y' and resid -22 through -3) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.080 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: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 33.890 Find NCS groups from input model: 0.410 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.096 32057 Z= 0.161 Angle : 0.525 14.940 43453 Z= 0.318 Chirality : 0.039 0.163 4921 Planarity : 0.003 0.051 5447 Dihedral : 15.467 134.811 12392 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.84 (0.14), residues: 3767 helix: 2.24 (0.13), residues: 1537 sheet: 1.14 (0.19), residues: 750 loop : 0.26 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 527 TYR 0.015 0.001 TYR 2 418 PHE 0.015 0.001 PHE 6 649 TRP 0.011 0.001 TRP 2 569 HIS 0.005 0.000 HIS 6 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.16 (32038) covalent geometry : angle 0.50010 / 0.32 (43429) hydrogen bonds : bond 0.15154 / 15.14 ( 1413) hydrogen bonds : angle 5.32574 / 5.37 ( 3976) metal coordination : bond 0.04338 / 5.66 ( 19) metal coordination : angle 6.81147 / 8.95 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 734 time to evaluate : 1.069 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: 2 793 MET cc_start: 0.8560 (tpt) cc_final: 0.8284 (tpp) REVERT: 3 123 CYS cc_start: 0.8381 (m) cc_final: 0.8011 (m) REVERT: 4 353 LYS cc_start: 0.7811 (mttt) cc_final: 0.7574 (mtmt) REVERT: 4 361 MET cc_start: 0.7128 (mmm) cc_final: 0.6831 (mtm) REVERT: 4 541 VAL cc_start: 0.7765 (t) cc_final: 0.7543 (p) REVERT: 5 196 LYS cc_start: 0.7851 (tptt) cc_final: 0.7591 (tmtt) REVERT: 6 155 THR cc_start: 0.2707 (p) cc_final: 0.2412 (p) REVERT: 7 221 TYR cc_start: 0.7293 (m-80) cc_final: 0.6679 (m-80) outliers start: 0 outliers final: 0 residues processed: 734 average time/residue: 0.2336 time to fit residues: 255.6539 Evaluate side-chains 287 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 4.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 301 HIS 2 420 ASN ** 2 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 298 GLN 3 334 HIS 3 553 HIS 4 231 GLN 4 521 GLN 4 606 GLN 5 261 ASN 5 692 HIS 6 27 GLN 6 187 ASN 6 328 GLN 6 635 HIS ** 7 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 212 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.121289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.093125 restraints weight = 58700.978| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.70 r_work: 0.3207 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32057 Z= 0.186 Angle : 0.621 10.012 43453 Z= 0.321 Chirality : 0.044 0.177 4921 Planarity : 0.005 0.062 5447 Dihedral : 12.433 131.972 4749 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.58 % Allowed : 7.28 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.14), residues: 3767 helix: 1.99 (0.13), residues: 1578 sheet: 0.91 (0.19), residues: 764 loop : 0.08 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG 7 133 TYR 0.018 0.002 TYR 7 562 PHE 0.021 0.002 PHE 6 649 TRP 0.015 0.002 TRP 2 185 HIS 0.010 0.001 HIS 2 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (32038) covalent geometry : angle 0.61532 / 0.32 (43429) hydrogen bonds : bond 0.04836 / 4.85 ( 1413) hydrogen bonds : angle 4.43573 / 4.42 ( 3976) metal coordination : bond 0.00903 / 1.13 ( 19) metal coordination : angle 3.52422 / 5.62 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 288 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 889 ASN cc_start: 0.8039 (m110) cc_final: 0.7655 (m-40) REVERT: 3 558 LYS cc_start: 0.6610 (mttt) cc_final: 0.6143 (pttm) REVERT: 4 197 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8451 (tt) REVERT: 4 541 VAL cc_start: 0.8051 (t) cc_final: 0.7825 (p) REVERT: 5 177 ASN cc_start: 0.7985 (m-40) cc_final: 0.7383 (m110) REVERT: 5 196 LYS cc_start: 0.8201 (tptt) cc_final: 0.7465 (tmtt) REVERT: 5 701 GLN cc_start: 0.7066 (mm-40) cc_final: 0.6225 (tt0) REVERT: 6 550 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8334 (mtt90) REVERT: 6 605 ASP cc_start: 0.7109 (t0) cc_final: 0.6425 (t0) REVERT: 7 621 MET cc_start: 0.7238 (mpp) cc_final: 0.7024 (mpp) outliers start: 53 outliers final: 31 residues processed: 326 average time/residue: 0.2094 time to fit residues: 108.5605 Evaluate side-chains 243 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 242 HIS Chi-restraints excluded: chain 2 residue 328 ASN Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 2 residue 534 LYS Chi-restraints excluded: chain 2 residue 547 THR Chi-restraints excluded: chain 2 residue 595 GLN Chi-restraints excluded: chain 2 residue 851 PHE Chi-restraints excluded: chain 3 residue 74 VAL Chi-restraints excluded: chain 3 residue 118 SER Chi-restraints excluded: chain 3 residue 243 CYS Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 656 LYS Chi-restraints excluded: chain 4 residue 197 LEU Chi-restraints excluded: chain 4 residue 534 SER Chi-restraints excluded: chain 4 residue 548 MET Chi-restraints excluded: chain 4 residue 556 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 633 THR Chi-restraints excluded: chain 5 residue 730 LEU Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 481 THR Chi-restraints excluded: chain 6 residue 492 THR Chi-restraints excluded: chain 6 residue 550 ARG Chi-restraints excluded: chain 6 residue 560 GLU Chi-restraints excluded: chain 6 residue 577 LEU Chi-restraints excluded: chain 7 residue 238 GLN Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain 7 residue 602 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 278 optimal weight: 10.0000 chunk 242 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 0.0870 chunk 172 optimal weight: 0.9990 chunk 103 optimal weight: 0.0270 chunk 332 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 249 optimal weight: 20.0000 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 196 HIS ** 2 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 777 HIS 2 781 HIS 2 792 ASN ** 2 893 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 145 HIS 6 494 ASN ** 7 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.094412 restraints weight = 58441.812| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.69 r_work: 0.3230 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32057 Z= 0.098 Angle : 0.496 7.776 43453 Z= 0.257 Chirality : 0.040 0.147 4921 Planarity : 0.003 0.048 5447 Dihedral : 12.332 133.997 4749 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.28 % Allowed : 8.33 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.70 (0.14), residues: 3767 helix: 2.16 (0.13), residues: 1583 sheet: 1.02 (0.19), residues: 763 loop : 0.06 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 133 TYR 0.016 0.001 TYR 7 73 PHE 0.021 0.001 PHE 6 649 TRP 0.011 0.001 TRP 6 751 HIS 0.006 0.001 HIS 6 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (32038) covalent geometry : angle 0.49148 / 0.26 (43429) hydrogen bonds : bond 0.03639 / 3.67 ( 1413) hydrogen bonds : angle 4.13642 / 4.12 ( 3976) metal coordination : bond 0.00543 / 0.71 ( 19) metal coordination : angle 2.92630 / 5.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 230 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: 2 196 HIS cc_start: 0.8378 (t70) cc_final: 0.7971 (t-170) REVERT: 3 558 LYS cc_start: 0.6591 (mttt) cc_final: 0.6120 (pttm) REVERT: 4 194 MET cc_start: 0.8778 (mmm) cc_final: 0.8320 (tpp) REVERT: 4 361 MET cc_start: 0.7768 (mmm) cc_final: 0.7333 (mtm) REVERT: 4 433 ASP cc_start: 0.7958 (t70) cc_final: 0.7521 (m-30) REVERT: 4 541 VAL cc_start: 0.7992 (t) cc_final: 0.7738 (p) REVERT: 5 177 ASN cc_start: 0.7961 (m-40) cc_final: 0.7261 (m-40) REVERT: 5 196 LYS cc_start: 0.8205 (tptt) cc_final: 0.7466 (tmtt) REVERT: 5 597 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7359 (tp30) REVERT: 5 701 GLN cc_start: 0.6970 (mm-40) cc_final: 0.6138 (tt0) REVERT: 6 550 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8295 (mtt90) REVERT: 7 621 MET cc_start: 0.7118 (mpp) cc_final: 0.6840 (mpp) outliers start: 43 outliers final: 18 residues processed: 261 average time/residue: 0.1969 time to fit residues: 83.3763 Evaluate side-chains 234 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 328 ASN Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 620 THR Chi-restraints excluded: chain 3 residue 656 LYS Chi-restraints excluded: chain 4 residue 434 GLU Chi-restraints excluded: chain 4 residue 534 SER Chi-restraints excluded: chain 4 residue 548 MET Chi-restraints excluded: chain 4 residue 556 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 469 ILE Chi-restraints excluded: chain 5 residue 597 GLU Chi-restraints excluded: chain 5 residue 633 THR Chi-restraints excluded: chain 5 residue 730 LEU Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 481 THR Chi-restraints excluded: chain 6 residue 550 ARG Chi-restraints excluded: chain 7 residue 94 VAL Chi-restraints excluded: chain 7 residue 199 THR Chi-restraints excluded: chain 7 residue 238 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 39 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 381 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 321 optimal weight: 7.9990 chunk 225 optimal weight: 0.9980 chunk 274 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 687 HIS 2 777 HIS 2 781 HIS ** 3 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 42 HIS 7 212 GLN 7 389 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.121101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.092587 restraints weight = 57943.991| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.77 r_work: 0.3184 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 32057 Z= 0.107 Angle : 0.489 7.114 43453 Z= 0.252 Chirality : 0.040 0.221 4921 Planarity : 0.003 0.046 5447 Dihedral : 12.344 133.687 4749 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.31 % Allowed : 8.83 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.74 (0.14), residues: 3767 helix: 2.24 (0.13), residues: 1586 sheet: 1.07 (0.19), residues: 740 loop : 0.02 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 589 TYR 0.018 0.001 TYR 7 73 PHE 0.019 0.001 PHE 6 649 TRP 0.014 0.001 TRP 6 751 HIS 0.005 0.001 HIS 2 893 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (32038) covalent geometry : angle 0.48472 / 0.25 (43429) hydrogen bonds : bond 0.03486 / 3.51 ( 1413) hydrogen bonds : angle 3.99149 / 4.00 ( 3976) metal coordination : bond 0.00505 / 0.66 ( 19) metal coordination : angle 2.62891 / 4.43 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 196 HIS cc_start: 0.8355 (t70) cc_final: 0.8120 (t-170) REVERT: 2 750 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9188 (tp) REVERT: 2 755 MET cc_start: 0.8464 (tpt) cc_final: 0.8230 (tpt) REVERT: 3 558 LYS cc_start: 0.6618 (mttt) cc_final: 0.6124 (pttm) REVERT: 4 194 MET cc_start: 0.8744 (mmm) cc_final: 0.8290 (tpp) REVERT: 4 299 MET cc_start: 0.9047 (tpp) cc_final: 0.8773 (tpp) REVERT: 4 324 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7122 (pm20) REVERT: 4 361 MET cc_start: 0.7874 (mmm) cc_final: 0.7431 (mtm) REVERT: 4 433 ASP cc_start: 0.7965 (t70) cc_final: 0.7522 (m-30) REVERT: 5 177 ASN cc_start: 0.7877 (m-40) cc_final: 0.7182 (m-40) REVERT: 5 196 LYS cc_start: 0.8236 (tptt) cc_final: 0.7501 (tmtt) REVERT: 5 597 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7332 (tp30) REVERT: 5 701 GLN cc_start: 0.6861 (mm-40) cc_final: 0.6083 (tt0) REVERT: 5 715 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8073 (mmm) REVERT: 6 176 GLN cc_start: 0.9080 (mt0) cc_final: 0.8382 (mm-40) REVERT: 6 550 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8301 (mtt90) REVERT: 7 621 MET cc_start: 0.7153 (mpp) cc_final: 0.6772 (mpp) outliers start: 44 outliers final: 28 residues processed: 261 average time/residue: 0.1927 time to fit residues: 81.7301 Evaluate side-chains 245 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 328 ASN Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 2 residue 534 LYS Chi-restraints excluded: chain 2 residue 547 THR Chi-restraints excluded: chain 2 residue 750 LEU Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 656 LYS Chi-restraints excluded: chain 4 residue 324 GLU Chi-restraints excluded: chain 4 residue 534 SER Chi-restraints excluded: chain 4 residue 556 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 469 ILE Chi-restraints excluded: chain 5 residue 482 CYS Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 597 GLU Chi-restraints excluded: chain 5 residue 633 THR Chi-restraints excluded: chain 5 residue 715 MET Chi-restraints excluded: chain 5 residue 730 LEU Chi-restraints excluded: chain 6 residue 43 GLU Chi-restraints excluded: chain 6 residue 98 VAL Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 481 THR Chi-restraints excluded: chain 6 residue 550 ARG Chi-restraints excluded: chain 6 residue 560 GLU Chi-restraints excluded: chain 6 residue 577 LEU Chi-restraints excluded: chain 7 residue 94 VAL Chi-restraints excluded: chain 7 residue 199 THR Chi-restraints excluded: chain 7 residue 238 GLN Chi-restraints excluded: chain 7 residue 292 LEU Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain 7 residue 602 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 276 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 378 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 237 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 777 HIS 2 843 GLN 2 893 HIS ** 3 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 408 HIS 7 214 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.113184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.085198 restraints weight = 59135.663| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.71 r_work: 0.3087 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 32057 Z= 0.200 Angle : 0.601 8.593 43453 Z= 0.312 Chirality : 0.044 0.290 4921 Planarity : 0.004 0.050 5447 Dihedral : 12.539 127.469 4749 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.91 % Allowed : 9.85 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3767 helix: 2.05 (0.13), residues: 1576 sheet: 0.76 (0.19), residues: 754 loop : -0.23 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 7 106 TYR 0.033 0.002 TYR 6 752 PHE 0.020 0.002 PHE 7 447 TRP 0.062 0.003 TRP 4 153 HIS 0.012 0.002 HIS 7 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (32038) covalent geometry : angle 0.59716 / 0.31 (43429) hydrogen bonds : bond 0.05123 / 5.22 ( 1413) hydrogen bonds : angle 4.27100 / 4.25 ( 3976) metal coordination : bond 0.00678 / 0.81 ( 19) metal coordination : angle 2.89816 / 5.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 228 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: 2 260 ASP cc_start: 0.7465 (m-30) cc_final: 0.7169 (m-30) REVERT: 2 755 MET cc_start: 0.8458 (tpt) cc_final: 0.8203 (tpt) REVERT: 3 233 ASP cc_start: 0.7907 (t0) cc_final: 0.7681 (t0) REVERT: 3 384 THR cc_start: 0.7613 (m) cc_final: 0.7363 (t) REVERT: 3 558 LYS cc_start: 0.6759 (mttt) cc_final: 0.6177 (pttm) REVERT: 4 548 MET cc_start: 0.6873 (ptm) cc_final: 0.6634 (ptm) REVERT: 4 635 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8168 (pp30) REVERT: 5 502 ASP cc_start: 0.8698 (m-30) cc_final: 0.8022 (t70) REVERT: 5 597 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7557 (tp30) REVERT: 5 701 GLN cc_start: 0.6877 (mm-40) cc_final: 0.6172 (tt0) REVERT: 5 715 MET cc_start: 0.8233 (mmm) cc_final: 0.7934 (mmm) REVERT: 6 176 GLN cc_start: 0.9141 (mt0) cc_final: 0.8417 (mm-40) REVERT: 6 550 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8500 (mtt90) REVERT: 6 722 ARG cc_start: 0.6920 (mtm-85) cc_final: 0.6711 (mtm180) REVERT: 7 621 MET cc_start: 0.7138 (mpp) cc_final: 0.6783 (mpp) outliers start: 64 outliers final: 39 residues processed: 280 average time/residue: 0.2019 time to fit residues: 91.3090 Evaluate side-chains 235 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 293 GLU Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 2 residue 534 LYS Chi-restraints excluded: chain 2 residue 547 THR Chi-restraints excluded: chain 2 residue 851 PHE Chi-restraints excluded: chain 2 residue 884 GLU Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 3 residue 155 ILE Chi-restraints excluded: chain 3 residue 243 CYS Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 620 THR Chi-restraints excluded: chain 3 residue 656 LYS Chi-restraints excluded: chain 4 residue 370 VAL Chi-restraints excluded: chain 4 residue 415 HIS Chi-restraints excluded: chain 4 residue 534 SER Chi-restraints excluded: chain 4 residue 556 LEU Chi-restraints excluded: chain 4 residue 635 GLN Chi-restraints excluded: chain 5 residue 404 THR Chi-restraints excluded: chain 5 residue 445 ASP Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 482 CYS Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 597 GLU Chi-restraints excluded: chain 5 residue 633 THR Chi-restraints excluded: chain 5 residue 706 HIS Chi-restraints excluded: chain 5 residue 730 LEU Chi-restraints excluded: chain 6 residue 43 GLU Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 492 THR Chi-restraints excluded: chain 6 residue 550 ARG Chi-restraints excluded: chain 6 residue 560 GLU Chi-restraints excluded: chain 6 residue 577 LEU Chi-restraints excluded: chain 7 residue 199 THR Chi-restraints excluded: chain 7 residue 238 GLN Chi-restraints excluded: chain 7 residue 292 LEU Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain 7 residue 602 SER Chi-restraints excluded: chain 7 residue 624 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 242 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 353 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 100 optimal weight: 0.1980 chunk 241 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 276 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 196 HIS 2 420 ASN ** 3 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 473 HIS ** 5 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 212 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.115435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.087575 restraints weight = 58007.245| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.72 r_work: 0.3139 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 32057 Z= 0.104 Angle : 0.502 9.069 43453 Z= 0.259 Chirality : 0.040 0.164 4921 Planarity : 0.003 0.047 5447 Dihedral : 12.461 130.816 4749 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.43 % Allowed : 11.19 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.14), residues: 3767 helix: 2.23 (0.13), residues: 1570 sheet: 0.81 (0.19), residues: 758 loop : -0.15 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 7 219 TYR 0.023 0.001 TYR 6 752 PHE 0.017 0.001 PHE 6 649 TRP 0.026 0.002 TRP 4 153 HIS 0.009 0.001 HIS 2 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (32038) covalent geometry : angle 0.49791 / 0.26 (43429) hydrogen bonds : bond 0.03737 / 3.78 ( 1413) hydrogen bonds : angle 4.01875 / 4.03 ( 3976) metal coordination : bond 0.00431 / 0.55 ( 19) metal coordination : angle 2.69864 / 4.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: 2 196 HIS cc_start: 0.8096 (OUTLIER) cc_final: 0.7751 (t70) REVERT: 2 755 MET cc_start: 0.8451 (tpt) cc_final: 0.8189 (tpt) REVERT: 3 233 ASP cc_start: 0.7851 (t0) cc_final: 0.7645 (t0) REVERT: 3 558 LYS cc_start: 0.6830 (mttt) cc_final: 0.6238 (pttm) REVERT: 4 324 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: 4 361 MET cc_start: 0.7774 (mmm) cc_final: 0.7473 (mtm) REVERT: 4 548 MET cc_start: 0.6803 (ptm) cc_final: 0.6418 (ptm) REVERT: 5 502 ASP cc_start: 0.8708 (m-30) cc_final: 0.8017 (t70) REVERT: 5 597 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7356 (tp30) REVERT: 5 715 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7970 (mmm) REVERT: 6 176 GLN cc_start: 0.9078 (mt0) cc_final: 0.8445 (mm-40) REVERT: 6 550 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8469 (mtt90) outliers start: 48 outliers final: 29 residues processed: 246 average time/residue: 0.2085 time to fit residues: 82.5057 Evaluate side-chains 229 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 HIS Chi-restraints excluded: chain 2 residue 274 TYR Chi-restraints excluded: chain 2 residue 293 GLU Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 750 LEU Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 620 THR Chi-restraints excluded: chain 3 residue 656 LYS Chi-restraints excluded: chain 4 residue 324 GLU Chi-restraints excluded: chain 4 residue 534 SER Chi-restraints excluded: chain 4 residue 556 LEU Chi-restraints excluded: chain 5 residue 404 THR Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 469 ILE Chi-restraints excluded: chain 5 residue 482 CYS Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 597 GLU Chi-restraints excluded: chain 5 residue 633 THR Chi-restraints excluded: chain 5 residue 715 MET Chi-restraints excluded: chain 5 residue 730 LEU Chi-restraints excluded: chain 6 residue 43 GLU Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 550 ARG Chi-restraints excluded: chain 6 residue 560 GLU Chi-restraints excluded: chain 6 residue 577 LEU Chi-restraints excluded: chain 7 residue 94 VAL Chi-restraints excluded: chain 7 residue 199 THR Chi-restraints excluded: chain 7 residue 238 GLN Chi-restraints excluded: chain 7 residue 292 LEU Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain 7 residue 602 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 316 optimal weight: 0.9980 chunk 278 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 356 optimal weight: 1.9990 chunk 296 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 340 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 875 HIS ** 3 33 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 = 0.3677 r_free = 0.3677 target = 0.115196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.087571 restraints weight = 58122.272| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.72 r_work: 0.3133 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32057 Z= 0.111 Angle : 0.494 9.075 43453 Z= 0.255 Chirality : 0.040 0.162 4921 Planarity : 0.003 0.045 5447 Dihedral : 12.413 130.430 4749 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.55 % Allowed : 11.13 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.57 (0.14), residues: 3767 helix: 2.25 (0.13), residues: 1571 sheet: 0.81 (0.19), residues: 757 loop : -0.15 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 6 435 TYR 0.023 0.001 TYR 6 752 PHE 0.017 0.001 PHE 6 649 TRP 0.038 0.002 TRP 4 153 HIS 0.020 0.001 HIS 2 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (32038) covalent geometry : angle 0.49047 / 0.25 (43429) hydrogen bonds : bond 0.03677 / 3.74 ( 1413) hydrogen bonds : angle 3.97208 / 3.98 ( 3976) metal coordination : bond 0.00441 / 0.57 ( 19) metal coordination : angle 2.45466 / 4.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: 2 755 MET cc_start: 0.8472 (tpt) cc_final: 0.8207 (tpt) REVERT: 3 384 THR cc_start: 0.7643 (m) cc_final: 0.7353 (t) REVERT: 3 558 LYS cc_start: 0.6920 (mttt) cc_final: 0.6308 (pttm) REVERT: 4 324 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7313 (pm20) REVERT: 4 548 MET cc_start: 0.6815 (ptm) cc_final: 0.6559 (ptm) REVERT: 5 502 ASP cc_start: 0.8716 (m-30) cc_final: 0.8025 (t70) REVERT: 5 597 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7331 (tp30) REVERT: 5 715 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7942 (mmm) REVERT: 6 176 GLN cc_start: 0.9067 (mt0) cc_final: 0.8440 (mm-40) REVERT: 6 550 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8486 (mtt90) outliers start: 52 outliers final: 39 residues processed: 250 average time/residue: 0.1907 time to fit residues: 77.4421 Evaluate side-chains 242 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 274 TYR Chi-restraints excluded: chain 2 residue 293 GLU Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 534 LYS Chi-restraints excluded: chain 2 residue 750 LEU Chi-restraints excluded: chain 2 residue 884 GLU Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 620 THR Chi-restraints excluded: chain 3 residue 656 LYS Chi-restraints excluded: chain 4 residue 253 ILE Chi-restraints excluded: chain 4 residue 324 GLU Chi-restraints excluded: chain 4 residue 370 VAL Chi-restraints excluded: chain 4 residue 433 ASP Chi-restraints excluded: chain 4 residue 534 SER Chi-restraints excluded: chain 4 residue 556 LEU Chi-restraints excluded: chain 5 residue 257 VAL Chi-restraints excluded: chain 5 residue 404 THR Chi-restraints excluded: chain 5 residue 445 ASP Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 469 ILE Chi-restraints excluded: chain 5 residue 482 CYS Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 597 GLU Chi-restraints excluded: chain 5 residue 633 THR Chi-restraints excluded: chain 5 residue 715 MET Chi-restraints excluded: chain 5 residue 730 LEU Chi-restraints excluded: chain 6 residue 43 GLU Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 550 ARG Chi-restraints excluded: chain 6 residue 560 GLU Chi-restraints excluded: chain 6 residue 577 LEU Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 7 residue 94 VAL Chi-restraints excluded: chain 7 residue 199 THR Chi-restraints excluded: chain 7 residue 238 GLN Chi-restraints excluded: chain 7 residue 292 LEU Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain 7 residue 602 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 212 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 299 optimal weight: 4.9990 chunk 326 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 312 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 323 optimal weight: 9.9990 chunk 106 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 287 HIS ** 3 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 38 GLN 7 240 HIS 7 541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.111035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.083032 restraints weight = 59174.644| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.72 r_work: 0.3051 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 32057 Z= 0.208 Angle : 0.603 10.108 43453 Z= 0.311 Chirality : 0.044 0.176 4921 Planarity : 0.005 0.063 5447 Dihedral : 12.540 124.267 4749 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.61 % Allowed : 11.55 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.14), residues: 3767 helix: 1.99 (0.13), residues: 1578 sheet: 0.52 (0.19), residues: 750 loop : -0.38 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 5 674 TYR 0.036 0.002 TYR 6 752 PHE 0.019 0.002 PHE 7 447 TRP 0.062 0.003 TRP 4 153 HIS 0.010 0.001 HIS 4 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.21 (32038) covalent geometry : angle 0.59977 / 0.31 (43429) hydrogen bonds : bond 0.05114 / 5.21 ( 1413) hydrogen bonds : angle 4.22646 / 4.22 ( 3976) metal coordination : bond 0.00632 / 0.74 ( 19) metal coordination : angle 2.88859 / 5.27 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: 2 755 MET cc_start: 0.8547 (tpt) cc_final: 0.8262 (tpt) REVERT: 3 180 GLU cc_start: 0.8118 (mp0) cc_final: 0.7880 (mp0) REVERT: 3 384 THR cc_start: 0.7771 (m) cc_final: 0.7432 (t) REVERT: 3 558 LYS cc_start: 0.6970 (mttt) cc_final: 0.6322 (pttm) REVERT: 4 324 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6514 (pm20) REVERT: 5 597 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7688 (tp30) REVERT: 5 715 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8051 (mmm) REVERT: 6 115 GLN cc_start: 0.8009 (mt0) cc_final: 0.7662 (tt0) REVERT: 6 550 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8559 (mtt90) REVERT: 7 426 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7144 (pt0) REVERT: 7 565 MET cc_start: 0.8775 (mtt) cc_final: 0.8553 (mtp) outliers start: 54 outliers final: 39 residues processed: 250 average time/residue: 0.2119 time to fit residues: 85.0866 Evaluate side-chains 232 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 242 HIS Chi-restraints excluded: chain 2 residue 274 TYR Chi-restraints excluded: chain 2 residue 293 GLU Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 480 SER Chi-restraints excluded: chain 2 residue 534 LYS Chi-restraints excluded: chain 2 residue 750 LEU Chi-restraints excluded: chain 2 residue 884 GLU Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 3 residue 155 ILE Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 455 VAL Chi-restraints excluded: chain 3 residue 620 THR Chi-restraints excluded: chain 3 residue 656 LYS Chi-restraints excluded: chain 4 residue 253 ILE Chi-restraints excluded: chain 4 residue 324 GLU Chi-restraints excluded: chain 4 residue 370 VAL Chi-restraints excluded: chain 4 residue 433 ASP Chi-restraints excluded: chain 4 residue 534 SER Chi-restraints excluded: chain 4 residue 556 LEU Chi-restraints excluded: chain 5 residue 404 THR Chi-restraints excluded: chain 5 residue 445 ASP Chi-restraints excluded: chain 5 residue 448 ASP Chi-restraints excluded: chain 5 residue 482 CYS Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 597 GLU Chi-restraints excluded: chain 5 residue 633 THR Chi-restraints excluded: chain 5 residue 706 HIS Chi-restraints excluded: chain 5 residue 715 MET Chi-restraints excluded: chain 5 residue 730 LEU Chi-restraints excluded: chain 6 residue 43 GLU Chi-restraints excluded: chain 6 residue 331 VAL Chi-restraints excluded: chain 6 residue 550 ARG Chi-restraints excluded: chain 6 residue 560 GLU Chi-restraints excluded: chain 6 residue 577 LEU Chi-restraints excluded: chain 7 residue 199 THR Chi-restraints excluded: chain 7 residue 238 GLN Chi-restraints excluded: chain 7 residue 292 LEU Chi-restraints excluded: chain 7 residue 336 LEU Chi-restraints excluded: chain 7 residue 412 VAL Chi-restraints excluded: chain 7 residue 602 SER Chi-restraints excluded: chain 7 residue 624 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 275 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 224 optimal weight: 3.9990 chunk 133 optimal weight: 0.0070 chunk 288 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 335 optimal weight: 0.0570 chunk 23 optimal weight: 0.7980 chunk 343 optimal weight: 3.9990 chunk 242 optimal weight: 0.4980 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 196 HIS ** 3 33 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 = 0.3672 r_free = 0.3672 target = 0.114771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087145 restraints weight = 57866.316| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.70 r_work: 0.3135 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 32057 Z= 0.097 Angle : 0.499 10.674 43453 Z= 0.259 Chirality : 0.040 0.172 4921 Planarity : 0.004 0.050 5447 Dihedral : 12.366 128.329 4749 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.01 % Allowed : 12.35 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.48 (0.14), residues: 3767 helix: 2.23 (0.13), residues: 1572 sheet: 0.67 (0.19), residues: 753 loop : -0.20 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 7 620 TYR 0.062 0.001 TYR 6 752 PHE 0.017 0.001 PHE 6 649 TRP 0.039 0.002 TRP 4 153 HIS 0.016 0.001 HIS 4 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 (32038) covalent geometry : angle 0.49604 / 0.26 (43429) hydrogen bonds : bond 0.03363 / 3.38 ( 1413) hydrogen bonds : angle 3.93161 / 3.97 ( 3976) metal coordination : bond 0.00381 / 0.51 ( 19) metal coordination : angle 2.38943 / 4.50 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 196 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7637 (t70) REVERT: 2 755 MET cc_start: 0.8533 (tpt) cc_final: 0.8242 (tpt) REVERT: 3 384 THR cc_start: 0.7748 (m) cc_final: 0.7385 (t) REVERT: 3 558 LYS cc_start: 0.7021 (mttt) cc_final: 0.6429 (pttm) REVERT: 4 324 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: 4 361 MET cc_start: 0.7731 (mmm) cc_final: 0.7441 (mtm) REVERT: 5 597 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7430 (tp30) REVERT: 5 715 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8007 (mmm) REVERT: 6 435 ARG cc_start: 0.7796 (mtt-85) cc_final: 0.7537 (mtt-85) REVERT: 6 745 ARG cc_start: 0.4153 (OUTLIER) cc_final: 0.2356 (ptp-170) REVERT: 7 235 MET cc_start: 0.8191 (ptp) cc_final: 0.7864 (ttp) REVERT: 7 426 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6993 (pt0) REVERT: 7 565 MET cc_start: 0.8699 (mtt) cc_final: 0.8455 (mtp) REVERT: 7 639 MET cc_start: 0.8528 (tpp) cc_final: 0.8105 (tpp) outliers start: 34 outliers final: 19 residues processed: 238 average time/residue: 0.2003 time to fit residues: 75.9129 Evaluate side-chains 221 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 HIS Chi-restraints excluded: chain 2 residue 274 TYR Chi-restraints excluded: chain 2 residue 293 GLU Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 750 LEU Chi-restraints excluded: chain 2 residue 884 GLU Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 620 THR Chi-restraints excluded: chain 3 residue 656 LYS Chi-restraints excluded: chain 4 residue 324 GLU Chi-restraints excluded: chain 4 residue 370 VAL Chi-restraints excluded: chain 4 residue 556 LEU Chi-restraints excluded: chain 5 residue 404 THR Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 597 GLU Chi-restraints excluded: chain 5 residue 715 MET Chi-restraints excluded: chain 5 residue 730 LEU Chi-restraints excluded: chain 6 residue 43 GLU Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 492 THR Chi-restraints excluded: chain 6 residue 745 ARG Chi-restraints excluded: chain 7 residue 292 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 351 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 314 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 328 optimal weight: 0.6980 chunk 221 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 185 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 242 HIS ** 3 33 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 = 0.3663 r_free = 0.3663 target = 0.114362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086455 restraints weight = 58445.839| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.75 r_work: 0.3125 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32057 Z= 0.101 Angle : 0.501 11.736 43453 Z= 0.257 Chirality : 0.041 0.192 4921 Planarity : 0.004 0.045 5447 Dihedral : 12.331 127.126 4749 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.84 % Allowed : 12.65 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.14), residues: 3767 helix: 2.23 (0.13), residues: 1572 sheet: 0.75 (0.19), residues: 752 loop : -0.18 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 3 17 TYR 0.063 0.001 TYR 6 752 PHE 0.026 0.001 PHE 2 891 TRP 0.038 0.002 TRP 4 153 HIS 0.033 0.001 HIS 2 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (32038) covalent geometry : angle 0.49856 / 0.26 (43429) hydrogen bonds : bond 0.03455 / 3.49 ( 1413) hydrogen bonds : angle 3.89942 / 3.94 ( 3976) metal coordination : bond 0.00388 / 0.51 ( 19) metal coordination : angle 2.18896 / 4.04 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 755 MET cc_start: 0.8540 (tpt) cc_final: 0.8245 (tpt) REVERT: 3 384 THR cc_start: 0.7714 (m) cc_final: 0.7410 (t) REVERT: 3 386 GLN cc_start: 0.7095 (mt0) cc_final: 0.6620 (pm20) REVERT: 3 558 LYS cc_start: 0.7007 (mttt) cc_final: 0.6424 (pttm) REVERT: 4 324 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: 4 361 MET cc_start: 0.7727 (mmm) cc_final: 0.7455 (mtm) REVERT: 5 145 MET cc_start: 0.9240 (mmt) cc_final: 0.8629 (tpt) REVERT: 5 597 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: 5 715 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7961 (mmm) REVERT: 6 115 GLN cc_start: 0.7882 (mt0) cc_final: 0.7482 (tt0) REVERT: 6 188 ARG cc_start: 0.6604 (ptm160) cc_final: 0.6207 (mtp85) REVERT: 6 194 ASP cc_start: 0.5666 (t0) cc_final: 0.5376 (t0) REVERT: 6 745 ARG cc_start: 0.4110 (OUTLIER) cc_final: 0.2335 (ptp-170) REVERT: 7 426 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7015 (pt0) REVERT: 7 565 MET cc_start: 0.8702 (mtt) cc_final: 0.8457 (mtp) REVERT: 7 637 MET cc_start: 0.8509 (mtm) cc_final: 0.8296 (mtp) REVERT: 7 639 MET cc_start: 0.8572 (tpp) cc_final: 0.8123 (tpp) outliers start: 28 outliers final: 21 residues processed: 226 average time/residue: 0.2010 time to fit residues: 73.1501 Evaluate side-chains 222 residues out of total 3353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 274 TYR Chi-restraints excluded: chain 2 residue 293 GLU Chi-restraints excluded: chain 2 residue 421 ASN Chi-restraints excluded: chain 2 residue 750 LEU Chi-restraints excluded: chain 2 residue 884 GLU Chi-restraints excluded: chain 3 residue 121 LEU Chi-restraints excluded: chain 3 residue 416 ASP Chi-restraints excluded: chain 3 residue 620 THR Chi-restraints excluded: chain 3 residue 656 LYS Chi-restraints excluded: chain 4 residue 239 MET Chi-restraints excluded: chain 4 residue 324 GLU Chi-restraints excluded: chain 4 residue 370 VAL Chi-restraints excluded: chain 4 residue 556 LEU Chi-restraints excluded: chain 5 residue 404 THR Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 597 GLU Chi-restraints excluded: chain 5 residue 715 MET Chi-restraints excluded: chain 5 residue 730 LEU Chi-restraints excluded: chain 6 residue 43 GLU Chi-restraints excluded: chain 6 residue 104 ILE Chi-restraints excluded: chain 6 residue 492 THR Chi-restraints excluded: chain 6 residue 618 VAL Chi-restraints excluded: chain 6 residue 745 ARG Chi-restraints excluded: chain 7 residue 292 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 13 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 336 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 375 optimal weight: 0.9990 chunk 264 optimal weight: 0.9980 chunk 369 optimal weight: 0.5980 chunk 143 optimal weight: 4.9990 chunk 226 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 242 HIS 2 875 HIS 4 368 HIS 7 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.114441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.086556 restraints weight = 58416.375| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.74 r_work: 0.3127 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 32057 Z= 0.100 Angle : 0.494 11.592 43453 Z= 0.253 Chirality : 0.040 0.162 4921 Planarity : 0.004 0.045 5447 Dihedral : 12.267 126.018 4749 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.90 % Allowed : 12.65 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.56 (0.14), residues: 3767 helix: 2.26 (0.13), residues: 1572 sheet: 0.78 (0.19), residues: 752 loop : -0.15 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 5 27 TYR 0.053 0.001 TYR 6 752 PHE 0.020 0.001 PHE 2 891 TRP 0.036 0.002 TRP 4 153 HIS 0.012 0.001 HIS 4 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (32038) covalent geometry : angle 0.49132 / 0.25 (43429) hydrogen bonds : bond 0.03354 / 3.38 ( 1413) hydrogen bonds : angle 3.86600 / 3.92 ( 3976) metal coordination : bond 0.00413 / 0.54 ( 19) metal coordination : angle 2.03975 / 3.66 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6043.86 seconds wall clock time: 104 minutes 44.29 seconds (6284.29 seconds total)