Starting phenix.real_space_refine on Sat Aug 8 10:56:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22vt_68728/08_2026/22vt_68728.cif Found real_map, /net/cci-nas-00/data/ceres_data/22vt_68728/08_2026/22vt_68728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22vt_68728/08_2026/22vt_68728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22vt_68728/08_2026/22vt_68728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22vt_68728/08_2026/22vt_68728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22vt_68728/08_2026/22vt_68728.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.010 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 4 6.06 5 P 13 5.49 5 Mg 3 5.21 5 S 128 5.16 5 C 16931 2.51 5 N 4812 2.21 5 O 5256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27147 Number of models: 1 Model: "" Number of chains: 11 Chain: "2" Number of atoms: 5327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5327 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 29, 'TRANS': 667} Chain breaks: 1 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'HIS:plan': 2, 'ARG:plan': 10, 'GLU:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 122 Chain: "3" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4468 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 20, 'TRANS': 584} Chain breaks: 4 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 16, 'ASP:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 5, 'GLU:plan': 10, 'PHE:plan': 1, 'HIS:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 198 Chain: "4" Number of atoms: 4951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 4951 Classifications: {'peptide': 663} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 25, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 7, 'ARG:plan': 14, 'GLN:plan1': 5, 'GLU:plan': 10, 'ASP:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 203 Chain: "6" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5252 Classifications: {'peptide': 667} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 21, 'TRANS': 645} Chain breaks: 3 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 6, 'PHE:plan': 1, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "7" Number of atoms: 4231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4231 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 25, 'TRANS': 538} Chain breaks: 3 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 4, 'PHE:plan': 1, 'ARG:plan': 14, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "5" Number of atoms: 2764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 2764 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 451} Link IDs: {'PTRANS': 21, 'TRANS': 529} Chain breaks: 6 Unresolved non-hydrogen bonds: 1645 Unresolved non-hydrogen angles: 2055 Unresolved non-hydrogen dihedrals: 1349 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 28, 'ARG:plan': 46, 'PHE:plan': 20, 'GLU:plan': 42, 'TYR:plan': 15, 'ASP:plan': 32, 'HIS:plan': 11, 'ASN:plan1': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 913 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "4" 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: "6" 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: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1134 SG CYS 2 329 95.630 92.273 78.713 1.00165.99 S ATOM 1157 SG CYS 2 332 96.678 94.906 81.111 1.00150.33 S ATOM 1308 SG CYS 2 352 93.085 93.588 81.260 1.00161.57 S ATOM 1330 SG CYS 2 355 94.121 95.837 78.455 1.00165.39 S ATOM 10831 SG CYS 4 306 112.907 102.792 97.103 1.00 91.94 S ATOM 10853 SG CYS 4 309 115.318 104.646 99.095 1.00 79.37 S ATOM 10999 SG CYS 4 328 113.286 106.226 96.108 1.00 85.85 S ATOM 11020 SG CYS 4 331 116.197 103.758 95.419 1.00111.36 S ATOM 15892 SG CYS 6 158 113.078 86.299 89.241 1.00135.48 S ATOM 15914 SG CYS 6 161 116.758 86.055 89.914 1.00143.93 S ATOM 16075 SG CYS 6 180 114.534 89.662 90.208 1.00140.79 S ATOM 16114 SG CYS 6 185 115.588 87.739 87.135 1.00144.31 S ATOM 21063 SG CYS 7 184 105.797 125.375 77.447 1.00159.42 S ATOM 21086 SG CYS 7 187 106.565 127.993 75.259 1.00173.41 S ATOM 21229 SG CYS 7 206 105.623 124.127 74.199 1.00175.36 S ATOM 21265 SG CYS 7 211 109.016 124.943 75.968 1.00183.48 S Time building chain proxies: 5.28, per 1000 atoms: 0.19 Number of scatterers: 27147 At special positions: 0 Unit cell: (135.45, 157.5, 175.35, 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 4 29.99 S 128 16.00 P 13 15.00 Mg 3 11.99 O 5256 8.00 N 4812 7.00 C 16931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 866.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21002 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 332 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 355 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 352 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 329 " 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 6 901 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 158 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 161 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 185 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 180 " pdb=" ZN 7 802 " pdb="ZN ZN 7 802 " - pdb=" SG CYS 7 184 " pdb="ZN ZN 7 802 " - pdb=" SG CYS 7 211 " pdb="ZN ZN 7 802 " - pdb=" SG CYS 7 187 " pdb="ZN ZN 7 802 " - pdb=" SG CYS 7 206 " Number of angles added : 24 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7132 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 41 sheets defined 44.7% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain '2' and resid 190 through 204 removed outlier: 4.364A pdb=" N GLU 2 194 " --> pdb=" O GLY 2 190 " (cutoff:3.500A) Processing helix chain '2' and resid 213 through 225 removed outlier: 3.554A pdb=" N GLU 2 217 " --> pdb=" O ASN 2 213 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS 2 223 " --> pdb=" O ILE 2 219 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS 2 224 " --> pdb=" O SER 2 220 " (cutoff:3.500A) Processing helix chain '2' and resid 234 through 239 Processing helix chain '2' and resid 241 through 251 Proline residue: 2 249 - end of helix Processing helix chain '2' and resid 251 through 271 removed outlier: 3.897A pdb=" N GLU 2 261 " --> pdb=" O GLN 2 257 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU 2 264 " --> pdb=" O ASP 2 260 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU 2 265 " --> pdb=" O GLU 2 261 " (cutoff:3.500A) Processing helix chain '2' and resid 293 through 297 removed outlier: 3.965A pdb=" N LEU 2 297 " --> pdb=" O LEU 2 294 " (cutoff:3.500A) Processing helix chain '2' and resid 298 through 302 removed outlier: 3.655A pdb=" N LEU 2 302 " --> pdb=" O GLN 2 299 " (cutoff:3.500A) Processing helix chain '2' and resid 458 through 470 removed outlier: 4.214A pdb=" N LYS 2 462 " --> pdb=" O ASP 2 458 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET 2 463 " --> pdb=" O GLU 2 459 " (cutoff:3.500A) Processing helix chain '2' and resid 472 through 481 removed outlier: 3.554A pdb=" N LYS 2 476 " --> pdb=" O GLN 2 472 " (cutoff:3.500A) Processing helix chain '2' and resid 488 through 501 Processing helix chain '2' and resid 528 through 540 removed outlier: 3.798A pdb=" N PHE 2 532 " --> pdb=" O ALA 2 528 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS 2 534 " --> pdb=" O SER 2 530 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU 2 537 " --> pdb=" O LEU 2 533 " (cutoff:3.500A) Processing helix chain '2' and resid 574 through 579 Processing helix chain '2' and resid 593 through 606 removed outlier: 3.976A pdb=" N THR 2 598 " --> pdb=" O ASP 2 594 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER 2 599 " --> pdb=" O GLN 2 595 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS 2 601 " --> pdb=" O ARG 2 597 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU 2 602 " --> pdb=" O THR 2 598 " (cutoff:3.500A) Processing helix chain '2' and resid 632 through 636 removed outlier: 3.617A pdb=" N GLY 2 635 " --> pdb=" O PRO 2 632 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG 2 636 " --> pdb=" O ILE 2 633 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 632 through 636' Processing helix chain '2' and resid 642 through 647 Processing helix chain '2' and resid 650 through 657 removed outlier: 3.661A pdb=" N PHE 2 657 " --> pdb=" O ILE 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 668 through 686 removed outlier: 3.618A pdb=" N PHE 2 678 " --> pdb=" O MET 2 674 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS 2 683 " --> pdb=" O VAL 2 679 " (cutoff:3.500A) Processing helix chain '2' and resid 719 through 727 removed outlier: 3.947A pdb=" N ILE 2 725 " --> pdb=" O LYS 2 721 " (cutoff:3.500A) Processing helix chain '2' and resid 739 through 757 Processing helix chain '2' and resid 763 through 781 removed outlier: 3.568A pdb=" N HIS 2 781 " --> pdb=" O HIS 2 777 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 803 Processing helix chain '2' and resid 807 through 816 removed outlier: 3.922A pdb=" N SER 2 813 " --> pdb=" O SER 2 809 " (cutoff:3.500A) Processing helix chain '2' and resid 818 through 823 Processing helix chain '2' and resid 829 through 851 removed outlier: 3.706A pdb=" N ILE 2 835 " --> pdb=" O LEU 2 831 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN 2 849 " --> pdb=" O THR 2 845 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG 2 850 " --> pdb=" O TYR 2 846 " (cutoff:3.500A) Processing helix chain '2' and resid 852 through 855 removed outlier: 3.962A pdb=" N GLN 2 855 " --> pdb=" O GLY 2 852 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 852 through 855' Processing helix chain '2' and resid 865 through 873 removed outlier: 3.920A pdb=" N ALA 2 869 " --> pdb=" O LEU 2 865 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLN 2 871 " --> pdb=" O ASP 2 867 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE 2 872 " --> pdb=" O LYS 2 868 " (cutoff:3.500A) Processing helix chain '2' and resid 877 through 883 Processing helix chain '2' and resid 883 through 889 removed outlier: 3.568A pdb=" N ARG 2 887 " --> pdb=" O SER 2 883 " (cutoff:3.500A) Processing helix chain '3' and resid 15 through 18 Processing helix chain '3' and resid 19 through 24 removed outlier: 3.838A pdb=" N LEU 3 23 " --> pdb=" O TYR 3 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP 3 24 " --> pdb=" O LEU 3 20 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 19 through 24' Processing helix chain '3' and resid 38 through 43 Processing helix chain '3' and resid 51 through 58 Processing helix chain '3' and resid 58 through 68 removed outlier: 3.586A pdb=" N LEU 3 66 " --> pdb=" O ALA 3 62 " (cutoff:3.500A) Processing helix chain '3' and resid 69 through 88 removed outlier: 3.741A pdb=" N VAL 3 74 " --> pdb=" O PHE 3 70 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA 3 75 " --> pdb=" O GLU 3 71 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 95 removed outlier: 4.043A pdb=" N ALA 3 92 " --> pdb=" O ASP 3 88 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 121 removed outlier: 3.795A pdb=" N PHE 3 120 " --> pdb=" O THR 3 117 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 291 Processing helix chain '3' and resid 295 through 302 removed outlier: 3.615A pdb=" N SER 3 302 " --> pdb=" O GLN 3 298 " (cutoff:3.500A) Processing helix chain '3' and resid 310 through 323 removed outlier: 3.609A pdb=" N LEU 3 318 " --> pdb=" O LYS 3 314 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS 3 319 " --> pdb=" O LYS 3 315 " (cutoff:3.500A) Processing helix chain '3' and resid 351 through 360 Processing helix chain '3' and resid 398 through 402 removed outlier: 3.510A pdb=" N ALA 3 401 " --> pdb=" O MET 3 398 " (cutoff:3.500A) Processing helix chain '3' and resid 411 through 414 removed outlier: 3.557A pdb=" N MET 3 414 " --> pdb=" O PHE 3 411 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 411 through 414' Processing helix chain '3' and resid 415 through 428 removed outlier: 3.767A pdb=" N HIS 3 423 " --> pdb=" O ARG 3 419 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) Processing helix chain '3' and resid 464 through 469 Processing helix chain '3' and resid 472 through 477 Processing helix chain '3' and resid 490 through 506 Processing helix chain '3' and resid 564 through 577 removed outlier: 3.535A pdb=" N LYS 3 570 " --> pdb=" O ALA 3 566 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA 3 575 " --> pdb=" O TYR 3 571 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE 3 577 " --> pdb=" O HIS 3 573 " (cutoff:3.500A) Processing helix chain '3' and resid 583 through 599 Processing helix chain '3' and resid 614 through 633 removed outlier: 3.829A pdb=" N LEU 3 618 " --> pdb=" O THR 3 614 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS 3 630 " --> pdb=" O THR 3 626 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA 3 631 " --> pdb=" O ALA 3 627 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG 3 632 " --> pdb=" O HIS 3 628 " (cutoff:3.500A) Processing helix chain '3' and resid 638 through 654 removed outlier: 3.583A pdb=" N GLU 3 644 " --> pdb=" O GLN 3 640 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA 3 645 " --> pdb=" O ASP 3 641 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU 3 647 " --> pdb=" O GLU 3 643 " (cutoff:3.500A) Processing helix chain '3' and resid 741 through 759 Processing helix chain '3' and resid 765 through 775 removed outlier: 3.536A pdb=" N ASP 3 775 " --> pdb=" O SER 3 771 " (cutoff:3.500A) Processing helix chain '3' and resid 781 through 795 Processing helix chain '4' and resid 159 through 172 removed outlier: 3.583A pdb=" N ARG 4 168 " --> pdb=" O GLU 4 164 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE 4 169 " --> pdb=" O ASN 4 165 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU 4 170 " --> pdb=" O PHE 4 166 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 200 removed outlier: 3.687A pdb=" N ARG 4 196 " --> pdb=" O LEU 4 192 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 4 197 " --> pdb=" O TYR 4 193 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE 4 200 " --> pdb=" O ARG 4 196 " (cutoff:3.500A) Processing helix chain '4' and resid 213 through 219 Processing helix chain '4' and resid 219 through 229 Processing helix chain '4' and resid 229 through 248 Proline residue: 4 235 - end of helix removed outlier: 3.661A pdb=" N MET 4 239 " --> pdb=" O PRO 4 235 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG 4 248 " --> pdb=" O ILE 4 244 " (cutoff:3.500A) Processing helix chain '4' and resid 275 through 279 Processing helix chain '4' and resid 341 through 344 removed outlier: 3.783A pdb=" N SER 4 344 " --> pdb=" O HIS 4 341 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 341 through 344' 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 444 through 454 removed outlier: 3.578A pdb=" N LEU 4 448 " --> pdb=" O LYS 4 444 " (cutoff:3.500A) Processing helix chain '4' and resid 457 through 465 Processing helix chain '4' and resid 473 through 486 Processing helix chain '4' and resid 518 through 527 removed outlier: 4.410A pdb=" N TYR 4 524 " --> pdb=" O LEU 4 520 " (cutoff:3.500A) Processing helix chain '4' and resid 561 through 566 Processing helix chain '4' and resid 580 through 593 Processing helix chain '4' and resid 629 through 635 Processing helix chain '4' and resid 637 through 642 Processing helix chain '4' and resid 655 through 671 Processing helix chain '4' and resid 676 through 696 removed outlier: 3.750A pdb=" N ASP 4 689 " --> pdb=" O ALA 4 685 " (cutoff:3.500A) Processing helix chain '4' and resid 703 through 723 removed outlier: 3.758A pdb=" N ILE 4 720 " --> pdb=" O ASP 4 716 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY 4 721 " --> pdb=" O MET 4 717 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER 4 723 " --> pdb=" O LYS 4 719 " (cutoff:3.500A) Processing helix chain '4' and resid 731 through 748 removed outlier: 3.862A pdb=" N GLU 4 735 " --> pdb=" O PRO 4 731 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG 4 739 " --> pdb=" O GLU 4 735 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG 4 748 " --> pdb=" O HIS 4 744 " (cutoff:3.500A) Processing helix chain '4' and resid 754 through 773 removed outlier: 3.755A pdb=" N VAL 4 758 " --> pdb=" O GLU 4 754 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN 4 771 " --> pdb=" O GLU 4 767 " (cutoff:3.500A) Processing helix chain '4' and resid 783 through 788 Processing helix chain '4' and resid 791 through 795 Processing helix chain '4' and resid 800 through 812 removed outlier: 4.084A pdb=" N LEU 4 808 " --> pdb=" O ALA 4 804 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER 4 811 " --> pdb=" O LYS 4 807 " (cutoff:3.500A) Processing helix chain '4' and resid 820 through 831 Processing helix chain '4' and resid 836 through 847 Processing helix chain '4' and resid 848 through 850 No H-bonds generated for 'chain '4' and resid 848 through 850' Processing helix chain '6' and resid 21 through 36 removed outlier: 3.557A pdb=" N LYS 6 25 " --> pdb=" O GLU 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 52 removed outlier: 3.999A pdb=" N GLN 6 48 " --> pdb=" O ILE 6 44 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU 6 49 " --> pdb=" O LYS 6 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 55 No H-bonds generated for 'chain '6' and resid 53 through 55' Processing helix chain '6' and resid 65 through 72 removed outlier: 3.762A pdb=" N GLN 6 70 " --> pdb=" O VAL 6 66 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE 6 71 " --> pdb=" O ASP 6 67 " (cutoff:3.500A) Processing helix chain '6' and resid 72 through 80 removed outlier: 3.526A pdb=" N GLN 6 80 " --> pdb=" O SER 6 76 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 100 removed outlier: 3.596A pdb=" N ARG 6 92 " --> pdb=" O PRO 6 88 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA 6 93 " --> pdb=" O TYR 6 89 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 126 Processing helix chain '6' and resid 186 through 189 removed outlier: 3.842A pdb=" N ARG 6 189 " --> pdb=" O ALA 6 186 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 186 through 189' Processing helix chain '6' and resid 231 through 233 No H-bonds generated for 'chain '6' and resid 231 through 233' Processing helix chain '6' and resid 321 through 329 Processing helix chain '6' and resid 330 through 343 removed outlier: 3.555A pdb=" N LYS 6 336 " --> pdb=" O LYS 6 332 " (cutoff:3.500A) Processing helix chain '6' and resid 345 through 355 removed outlier: 4.089A pdb=" N CYS 6 351 " --> pdb=" O TYR 6 347 " (cutoff:3.500A) Processing helix chain '6' and resid 361 through 374 removed outlier: 3.590A pdb=" N LEU 6 372 " --> pdb=" O VAL 6 368 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE 6 373 " --> pdb=" O LEU 6 369 " (cutoff:3.500A) Processing helix chain '6' and resid 401 through 413 removed outlier: 3.513A pdb=" N PHE 6 405 " --> pdb=" O ALA 6 401 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU 6 406 " --> pdb=" O LYS 6 402 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL 6 409 " --> pdb=" O PHE 6 405 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU 6 410 " --> pdb=" O LEU 6 406 " (cutoff:3.500A) Processing helix chain '6' and resid 462 through 465 removed outlier: 3.708A pdb=" N MET 6 465 " --> pdb=" O PHE 6 462 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 462 through 465' Processing helix chain '6' and resid 466 through 476 removed outlier: 3.695A pdb=" N VAL 6 471 " --> pdb=" O VAL 6 467 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA 6 472 " --> pdb=" O ARG 6 468 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU 6 475 " --> pdb=" O VAL 6 471 " (cutoff:3.500A) Processing helix chain '6' and resid 515 through 519 Processing helix chain '6' and resid 523 through 530 Processing helix chain '6' and resid 542 through 558 removed outlier: 3.503A pdb=" N TYR 6 546 " --> pdb=" O GLU 6 542 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA 6 547 " --> pdb=" O VAL 6 543 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG 6 551 " --> pdb=" O ALA 6 547 " (cutoff:3.500A) Processing helix chain '6' and resid 571 through 582 removed outlier: 3.707A pdb=" N GLN 6 581 " --> pdb=" O LEU 6 577 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE 6 582 " --> pdb=" O PHE 6 578 " (cutoff:3.500A) Processing helix chain '6' and resid 587 through 605 removed outlier: 3.684A pdb=" N ASP 6 592 " --> pdb=" O LYS 6 588 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP 6 605 " --> pdb=" O LEU 6 601 " (cutoff:3.500A) Processing helix chain '6' and resid 618 through 635 Processing helix chain '6' and resid 641 through 656 removed outlier: 3.722A pdb=" N VAL 6 645 " --> pdb=" O GLN 6 641 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 6 652 " --> pdb=" O ALA 6 648 " (cutoff:3.500A) Processing helix chain '6' and resid 721 through 739 removed outlier: 3.616A pdb=" N VAL 6 728 " --> pdb=" O SER 6 724 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU 6 736 " --> pdb=" O ARG 6 732 " (cutoff:3.500A) Processing helix chain '6' and resid 751 through 759 removed outlier: 3.729A pdb=" N ILE 6 756 " --> pdb=" O TYR 6 752 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU 6 759 " --> pdb=" O GLU 6 755 " (cutoff:3.500A) Processing helix chain '6' and resid 767 through 777 removed outlier: 4.185A pdb=" N ARG 6 771 " --> pdb=" O ILE 6 767 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU 6 774 " --> pdb=" O LYS 6 770 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS 6 775 " --> pdb=" O ARG 6 771 " (cutoff:3.500A) Processing helix chain '7' and resid 31 through 40 removed outlier: 3.984A pdb=" N VAL 7 38 " --> pdb=" O GLY 7 34 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU 7 40 " --> pdb=" O GLN 7 36 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 59 removed outlier: 3.638A pdb=" N VAL 7 55 " --> pdb=" O ASP 7 51 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU 7 57 " --> pdb=" O ASP 7 53 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP 7 59 " --> pdb=" O VAL 7 55 " (cutoff:3.500A) Processing helix chain '7' and resid 59 through 69 removed outlier: 3.786A pdb=" N VAL 7 63 " --> pdb=" O ASP 7 59 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP 7 64 " --> pdb=" O PRO 7 60 " (cutoff:3.500A) Processing helix chain '7' and resid 69 through 84 removed outlier: 3.528A pdb=" N ALA 7 78 " --> pdb=" O ALA 7 74 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP 7 79 " --> pdb=" O LYS 7 75 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA 7 80 " --> pdb=" O LEU 7 76 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL 7 81 " --> pdb=" O PHE 7 77 " (cutoff:3.500A) Processing helix chain '7' and resid 148 through 152 Processing helix chain '7' and resid 208 through 215 removed outlier: 3.612A pdb=" N GLN 7 212 " --> pdb=" O SER 7 208 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR 7 213 " --> pdb=" O GLN 7 209 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN 7 214 " --> pdb=" O GLU 7 210 " (cutoff:3.500A) Processing helix chain '7' and resid 332 through 340 Processing helix chain '7' and resid 347 through 360 removed outlier: 3.563A pdb=" N LEU 7 357 " --> pdb=" O ALA 7 353 " (cutoff:3.500A) Processing helix chain '7' and resid 386 through 398 removed outlier: 3.707A pdb=" N ARG 7 396 " --> pdb=" O SER 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 406 through 410 removed outlier: 3.524A pdb=" N SER 7 410 " --> pdb=" O ARG 7 407 " (cutoff:3.500A) Processing helix chain '7' and resid 424 through 428 removed outlier: 3.724A pdb=" N LEU 7 427 " --> pdb=" O SER 7 424 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR 7 428 " --> pdb=" O GLY 7 425 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 424 through 428' Processing helix chain '7' and resid 451 through 465 removed outlier: 3.792A pdb=" N THR 7 456 " --> pdb=" O GLU 7 452 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA 7 457 " --> pdb=" O ALA 7 453 " (cutoff:3.500A) Processing helix chain '7' and resid 500 through 505 Processing helix chain '7' and resid 508 through 515 removed outlier: 3.507A pdb=" N ARG 7 514 " --> pdb=" O ALA 7 510 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE 7 515 " --> pdb=" O LEU 7 511 " (cutoff:3.500A) Processing helix chain '7' and resid 526 through 544 removed outlier: 4.130A pdb=" N ARG 7 532 " --> pdb=" O ASP 7 528 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N HIS 7 543 " --> pdb=" O TYR 7 539 " (cutoff:3.500A) Processing helix chain '7' and resid 555 through 566 removed outlier: 3.583A pdb=" N ARG 7 560 " --> pdb=" O MET 7 556 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG 7 561 " --> pdb=" O LYS 7 557 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 576 No H-bonds generated for 'chain '7' and resid 574 through 576' Processing helix chain '7' and resid 577 through 596 removed outlier: 3.531A pdb=" N ALA 7 583 " --> pdb=" O ASP 7 579 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU 7 587 " --> pdb=" O ALA 7 583 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS 7 596 " --> pdb=" O ALA 7 592 " (cutoff:3.500A) Processing helix chain '7' and resid 602 through 620 removed outlier: 3.994A pdb=" N LEU 7 606 " --> pdb=" O SER 7 602 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU 7 607 " --> pdb=" O ALA 7 603 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA 7 615 " --> pdb=" O ARG 7 611 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 7 617 " --> pdb=" O SER 7 613 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG 7 618 " --> pdb=" O THR 7 614 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU 7 619 " --> pdb=" O ALA 7 615 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 641 removed outlier: 3.730A pdb=" N VAL 7 630 " --> pdb=" O GLU 7 626 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU 7 632 " --> pdb=" O GLU 7 628 " (cutoff:3.500A) Processing helix chain '5' and resid 30 through 37 Processing helix chain '5' and resid 46 through 52 removed outlier: 3.604A pdb=" N THR 5 49 " --> pdb=" O THR 5 46 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY 5 50 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE 5 51 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR 5 52 " --> pdb=" O THR 5 49 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 46 through 52' Processing helix chain '5' and resid 53 through 63 removed outlier: 3.704A pdb=" N ARG 5 61 " --> pdb=" O ASP 5 57 " (cutoff:3.500A) Processing helix chain '5' and resid 73 through 79 Processing helix chain '5' and resid 81 through 91 removed outlier: 3.914A pdb=" N ALA 5 85 " --> pdb=" O ASP 5 81 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 108 removed outlier: 4.672A pdb=" N GLN 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU 5 98 " --> pdb=" O GLU 5 94 " (cutoff:3.500A) Processing helix chain '5' and resid 141 through 145 removed outlier: 3.644A pdb=" N MET 5 145 " --> pdb=" O SER 5 142 " (cutoff:3.500A) Processing helix chain '5' and resid 316 through 320 Processing helix chain '5' and resid 320 through 328 Processing helix chain '5' and resid 329 through 338 removed outlier: 3.847A pdb=" N GLU 5 333 " --> pdb=" O PRO 5 329 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE 5 335 " --> pdb=" O VAL 5 331 " (cutoff:3.500A) Processing helix chain '5' and resid 346 through 359 removed outlier: 4.351A pdb=" N ALA 5 352 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU 5 357 " --> pdb=" O ILE 5 353 " (cutoff:3.500A) Processing helix chain '5' and resid 383 through 398 removed outlier: 3.604A pdb=" N LEU 5 391 " --> pdb=" O LYS 5 387 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS 5 392 " --> pdb=" O SER 5 388 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU 5 395 " --> pdb=" O LEU 5 391 " (cutoff:3.500A) Processing helix chain '5' and resid 432 through 437 removed outlier: 3.529A pdb=" N ALA 5 437 " --> pdb=" O ALA 5 433 " (cutoff:3.500A) Processing helix chain '5' and resid 446 through 450 removed outlier: 3.559A pdb=" N LYS 5 449 " --> pdb=" O GLU 5 446 " (cutoff:3.500A) Processing helix chain '5' and resid 451 through 465 Processing helix chain '5' and resid 507 through 514 removed outlier: 3.651A pdb=" N SER 5 512 " --> pdb=" O THR 5 509 " (cutoff:3.500A) Processing helix chain '5' and resid 555 through 569 removed outlier: 3.623A pdb=" N LYS 5 561 " --> pdb=" O ALA 5 557 " (cutoff:3.500A) Processing helix chain '5' and resid 575 through 590 removed outlier: 3.947A pdb=" N ALA 5 579 " --> pdb=" O SER 5 575 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS 5 581 " --> pdb=" O GLU 5 577 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS 5 583 " --> pdb=" O ALA 5 579 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN 5 584 " --> pdb=" O GLU 5 580 " (cutoff:3.500A) Processing helix chain '5' and resid 597 through 602 Processing helix chain '5' and resid 609 through 627 Processing helix chain '5' and resid 633 through 652 removed outlier: 3.856A pdb=" N GLU 5 639 " --> pdb=" O ALA 5 635 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE 5 644 " --> pdb=" O ALA 5 640 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN 5 645 " --> pdb=" O LEU 5 641 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL 5 646 " --> pdb=" O ARG 5 642 " (cutoff:3.500A) Processing helix chain '5' and resid 664 through 683 removed outlier: 3.900A pdb=" N MET 5 671 " --> pdb=" O GLU 5 667 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG 5 681 " --> pdb=" O LYS 5 677 " (cutoff:3.500A) Processing helix chain '5' and resid 691 through 701 Processing helix chain '5' and resid 704 through 718 removed outlier: 3.687A pdb=" N LYS 5 710 " --> pdb=" O HIS 5 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 230 through 233 Processing sheet with id=AA2, first strand: chain '2' and resid 417 through 422 removed outlier: 9.830A pdb=" N SER 2 393 " --> pdb=" O THR 2 437 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N ILE 2 439 " --> pdb=" O SER 2 393 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASP 2 395 " --> pdb=" O ILE 2 439 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 314 through 315 Processing sheet with id=AA4, first strand: chain '2' and resid 335 through 340 removed outlier: 6.066A pdb=" N TYR 2 327 " --> pdb=" O LEU 2 336 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL 2 325 " --> pdb=" O PRO 2 338 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N CYS 2 340 " --> pdb=" O SER 2 323 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER 2 323 " --> pdb=" O CYS 2 340 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU 2 322 " --> pdb=" O ILE 2 369 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET 2 365 " --> pdb=" O LYS 2 326 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASN 2 328 " --> pdb=" O VAL 2 363 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL 2 363 " --> pdb=" O ASN 2 328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 546 through 547 removed outlier: 6.761A pdb=" N THR 2 546 " --> pdb=" O ASP 2 587 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE 2 586 " --> pdb=" O ALA 2 629 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU 2 520 " --> pdb=" O CYS 2 661 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL 2 663 " --> pdb=" O LEU 2 520 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS 2 522 " --> pdb=" O VAL 2 663 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 582 through 583 removed outlier: 6.933A pdb=" N GLY 2 582 " --> pdb=" O THR 2 625 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '2' and resid 610 through 613 Processing sheet with id=AA8, first strand: chain '3' and resid 47 through 50 removed outlier: 5.868A pdb=" N LEU 3 47 " --> pdb=" O GLY 3 101 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU 3 103 " --> pdb=" O LEU 3 47 " (cutoff:3.500A) removed outlier: 5.576A 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 126 Processing sheet with id=AB1, first strand: chain '3' and resid 234 through 235 removed outlier: 6.728A pdb=" N THR 3 200 " --> pdb=" O THR 3 132 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS 3 134 " --> pdb=" O THR 3 198 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR 3 198 " --> pdb=" O CYS 3 134 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL 3 217 " --> pdb=" O ILE 3 201 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASP 3 218 " --> pdb=" O LEU 3 260 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 234 through 235 Processing sheet with id=AB3, first strand: chain '3' and resid 327 through 328 removed outlier: 3.667A pdb=" N ARG 3 327 " --> pdb=" O ILE 3 335 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 404 through 409 removed outlier: 7.239A pdb=" N GLY 3 404 " --> pdb=" O SER 3 447 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU 3 449 " --> pdb=" O GLY 3 404 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL 3 406 " --> pdb=" O LEU 3 449 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA 3 451 " --> pdb=" O VAL 3 406 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE 3 408 " --> pdb=" O ALA 3 451 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY 3 345 " --> pdb=" O ALA 3 452 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 430 through 432 Processing sheet with id=AB6, first strand: chain '3' and resid 762 through 764 Processing sheet with id=AB7, first strand: chain '4' and resid 282 through 285 removed outlier: 3.593A pdb=" N GLY 4 392 " --> pdb=" O ILE 4 283 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE 4 371 " --> pdb=" O ILE 4 416 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG 4 291 " --> pdb=" O LYS 4 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 299 through 300 Processing sheet with id=AB9, first strand: chain '4' and resid 312 through 313 Processing sheet with id=AC1, first strand: chain '4' and resid 317 through 318 Processing sheet with id=AC2, first strand: chain '4' and resid 408 through 409 Processing sheet with id=AC3, first strand: chain '4' and resid 533 through 534 removed outlier: 6.953A pdb=" N THR 4 533 " --> pdb=" O ASP 4 574 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE 4 506 " --> pdb=" O ALA 4 615 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ALA 4 617 " --> pdb=" O ILE 4 506 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU 4 508 " --> pdb=" O ALA 4 617 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU 4 507 " --> pdb=" O PHE 4 648 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 546 through 550 removed outlier: 3.738A pdb=" N GLN 4 555 " --> pdb=" O ASP 4 550 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '4' and resid 595 through 600 removed outlier: 3.593A pdb=" N LYS 4 600 " --> pdb=" O ILE 4 603 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '6' and resid 60 through 64 removed outlier: 6.061A pdb=" N LEU 6 61 " --> pdb=" O ALA 6 113 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLN 6 115 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL 6 63 " --> pdb=" O GLN 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain '6' and resid 134 through 135 removed outlier: 8.342A pdb=" N LYS 6 241 " --> pdb=" O PRO 6 305 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP 6 243 " --> pdb=" O VAL 6 303 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL 6 303 " --> pdb=" O ASP 6 243 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR 6 245 " --> pdb=" O CYS 6 301 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N SER 6 223 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N PHE 6 298 " --> pdb=" O SER 6 223 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU 6 225 " --> pdb=" O PHE 6 298 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ALA 6 300 " --> pdb=" O GLU 6 225 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG 6 207 " --> pdb=" O VAL 6 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '6' and resid 164 through 169 removed outlier: 6.125A pdb=" N VAL 6 164 " --> pdb=" O CYS 6 158 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N CYS 6 158 " --> pdb=" O VAL 6 164 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG 6 166 " --> pdb=" O PHE 6 156 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE 6 156 " --> pdb=" O ARG 6 166 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU 6 192 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '6' and resid 164 through 169 removed outlier: 6.125A pdb=" N VAL 6 164 " --> pdb=" O CYS 6 158 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N CYS 6 158 " --> pdb=" O VAL 6 164 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG 6 166 " --> pdb=" O PHE 6 156 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE 6 156 " --> pdb=" O ARG 6 166 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS 6 148 " --> pdb=" O PHE 6 203 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE 6 203 " --> pdb=" O HIS 6 148 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ARG 6 199 " --> pdb=" O VAL 6 152 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '6' and resid 378 through 379 Processing sheet with id=AD2, first strand: chain '6' and resid 417 through 420 removed outlier: 3.617A pdb=" N CYS 6 457 " --> pdb=" O SER 6 498 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY 6 396 " --> pdb=" O ALA 6 503 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 433 through 435 Processing sheet with id=AD4, first strand: chain '6' and resid 481 through 486 Processing sheet with id=AD5, first strand: chain '6' and resid 585 through 586 removed outlier: 7.157A pdb=" N LYS 6 585 " --> pdb=" O VAL 6 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain '7' and resid 47 through 49 Processing sheet with id=AD7, first strand: chain '7' and resid 270 through 271 removed outlier: 3.632A pdb=" N LYS 7 236 " --> pdb=" O THR 7 168 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL 7 170 " --> pdb=" O GLU 7 234 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLU 7 234 " --> pdb=" O VAL 7 170 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '7' and resid 190 through 194 removed outlier: 3.545A pdb=" N ALA 7 180 " --> pdb=" O GLN 7 193 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N PHE 7 232 " --> pdb=" O PRO 7 175 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N MET 7 177 " --> pdb=" O ILE 7 230 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE 7 230 " --> pdb=" O MET 7 177 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL 7 179 " --> pdb=" O ARG 7 228 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR 7 181 " --> pdb=" O GLY 7 226 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY 7 226 " --> pdb=" O THR 7 181 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N THR 7 183 " --> pdb=" O THR 7 224 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N THR 7 224 " --> pdb=" O THR 7 183 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '7' and resid 401 through 404 removed outlier: 6.680A pdb=" N CYS 7 442 " --> pdb=" O LEU 7 485 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '5' and resid 244 through 246 removed outlier: 6.807A pdb=" N LYS 5 228 " --> pdb=" O ILE 5 156 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '5' and resid 266 through 268 removed outlier: 6.877A pdb=" N MET 5 266 " --> pdb=" O LEU 5 297 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '5' and resid 401 through 403 removed outlier: 3.560A pdb=" N CYS 5 443 " --> pdb=" O VAL 5 402 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '5' and resid 417 through 418 Processing sheet with id=AE5, first strand: chain '5' and resid 688 through 690 1113 hydrogen bonds defined for protein. 3171 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.58 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9398 1.35 - 1.47: 5642 1.47 - 1.59: 12289 1.59 - 1.71: 21 1.71 - 1.83: 197 Bond restraints: 27547 Sorted by residual: bond pdb=" N ILE 3 763 " pdb=" CA ILE 3 763 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.72e+00 bond pdb=" N ILE 3 804 " pdb=" CA ILE 3 804 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.24e+00 bond pdb=" N ILE 3 805 " pdb=" CA ILE 3 805 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.06e+00 bond pdb=" N ILE 2 477 " pdb=" CA ILE 2 477 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.01e+00 bond pdb=" CA SER 4 515 " pdb=" CB SER 4 515 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.33e-02 5.65e+03 8.54e+00 ... (remaining 27542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 36905 2.21 - 4.42: 547 4.42 - 6.63: 51 6.63 - 8.84: 3 8.84 - 11.06: 4 Bond angle restraints: 37510 Sorted by residual: angle pdb=" PA ATP 21001 " pdb=" O3A ATP 21001 " pdb=" PB ATP 21001 " ideal model delta sigma weight residual 136.83 125.77 11.06 1.00e+00 1.00e+00 1.22e+02 angle pdb=" PA ATP 6 902 " pdb=" O3A ATP 6 902 " pdb=" PB ATP 6 902 " ideal model delta sigma weight residual 136.83 126.31 10.52 1.00e+00 1.00e+00 1.11e+02 angle pdb=" PB ATP 4 902 " pdb=" O3B ATP 4 902 " pdb=" PG ATP 4 902 " ideal model delta sigma weight residual 139.87 129.52 10.35 1.00e+00 1.00e+00 1.07e+02 angle pdb=" PB ATP 6 902 " pdb=" O3B ATP 6 902 " pdb=" PG ATP 6 902 " ideal model delta sigma weight residual 139.87 130.39 9.48 1.00e+00 1.00e+00 8.99e+01 angle pdb=" PB ATP 21001 " pdb=" O3B ATP 21001 " pdb=" PG ATP 21001 " ideal model delta sigma weight residual 139.87 131.40 8.47 1.00e+00 1.00e+00 7.18e+01 ... (remaining 37505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 15683 17.17 - 34.35: 894 34.35 - 51.52: 116 51.52 - 68.69: 140 68.69 - 85.86: 7 Dihedral angle restraints: 16840 sinusoidal: 5901 harmonic: 10939 Sorted by residual: dihedral pdb=" CA PRO 4 297 " pdb=" C PRO 4 297 " pdb=" N GLU 4 298 " pdb=" CA GLU 4 298 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASP 3 402 " pdb=" CB ASP 3 402 " pdb=" CG ASP 3 402 " pdb=" OD1 ASP 3 402 " ideal model delta sinusoidal sigma weight residual -30.00 -88.81 58.81 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP 3 412 " pdb=" CB ASP 3 412 " pdb=" CG ASP 3 412 " pdb=" OD1 ASP 3 412 " ideal model delta sinusoidal sigma weight residual -30.00 -88.48 58.48 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 16837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3437 0.047 - 0.094: 736 0.094 - 0.140: 260 0.140 - 0.187: 22 0.187 - 0.234: 13 Chirality restraints: 4468 Sorted by residual: chirality pdb=" CA ILE 2 762 " pdb=" N ILE 2 762 " pdb=" C ILE 2 762 " pdb=" CB ILE 2 762 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA VAL 2 731 " pdb=" N VAL 2 731 " pdb=" C VAL 2 731 " pdb=" CB VAL 2 731 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA VAL 6 226 " pdb=" N VAL 6 226 " pdb=" C VAL 6 226 " pdb=" CB VAL 6 226 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 4465 not shown) Planarity restraints: 4934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 751 " 0.245 9.50e-02 1.11e+02 1.10e-01 7.42e+00 pdb=" NE ARG 2 751 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG 2 751 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 751 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 751 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE 6 104 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO 6 105 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO 6 105 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO 6 105 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY 2 190 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO 2 191 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO 2 191 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO 2 191 " 0.028 5.00e-02 4.00e+02 ... (remaining 4931 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 7 2.36 - 2.99: 13849 2.99 - 3.63: 40763 3.63 - 4.26: 58861 4.26 - 4.90: 95898 Nonbonded interactions: 209378 Sorted by model distance: nonbonded pdb=" OG SER 2 530 " pdb="MG MG 21003 " model vdw 1.720 2.170 nonbonded pdb=" O1B ATP 4 902 " pdb="MG MG 4 903 " model vdw 1.733 2.170 nonbonded pdb=" CB SER 7 208 " pdb="ZN ZN 7 802 " model vdw 1.996 2.630 nonbonded pdb=" OG SER 6 403 " pdb="MG MG 6 903 " model vdw 2.065 2.170 nonbonded pdb=" OD2 ASP 6 460 " pdb="MG MG 6 903 " model vdw 2.095 2.170 ... (remaining 209373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.140 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 27.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.004 0.052 27563 Z= 0.233 Angle : 0.636 21.643 37534 Z= 0.384 Chirality : 0.045 0.234 4468 Planarity : 0.004 0.110 4934 Dihedral : 12.829 85.863 9708 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 0.08 % Allowed : 0.35 % Favored : 99.57 % 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: -1.21 (0.14), residues: 3695 helix: -0.38 (0.13), residues: 1425 sheet: -1.53 (0.25), residues: 470 loop : -0.82 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 6 529 TYR 0.009 0.001 TYR 4 249 PHE 0.012 0.001 PHE 6 530 TRP 0.007 0.001 TRP 6 614 HIS 0.003 0.000 HIS 4 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.23 (27547) covalent geometry : angle 0.60146 / 0.38 (37510) hydrogen bonds : bond 0.25614 / 17.46 ( 1109) hydrogen bonds : angle 8.09902 / 5.65 ( 3171) metal coordination : bond 0.00727 / 0.39 ( 16) metal coordination : angle 8.20351 / 5.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 339 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 828 ASN cc_start: 0.8280 (m-40) cc_final: 0.7761 (t0) REVERT: 2 890 LYS cc_start: 0.9102 (tptt) cc_final: 0.8516 (tttm) REVERT: 4 541 VAL cc_start: 0.8713 (t) cc_final: 0.8463 (t) REVERT: 6 521 ASN cc_start: 0.8199 (t0) cc_final: 0.7969 (t0) outliers start: 2 outliers final: 0 residues processed: 341 average time/residue: 0.1588 time to fit residues: 86.8044 Evaluate side-chains 188 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0010 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 287 HIS 2 299 GLN 2 321 GLN ** 2 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 511 HIS 2 621 GLN 2 849 ASN ** 3 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 766 ASN ** 3 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 171 GLN 4 214 HIS ** 4 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 420 HIS ** 4 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 187 ASN 6 345 ASN ** 6 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 18 GLN ** 7 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 186 GLN 7 270 HIS 7 479 ASN 7 504 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.090066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061641 restraints weight = 115904.815| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 4.79 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27563 Z= 0.136 Angle : 0.599 13.651 37534 Z= 0.298 Chirality : 0.042 0.177 4468 Planarity : 0.004 0.054 4934 Dihedral : 5.979 83.556 4099 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 0.86 % Allowed : 6.21 % Favored : 92.93 % 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: -0.68 (0.14), residues: 3695 helix: 0.43 (0.14), residues: 1483 sheet: -1.53 (0.24), residues: 503 loop : -0.78 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 6 619 TYR 0.015 0.001 TYR 6 347 PHE 0.018 0.001 PHE 7 515 TRP 0.019 0.001 TRP 7 593 HIS 0.008 0.001 HIS 2 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (27547) covalent geometry : angle 0.57790 / 0.30 (37510) hydrogen bonds : bond 0.05060 / 3.48 ( 1109) hydrogen bonds : angle 5.42497 / 3.72 ( 3171) metal coordination : bond 0.00912 / 0.51 ( 16) metal coordination : angle 6.27858 / 4.41 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 299 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8244 (pp30) REVERT: 2 674 MET cc_start: 0.9228 (tpp) cc_final: 0.8948 (tpt) REVERT: 2 793 MET cc_start: 0.9440 (tpp) cc_final: 0.9078 (tpp) REVERT: 2 828 ASN cc_start: 0.8976 (m-40) cc_final: 0.8192 (t0) REVERT: 2 836 LEU cc_start: 0.9401 (mt) cc_final: 0.9164 (tt) REVERT: 2 890 LYS cc_start: 0.9053 (tptt) cc_final: 0.8375 (tttm) REVERT: 3 303 LEU cc_start: 0.8885 (mt) cc_final: 0.8571 (mt) REVERT: 3 438 ILE cc_start: 0.7809 (mt) cc_final: 0.7511 (pt) REVERT: 3 799 MET cc_start: 0.9412 (ttp) cc_final: 0.9087 (ttp) REVERT: 4 271 MET cc_start: 0.7723 (ptt) cc_final: 0.7437 (ptm) REVERT: 4 317 MET cc_start: 0.7382 (tpp) cc_final: 0.7035 (tpp) REVERT: 4 531 GLN cc_start: 0.7035 (tm-30) cc_final: 0.6759 (tm-30) REVERT: 4 699 MET cc_start: 0.8699 (mmt) cc_final: 0.8458 (mmm) REVERT: 4 738 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8236 (mp) REVERT: 4 742 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8201 (mt-10) REVERT: 6 82 GLU cc_start: 0.8216 (pm20) cc_final: 0.8014 (pm20) REVERT: 6 496 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7844 (mtm-85) REVERT: 6 521 ASN cc_start: 0.9199 (t0) cc_final: 0.8675 (t0) REVERT: 7 446 GLU cc_start: 0.9152 (tt0) cc_final: 0.8624 (tt0) REVERT: 7 450 MET cc_start: 0.7187 (mmm) cc_final: 0.6965 (mmm) outliers start: 22 outliers final: 12 residues processed: 216 average time/residue: 0.1481 time to fit residues: 53.2198 Evaluate side-chains 198 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 299 GLN Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 134 CYS Chi-restraints excluded: chain 3 residue 433 ILE Chi-restraints excluded: chain 4 residue 419 ILE Chi-restraints excluded: chain 4 residue 622 SER Chi-restraints excluded: chain 4 residue 669 LEU Chi-restraints excluded: chain 4 residue 738 ILE Chi-restraints excluded: chain 6 residue 122 LYS Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 249 ILE Chi-restraints excluded: chain 6 residue 251 VAL Chi-restraints excluded: chain 6 residue 496 ARG Chi-restraints excluded: chain 7 residue 436 LEU Chi-restraints excluded: chain 7 residue 461 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 291 optimal weight: 7.9990 chunk 353 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 193 optimal weight: 50.0000 chunk 129 optimal weight: 20.0000 chunk 280 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 284 optimal weight: 20.0000 chunk 362 optimal weight: 30.0000 chunk 55 optimal weight: 0.8980 chunk 341 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 299 GLN 2 838 GLN ** 3 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 665 HIS ** 6 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 556 HIS ** 6 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 465 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.087803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059268 restraints weight = 114332.842| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 4.68 r_work: 0.2951 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27563 Z= 0.193 Angle : 0.585 8.648 37534 Z= 0.294 Chirality : 0.042 0.183 4468 Planarity : 0.004 0.050 4934 Dihedral : 5.957 83.789 4099 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.49 % Favored : 94.48 % Rotamer: Outliers : 1.21 % Allowed : 8.32 % Favored : 90.47 % 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: -0.53 (0.14), residues: 3695 helix: 0.64 (0.14), residues: 1501 sheet: -1.56 (0.23), residues: 517 loop : -0.77 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 6 619 TYR 0.020 0.001 TYR 2 535 PHE 0.014 0.001 PHE 6 172 TRP 0.013 0.001 TRP 7 593 HIS 0.006 0.001 HIS 2 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (27547) covalent geometry : angle 0.57299 / 0.29 (37510) hydrogen bonds : bond 0.03794 / 2.62 ( 1109) hydrogen bonds : angle 4.95832 / 3.40 ( 3171) metal coordination : bond 0.01121 / 0.58 ( 16) metal coordination : angle 4.68318 / 3.20 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 222 MET cc_start: 0.9214 (tmm) cc_final: 0.8997 (tmm) REVERT: 2 674 MET cc_start: 0.9562 (tpp) cc_final: 0.9249 (tpp) REVERT: 2 755 MET cc_start: 0.9025 (ptp) cc_final: 0.8729 (ppp) REVERT: 2 793 MET cc_start: 0.9588 (tpp) cc_final: 0.9330 (tpp) REVERT: 2 890 LYS cc_start: 0.9136 (tptt) cc_final: 0.8333 (tttm) REVERT: 3 303 LEU cc_start: 0.9028 (mt) cc_final: 0.8737 (mt) REVERT: 3 438 ILE cc_start: 0.7476 (mt) cc_final: 0.7202 (pt) REVERT: 3 799 MET cc_start: 0.9537 (ttp) cc_final: 0.9172 (ttp) REVERT: 4 317 MET cc_start: 0.7759 (tpp) cc_final: 0.7363 (tpp) REVERT: 4 559 GLN cc_start: 0.8959 (mm110) cc_final: 0.8499 (tm-30) REVERT: 4 699 MET cc_start: 0.9274 (mmt) cc_final: 0.9024 (mmm) REVERT: 4 738 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8546 (mp) REVERT: 4 742 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8771 (mt-10) REVERT: 6 475 GLU cc_start: 0.8942 (tp30) cc_final: 0.8586 (tp30) REVERT: 6 496 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8245 (mtm-85) REVERT: 6 521 ASN cc_start: 0.9482 (t0) cc_final: 0.9007 (t0) REVERT: 7 446 GLU cc_start: 0.9215 (tt0) cc_final: 0.8647 (tt0) REVERT: 7 559 MET cc_start: 0.8212 (mmm) cc_final: 0.7882 (mmm) outliers start: 31 outliers final: 17 residues processed: 204 average time/residue: 0.1390 time to fit residues: 48.1951 Evaluate side-chains 185 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 399 LEU Chi-restraints excluded: chain 2 residue 544 ILE Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 134 CYS Chi-restraints excluded: chain 3 residue 433 ILE Chi-restraints excluded: chain 4 residue 419 ILE Chi-restraints excluded: chain 4 residue 598 ILE Chi-restraints excluded: chain 4 residue 669 LEU Chi-restraints excluded: chain 4 residue 738 ILE Chi-restraints excluded: chain 6 residue 122 LYS Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 249 ILE Chi-restraints excluded: chain 6 residue 329 MET Chi-restraints excluded: chain 6 residue 411 GLU Chi-restraints excluded: chain 6 residue 496 ARG Chi-restraints excluded: chain 7 residue 131 MET Chi-restraints excluded: chain 7 residue 441 VAL Chi-restraints excluded: chain 7 residue 461 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 126 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 274 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 344 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 325 optimal weight: 40.0000 chunk 226 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 chunk 82 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 299 GLN ** 3 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 483 GLN ** 6 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 509 HIS 6 635 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.087286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.058680 restraints weight = 114532.634| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.69 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27563 Z= 0.182 Angle : 0.566 9.043 37534 Z= 0.283 Chirality : 0.042 0.178 4468 Planarity : 0.003 0.047 4934 Dihedral : 5.991 87.268 4099 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 1.21 % Allowed : 10.12 % Favored : 88.67 % 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: -0.44 (0.14), residues: 3695 helix: 0.78 (0.14), residues: 1504 sheet: -1.61 (0.23), residues: 529 loop : -0.74 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 6 619 TYR 0.014 0.001 TYR 2 535 PHE 0.013 0.001 PHE 6 172 TRP 0.011 0.001 TRP 7 593 HIS 0.005 0.001 HIS 4 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (27547) covalent geometry : angle 0.55673 / 0.28 (37510) hydrogen bonds : bond 0.03284 / 2.26 ( 1109) hydrogen bonds : angle 4.70738 / 3.23 ( 3171) metal coordination : bond 0.01052 / 0.57 ( 16) metal coordination : angle 4.12219 / 2.65 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 1.024 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: 2 423 ASP cc_start: 0.8402 (t0) cc_final: 0.8116 (t0) REVERT: 2 674 MET cc_start: 0.9297 (tpp) cc_final: 0.8913 (tpp) REVERT: 2 755 MET cc_start: 0.8992 (ptp) cc_final: 0.8715 (ppp) REVERT: 2 773 MET cc_start: 0.9114 (mtm) cc_final: 0.8891 (mtm) REVERT: 2 793 MET cc_start: 0.9462 (tpp) cc_final: 0.9075 (tpp) REVERT: 2 836 LEU cc_start: 0.9439 (mt) cc_final: 0.9191 (tt) REVERT: 2 890 LYS cc_start: 0.9117 (tptt) cc_final: 0.8392 (tttm) REVERT: 3 303 LEU cc_start: 0.8952 (mt) cc_final: 0.8589 (mt) REVERT: 3 438 ILE cc_start: 0.7942 (mt) cc_final: 0.7629 (pt) REVERT: 4 317 MET cc_start: 0.7586 (tpp) cc_final: 0.7224 (tpp) REVERT: 4 559 GLN cc_start: 0.8863 (mm110) cc_final: 0.8380 (tm-30) REVERT: 4 738 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8395 (mp) REVERT: 4 742 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8142 (mt-10) REVERT: 6 475 GLU cc_start: 0.8715 (tp30) cc_final: 0.8174 (tp30) REVERT: 6 496 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7908 (mtm-85) REVERT: 6 521 ASN cc_start: 0.9208 (t0) cc_final: 0.8712 (t0) REVERT: 7 446 GLU cc_start: 0.9078 (tt0) cc_final: 0.8486 (tt0) outliers start: 31 outliers final: 21 residues processed: 197 average time/residue: 0.1387 time to fit residues: 47.3408 Evaluate side-chains 187 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 399 LEU Chi-restraints excluded: chain 2 residue 544 ILE Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 134 CYS Chi-restraints excluded: chain 3 residue 408 ILE Chi-restraints excluded: chain 3 residue 433 ILE Chi-restraints excluded: chain 4 residue 208 LEU Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 419 ILE Chi-restraints excluded: chain 4 residue 598 ILE Chi-restraints excluded: chain 4 residue 622 SER Chi-restraints excluded: chain 4 residue 669 LEU Chi-restraints excluded: chain 4 residue 738 ILE Chi-restraints excluded: chain 6 residue 122 LYS Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 249 ILE Chi-restraints excluded: chain 6 residue 329 MET Chi-restraints excluded: chain 6 residue 376 VAL Chi-restraints excluded: chain 6 residue 411 GLU Chi-restraints excluded: chain 6 residue 496 ARG Chi-restraints excluded: chain 7 residue 264 ILE Chi-restraints excluded: chain 7 residue 441 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 257 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 245 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.086270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.057699 restraints weight = 113962.799| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 4.63 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27563 Z= 0.192 Angle : 0.580 11.021 37534 Z= 0.288 Chirality : 0.042 0.178 4468 Planarity : 0.003 0.044 4934 Dihedral : 6.023 88.317 4099 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.13 % Rotamer: Outliers : 1.45 % Allowed : 11.06 % Favored : 87.50 % 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: -0.35 (0.14), residues: 3695 helix: 0.91 (0.14), residues: 1503 sheet: -1.57 (0.23), residues: 542 loop : -0.73 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 6 619 TYR 0.013 0.001 TYR 2 535 PHE 0.014 0.001 PHE 6 172 TRP 0.011 0.001 TRP 2 569 HIS 0.006 0.001 HIS 4 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (27547) covalent geometry : angle 0.57158 / 0.29 (37510) hydrogen bonds : bond 0.03126 / 2.15 ( 1109) hydrogen bonds : angle 4.58442 / 3.15 ( 3171) metal coordination : bond 0.01095 / 0.58 ( 16) metal coordination : angle 4.01244 / 2.47 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 423 ASP cc_start: 0.8414 (t0) cc_final: 0.8045 (t0) REVERT: 2 674 MET cc_start: 0.9321 (tpp) cc_final: 0.8903 (tpp) REVERT: 2 755 MET cc_start: 0.9043 (ptp) cc_final: 0.8715 (ppp) REVERT: 2 793 MET cc_start: 0.9479 (tpp) cc_final: 0.9027 (tpp) REVERT: 2 814 MET cc_start: 0.9714 (mmt) cc_final: 0.9294 (mmm) REVERT: 2 890 LYS cc_start: 0.9128 (tptt) cc_final: 0.8401 (tttm) REVERT: 3 303 LEU cc_start: 0.9050 (mt) cc_final: 0.8621 (mt) REVERT: 4 271 MET cc_start: 0.8279 (ptt) cc_final: 0.8079 (ptm) REVERT: 4 317 MET cc_start: 0.7657 (tpp) cc_final: 0.7249 (tpp) REVERT: 4 559 GLN cc_start: 0.8859 (mm110) cc_final: 0.8344 (tm-30) REVERT: 4 738 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8426 (mp) REVERT: 4 742 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8136 (mt-10) REVERT: 6 389 ASP cc_start: 0.8362 (m-30) cc_final: 0.7298 (p0) REVERT: 6 475 GLU cc_start: 0.8818 (tp30) cc_final: 0.8334 (tp30) REVERT: 6 496 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7781 (mtm-85) REVERT: 6 521 ASN cc_start: 0.9224 (t0) cc_final: 0.8733 (t0) REVERT: 7 446 GLU cc_start: 0.9080 (tt0) cc_final: 0.8490 (tt0) REVERT: 7 450 MET cc_start: 0.7221 (mmm) cc_final: 0.6920 (mmm) REVERT: 7 556 MET cc_start: 0.8533 (mmm) cc_final: 0.7986 (mmm) outliers start: 37 outliers final: 24 residues processed: 195 average time/residue: 0.1384 time to fit residues: 46.1516 Evaluate side-chains 183 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 399 LEU Chi-restraints excluded: chain 2 residue 544 ILE Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 134 CYS Chi-restraints excluded: chain 3 residue 408 ILE Chi-restraints excluded: chain 3 residue 433 ILE Chi-restraints excluded: chain 4 residue 208 LEU Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 419 ILE Chi-restraints excluded: chain 4 residue 563 LEU Chi-restraints excluded: chain 4 residue 598 ILE Chi-restraints excluded: chain 4 residue 669 LEU Chi-restraints excluded: chain 4 residue 738 ILE Chi-restraints excluded: chain 6 residue 122 LYS Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 249 ILE Chi-restraints excluded: chain 6 residue 329 MET Chi-restraints excluded: chain 6 residue 376 VAL Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 411 GLU Chi-restraints excluded: chain 6 residue 496 ARG Chi-restraints excluded: chain 7 residue 264 ILE Chi-restraints excluded: chain 7 residue 441 VAL Chi-restraints excluded: chain 7 residue 462 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 0.0040 chunk 251 optimal weight: 0.9980 chunk 322 optimal weight: 50.0000 chunk 352 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 307 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 chunk 266 optimal weight: 7.9990 chunk 293 optimal weight: 20.0000 chunk 235 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 144 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.087124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.058797 restraints weight = 113903.326| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.64 r_work: 0.2940 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27563 Z= 0.130 Angle : 0.549 11.273 37534 Z= 0.270 Chirality : 0.042 0.177 4468 Planarity : 0.003 0.042 4934 Dihedral : 5.940 88.201 4099 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 1.25 % Allowed : 12.08 % Favored : 86.67 % 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: -0.25 (0.14), residues: 3695 helix: 0.98 (0.14), residues: 1510 sheet: -1.46 (0.23), residues: 535 loop : -0.71 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 6 619 TYR 0.015 0.001 TYR 2 535 PHE 0.010 0.001 PHE 6 172 TRP 0.008 0.001 TRP 7 593 HIS 0.004 0.001 HIS 4 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (27547) covalent geometry : angle 0.54037 / 0.27 (37510) hydrogen bonds : bond 0.02868 / 1.98 ( 1109) hydrogen bonds : angle 4.39966 / 3.02 ( 3171) metal coordination : bond 0.00810 / 0.43 ( 16) metal coordination : angle 3.77991 / 2.25 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 423 ASP cc_start: 0.8910 (t0) cc_final: 0.8564 (t0) REVERT: 2 674 MET cc_start: 0.9621 (tpp) cc_final: 0.9236 (tpp) REVERT: 2 755 MET cc_start: 0.9162 (ptp) cc_final: 0.8806 (ppp) REVERT: 2 793 MET cc_start: 0.9602 (tpp) cc_final: 0.9289 (tpp) REVERT: 2 890 LYS cc_start: 0.9162 (tptt) cc_final: 0.8321 (tttm) REVERT: 3 303 LEU cc_start: 0.8992 (mt) cc_final: 0.8640 (mt) REVERT: 4 271 MET cc_start: 0.8359 (ptt) cc_final: 0.8149 (ptm) REVERT: 4 317 MET cc_start: 0.7848 (tpp) cc_final: 0.7355 (tpp) REVERT: 4 378 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9139 (mm) REVERT: 4 559 GLN cc_start: 0.8928 (mm110) cc_final: 0.8415 (tm-30) REVERT: 4 738 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8633 (mp) REVERT: 4 742 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8732 (mt-10) REVERT: 6 117 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8967 (mm) REVERT: 6 389 ASP cc_start: 0.8681 (m-30) cc_final: 0.7533 (p0) REVERT: 6 475 GLU cc_start: 0.9166 (tp30) cc_final: 0.8720 (tp30) REVERT: 6 521 ASN cc_start: 0.9480 (t0) cc_final: 0.9022 (t0) REVERT: 7 446 GLU cc_start: 0.9190 (tt0) cc_final: 0.8647 (tt0) REVERT: 7 604 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8630 (mtp180) outliers start: 32 outliers final: 20 residues processed: 191 average time/residue: 0.1426 time to fit residues: 46.7364 Evaluate side-chains 183 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 399 LEU Chi-restraints excluded: chain 2 residue 544 ILE Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 134 CYS Chi-restraints excluded: chain 3 residue 295 ILE Chi-restraints excluded: chain 3 residue 408 ILE Chi-restraints excluded: chain 3 residue 433 ILE Chi-restraints excluded: chain 4 residue 208 LEU Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 378 LEU Chi-restraints excluded: chain 4 residue 419 ILE Chi-restraints excluded: chain 4 residue 598 ILE Chi-restraints excluded: chain 4 residue 738 ILE Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 122 LYS Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 249 ILE Chi-restraints excluded: chain 6 residue 376 VAL Chi-restraints excluded: chain 6 residue 411 GLU Chi-restraints excluded: chain 6 residue 496 ARG Chi-restraints excluded: chain 7 residue 264 ILE Chi-restraints excluded: chain 7 residue 462 MET Chi-restraints excluded: chain 7 residue 604 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 292 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 323 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 358 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 483 GLN ** 7 36 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 = 0.3914 r_free = 0.3914 target = 0.087155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.058743 restraints weight = 113365.685| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.63 r_work: 0.2944 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27563 Z= 0.124 Angle : 0.554 12.744 37534 Z= 0.271 Chirality : 0.042 0.176 4468 Planarity : 0.003 0.041 4934 Dihedral : 5.888 89.325 4099 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.52 % Allowed : 12.27 % Favored : 86.21 % 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: -0.21 (0.14), residues: 3695 helix: 1.02 (0.14), residues: 1510 sheet: -1.42 (0.23), residues: 525 loop : -0.71 (0.16), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 6 619 TYR 0.014 0.001 TYR 2 535 PHE 0.010 0.001 PHE 6 373 TRP 0.008 0.001 TRP 7 593 HIS 0.004 0.001 HIS 4 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (27547) covalent geometry : angle 0.54769 / 0.27 (37510) hydrogen bonds : bond 0.02805 / 1.93 ( 1109) hydrogen bonds : angle 4.33148 / 2.96 ( 3171) metal coordination : bond 0.00704 / 0.36 ( 16) metal coordination : angle 3.33532 / 2.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 423 ASP cc_start: 0.8979 (t0) cc_final: 0.8619 (t0) REVERT: 2 674 MET cc_start: 0.9610 (tpp) cc_final: 0.9209 (tpp) REVERT: 2 755 MET cc_start: 0.9201 (ptp) cc_final: 0.8792 (ppp) REVERT: 2 793 MET cc_start: 0.9607 (tpp) cc_final: 0.9292 (tpp) REVERT: 2 814 MET cc_start: 0.9793 (mmt) cc_final: 0.9310 (mmm) REVERT: 2 890 LYS cc_start: 0.9169 (tptt) cc_final: 0.8335 (tttm) REVERT: 3 303 LEU cc_start: 0.8986 (mt) cc_final: 0.8619 (mt) REVERT: 3 799 MET cc_start: 0.9541 (ttp) cc_final: 0.8610 (ppp) REVERT: 3 804 ILE cc_start: 0.9680 (mp) cc_final: 0.9409 (mt) REVERT: 4 271 MET cc_start: 0.8338 (ptt) cc_final: 0.8136 (ptm) REVERT: 4 317 MET cc_start: 0.7900 (tpp) cc_final: 0.7449 (tpp) REVERT: 4 378 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9164 (mm) REVERT: 4 548 MET cc_start: 0.8326 (tmm) cc_final: 0.8004 (ppp) REVERT: 4 559 GLN cc_start: 0.8962 (mm110) cc_final: 0.8450 (tm-30) REVERT: 4 684 MET cc_start: 0.9017 (tmm) cc_final: 0.8762 (tmm) REVERT: 4 738 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8696 (mp) REVERT: 4 742 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8717 (mt-10) REVERT: 6 117 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8994 (mm) REVERT: 6 329 MET cc_start: 0.8843 (ptt) cc_final: 0.8617 (ppp) REVERT: 6 389 ASP cc_start: 0.8695 (m-30) cc_final: 0.7577 (p0) REVERT: 6 475 GLU cc_start: 0.9183 (tp30) cc_final: 0.8729 (tp30) REVERT: 6 521 ASN cc_start: 0.9454 (t0) cc_final: 0.9010 (t0) REVERT: 7 446 GLU cc_start: 0.9200 (tt0) cc_final: 0.8697 (tt0) outliers start: 39 outliers final: 26 residues processed: 194 average time/residue: 0.1370 time to fit residues: 45.2705 Evaluate side-chains 188 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 399 LEU Chi-restraints excluded: chain 2 residue 544 ILE Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 134 CYS Chi-restraints excluded: chain 3 residue 295 ILE Chi-restraints excluded: chain 3 residue 408 ILE Chi-restraints excluded: chain 3 residue 433 ILE Chi-restraints excluded: chain 4 residue 208 LEU Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 378 LEU Chi-restraints excluded: chain 4 residue 413 LYS Chi-restraints excluded: chain 4 residue 419 ILE Chi-restraints excluded: chain 4 residue 598 ILE Chi-restraints excluded: chain 4 residue 738 ILE Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 122 LYS Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 249 ILE Chi-restraints excluded: chain 6 residue 376 VAL Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 411 GLU Chi-restraints excluded: chain 6 residue 496 ARG Chi-restraints excluded: chain 6 residue 635 HIS Chi-restraints excluded: chain 7 residue 131 MET Chi-restraints excluded: chain 7 residue 264 ILE Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 462 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 302 optimal weight: 9.9990 chunk 24 optimal weight: 0.0370 chunk 122 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 chunk 169 optimal weight: 0.4980 chunk 75 optimal weight: 8.9990 chunk 358 optimal weight: 0.0010 chunk 16 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 335 optimal weight: 50.0000 chunk 366 optimal weight: 8.9990 overall best weight: 2.3068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 593 ASN ** 3 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 465 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.087146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.058755 restraints weight = 114016.781| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.64 r_work: 0.2946 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27563 Z= 0.123 Angle : 0.564 12.761 37534 Z= 0.273 Chirality : 0.042 0.275 4468 Planarity : 0.003 0.042 4934 Dihedral : 5.828 89.521 4099 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.41 % Allowed : 12.58 % Favored : 86.01 % 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: -0.17 (0.14), residues: 3695 helix: 1.06 (0.14), residues: 1512 sheet: -1.38 (0.23), residues: 525 loop : -0.69 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 6 619 TYR 0.014 0.001 TYR 2 535 PHE 0.014 0.001 PHE 2 432 TRP 0.007 0.001 TRP 7 593 HIS 0.004 0.001 HIS 2 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (27547) covalent geometry : angle 0.55816 / 0.27 (37510) hydrogen bonds : bond 0.02776 / 1.92 ( 1109) hydrogen bonds : angle 4.25618 / 2.90 ( 3171) metal coordination : bond 0.00705 / 0.37 ( 16) metal coordination : angle 3.29183 / 2.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 423 ASP cc_start: 0.8998 (t0) cc_final: 0.8640 (t0) REVERT: 2 604 MET cc_start: 0.9168 (mtm) cc_final: 0.8903 (mtm) REVERT: 2 674 MET cc_start: 0.9619 (tpp) cc_final: 0.9211 (tpp) REVERT: 2 755 MET cc_start: 0.9172 (ptp) cc_final: 0.8762 (ppp) REVERT: 2 793 MET cc_start: 0.9607 (tpp) cc_final: 0.9287 (tpp) REVERT: 2 890 LYS cc_start: 0.9169 (tptt) cc_final: 0.8324 (tttm) REVERT: 3 303 LEU cc_start: 0.8992 (mt) cc_final: 0.8626 (mt) REVERT: 3 799 MET cc_start: 0.9465 (ttp) cc_final: 0.8673 (ppp) REVERT: 3 804 ILE cc_start: 0.9698 (mp) cc_final: 0.9425 (mt) REVERT: 4 317 MET cc_start: 0.7896 (tpp) cc_final: 0.7430 (tpp) REVERT: 4 378 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9166 (mm) REVERT: 4 548 MET cc_start: 0.8352 (tmm) cc_final: 0.8020 (ppp) REVERT: 4 559 GLN cc_start: 0.8959 (mm110) cc_final: 0.8487 (tm-30) REVERT: 4 684 MET cc_start: 0.9022 (tmm) cc_final: 0.8775 (tmm) REVERT: 4 738 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8688 (mp) REVERT: 4 742 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8744 (mt-10) REVERT: 6 81 GLU cc_start: 0.9351 (mt-10) cc_final: 0.9009 (mt-10) REVERT: 6 389 ASP cc_start: 0.8709 (m-30) cc_final: 0.7618 (p0) REVERT: 6 475 GLU cc_start: 0.9190 (tp30) cc_final: 0.8720 (tp30) REVERT: 6 521 ASN cc_start: 0.9463 (t0) cc_final: 0.9028 (t0) REVERT: 7 177 MET cc_start: 0.9026 (tpp) cc_final: 0.8663 (tpp) REVERT: 7 446 GLU cc_start: 0.9200 (tt0) cc_final: 0.8670 (tt0) REVERT: 7 460 GLU cc_start: 0.8683 (tt0) cc_final: 0.8465 (tm-30) outliers start: 36 outliers final: 22 residues processed: 197 average time/residue: 0.1409 time to fit residues: 48.2875 Evaluate side-chains 184 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 399 LEU Chi-restraints excluded: chain 2 residue 544 ILE Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 134 CYS Chi-restraints excluded: chain 3 residue 295 ILE Chi-restraints excluded: chain 3 residue 433 ILE Chi-restraints excluded: chain 4 residue 208 LEU Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 378 LEU Chi-restraints excluded: chain 4 residue 413 LYS Chi-restraints excluded: chain 4 residue 419 ILE Chi-restraints excluded: chain 4 residue 738 ILE Chi-restraints excluded: chain 6 residue 122 LYS Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 249 ILE Chi-restraints excluded: chain 6 residue 376 VAL Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 411 GLU Chi-restraints excluded: chain 6 residue 635 HIS Chi-restraints excluded: chain 7 residue 264 ILE Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 462 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 58 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 92 optimal weight: 0.0770 chunk 152 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 285 optimal weight: 8.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 HIS ** 3 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 187 ASN ** 7 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.086555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.058280 restraints weight = 114495.944| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 4.61 r_work: 0.2930 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27563 Z= 0.159 Angle : 0.587 12.398 37534 Z= 0.285 Chirality : 0.042 0.265 4468 Planarity : 0.003 0.041 4934 Dihedral : 5.852 87.852 4099 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.25 % Allowed : 13.17 % Favored : 85.58 % 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: -0.15 (0.14), residues: 3695 helix: 1.11 (0.14), residues: 1506 sheet: -1.40 (0.23), residues: 525 loop : -0.71 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 6 496 TYR 0.015 0.001 TYR 2 535 PHE 0.012 0.001 PHE 6 530 TRP 0.009 0.002 TRP 2 569 HIS 0.006 0.001 HIS 4 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (27547) covalent geometry : angle 0.58073 / 0.28 (37510) hydrogen bonds : bond 0.02833 / 1.94 ( 1109) hydrogen bonds : angle 4.31324 / 2.94 ( 3171) metal coordination : bond 0.00896 / 0.47 ( 16) metal coordination : angle 3.36500 / 2.15 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 423 ASP cc_start: 0.9011 (t0) cc_final: 0.8621 (t0) REVERT: 2 604 MET cc_start: 0.9204 (mtm) cc_final: 0.8952 (mtm) REVERT: 2 674 MET cc_start: 0.9634 (tpp) cc_final: 0.9228 (tpp) REVERT: 2 755 MET cc_start: 0.9169 (ptp) cc_final: 0.8773 (ppp) REVERT: 2 814 MET cc_start: 0.9791 (mmt) cc_final: 0.9373 (mmm) REVERT: 2 890 LYS cc_start: 0.9177 (tptt) cc_final: 0.8335 (tptt) REVERT: 3 204 MET cc_start: 0.8358 (pmm) cc_final: 0.7616 (pmm) REVERT: 3 303 LEU cc_start: 0.8968 (mt) cc_final: 0.8574 (mt) REVERT: 3 792 MET cc_start: 0.9417 (mtm) cc_final: 0.9207 (ptp) REVERT: 3 799 MET cc_start: 0.9495 (ttp) cc_final: 0.8849 (tmm) REVERT: 3 804 ILE cc_start: 0.9694 (mp) cc_final: 0.9407 (mt) REVERT: 4 317 MET cc_start: 0.7886 (tpp) cc_final: 0.7426 (tpp) REVERT: 4 378 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9123 (mm) REVERT: 4 548 MET cc_start: 0.8345 (tmm) cc_final: 0.7993 (ppp) REVERT: 4 559 GLN cc_start: 0.8965 (mm110) cc_final: 0.8458 (tm-30) REVERT: 4 684 MET cc_start: 0.9010 (tmm) cc_final: 0.8758 (tmm) REVERT: 4 738 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8707 (mp) REVERT: 4 742 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8770 (mt-10) REVERT: 6 81 GLU cc_start: 0.9358 (mt-10) cc_final: 0.8998 (mt-10) REVERT: 6 389 ASP cc_start: 0.8784 (m-30) cc_final: 0.7608 (p0) REVERT: 6 521 ASN cc_start: 0.9493 (t0) cc_final: 0.9050 (t0) REVERT: 6 634 MET cc_start: 0.9273 (ttp) cc_final: 0.9023 (tmm) REVERT: 7 174 LYS cc_start: 0.8368 (mmtp) cc_final: 0.8137 (mmtp) REVERT: 7 446 GLU cc_start: 0.9169 (tt0) cc_final: 0.8670 (tt0) outliers start: 32 outliers final: 23 residues processed: 187 average time/residue: 0.1262 time to fit residues: 40.9817 Evaluate side-chains 185 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 399 LEU Chi-restraints excluded: chain 2 residue 544 ILE Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 134 CYS Chi-restraints excluded: chain 3 residue 295 ILE Chi-restraints excluded: chain 3 residue 433 ILE Chi-restraints excluded: chain 4 residue 208 LEU Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 378 LEU Chi-restraints excluded: chain 4 residue 413 LYS Chi-restraints excluded: chain 4 residue 419 ILE Chi-restraints excluded: chain 4 residue 738 ILE Chi-restraints excluded: chain 6 residue 122 LYS Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 249 ILE Chi-restraints excluded: chain 6 residue 376 VAL Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 411 GLU Chi-restraints excluded: chain 6 residue 635 HIS Chi-restraints excluded: chain 7 residue 131 MET Chi-restraints excluded: chain 7 residue 264 ILE Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 462 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 94 optimal weight: 8.9990 chunk 200 optimal weight: 0.9990 chunk 285 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 288 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 188 optimal weight: 0.0870 chunk 161 optimal weight: 5.9990 chunk 134 optimal weight: 0.2980 overall best weight: 2.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 638 HIS ** 7 36 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 = 0.3914 r_free = 0.3914 target = 0.087137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.058923 restraints weight = 114649.919| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 4.63 r_work: 0.2949 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27563 Z= 0.119 Angle : 0.579 13.027 37534 Z= 0.279 Chirality : 0.042 0.245 4468 Planarity : 0.003 0.041 4934 Dihedral : 5.778 84.062 4099 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.06 % Allowed : 13.44 % Favored : 85.50 % 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: -0.13 (0.14), residues: 3695 helix: 1.14 (0.14), residues: 1508 sheet: -1.41 (0.23), residues: 542 loop : -0.69 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG 7 43 TYR 0.014 0.001 TYR 2 535 PHE 0.015 0.001 PHE 2 432 TRP 0.007 0.001 TRP 2 569 HIS 0.005 0.001 HIS 4 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (27547) covalent geometry : angle 0.57360 / 0.28 (37510) hydrogen bonds : bond 0.02720 / 1.88 ( 1109) hydrogen bonds : angle 4.19997 / 2.86 ( 3171) metal coordination : bond 0.00655 / 0.35 ( 16) metal coordination : angle 3.30243 / 2.04 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7390 Ramachandran restraints generated. 3695 Oldfield, 0 Emsley, 3695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 423 ASP cc_start: 0.9024 (t0) cc_final: 0.8655 (t0) REVERT: 2 604 MET cc_start: 0.9129 (mtm) cc_final: 0.8926 (mtm) REVERT: 2 674 MET cc_start: 0.9627 (tpp) cc_final: 0.9211 (tpp) REVERT: 2 755 MET cc_start: 0.9195 (ptp) cc_final: 0.8785 (ppp) REVERT: 2 793 MET cc_start: 0.9598 (tpp) cc_final: 0.9309 (tpp) REVERT: 2 814 MET cc_start: 0.9794 (mmt) cc_final: 0.9379 (mmm) REVERT: 2 890 LYS cc_start: 0.9175 (tptt) cc_final: 0.8317 (tptt) REVERT: 3 204 MET cc_start: 0.8339 (pmm) cc_final: 0.7624 (pmm) REVERT: 3 303 LEU cc_start: 0.8960 (mt) cc_final: 0.8589 (mt) REVERT: 3 799 MET cc_start: 0.9374 (ttp) cc_final: 0.8799 (tmm) REVERT: 3 804 ILE cc_start: 0.9689 (mp) cc_final: 0.9389 (mt) REVERT: 4 317 MET cc_start: 0.7921 (tpp) cc_final: 0.7464 (tpp) REVERT: 4 378 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9162 (mm) REVERT: 4 548 MET cc_start: 0.8391 (tmm) cc_final: 0.8041 (ppp) REVERT: 4 559 GLN cc_start: 0.8973 (mm110) cc_final: 0.8506 (tm-30) REVERT: 4 684 MET cc_start: 0.9020 (tmm) cc_final: 0.8771 (tmm) REVERT: 4 738 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8368 (mt) REVERT: 4 742 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8687 (mp0) REVERT: 6 81 GLU cc_start: 0.9386 (mt-10) cc_final: 0.9021 (mt-10) REVERT: 6 389 ASP cc_start: 0.8754 (m-30) cc_final: 0.7660 (p0) REVERT: 6 475 GLU cc_start: 0.9100 (tp30) cc_final: 0.8825 (tp30) REVERT: 6 521 ASN cc_start: 0.9458 (t0) cc_final: 0.9028 (t0) REVERT: 6 634 MET cc_start: 0.9255 (ttp) cc_final: 0.9007 (tmm) REVERT: 7 174 LYS cc_start: 0.8380 (mmtp) cc_final: 0.8158 (mmtp) REVERT: 7 177 MET cc_start: 0.9020 (tpp) cc_final: 0.8721 (tpp) REVERT: 7 460 GLU cc_start: 0.8659 (tt0) cc_final: 0.8436 (tm-30) outliers start: 27 outliers final: 23 residues processed: 186 average time/residue: 0.1313 time to fit residues: 42.6897 Evaluate side-chains 186 residues out of total 3276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 399 LEU Chi-restraints excluded: chain 2 residue 544 ILE Chi-restraints excluded: chain 3 residue 124 VAL Chi-restraints excluded: chain 3 residue 134 CYS Chi-restraints excluded: chain 3 residue 295 ILE Chi-restraints excluded: chain 3 residue 433 ILE Chi-restraints excluded: chain 4 residue 208 LEU Chi-restraints excluded: chain 4 residue 215 ILE Chi-restraints excluded: chain 4 residue 378 LEU Chi-restraints excluded: chain 4 residue 413 LYS Chi-restraints excluded: chain 4 residue 419 ILE Chi-restraints excluded: chain 4 residue 598 ILE Chi-restraints excluded: chain 4 residue 738 ILE Chi-restraints excluded: chain 6 residue 147 VAL Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 249 ILE Chi-restraints excluded: chain 6 residue 376 VAL Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 411 GLU Chi-restraints excluded: chain 6 residue 635 HIS Chi-restraints excluded: chain 7 residue 131 MET Chi-restraints excluded: chain 7 residue 264 ILE Chi-restraints excluded: chain 7 residue 397 LEU Chi-restraints excluded: chain 7 residue 462 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 163 optimal weight: 5.9990 chunk 343 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 332 optimal weight: 40.0000 chunk 155 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 366 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 77 GLN ** 3 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 350 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 = 0.3901 r_free = 0.3901 target = 0.086135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.057699 restraints weight = 113265.462| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 4.62 r_work: 0.2927 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27563 Z= 0.159 Angle : 0.595 12.837 37534 Z= 0.289 Chirality : 0.042 0.219 4468 Planarity : 0.003 0.042 4934 Dihedral : 5.802 83.929 4099 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.21 % Allowed : 13.52 % Favored : 85.27 % 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: -0.12 (0.14), residues: 3695 helix: 1.16 (0.14), residues: 1510 sheet: -1.44 (0.23), residues: 545 loop : -0.69 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 7 43 TYR 0.015 0.001 TYR 2 535 PHE 0.012 0.001 PHE 6 530 TRP 0.010 0.001 TRP 2 569 HIS 0.004 0.001 HIS 2 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (27547) covalent geometry : angle 0.58957 / 0.29 (37510) hydrogen bonds : bond 0.02832 / 1.94 ( 1109) hydrogen bonds : angle 4.25049 / 2.89 ( 3171) metal coordination : bond 0.00879 / 0.46 ( 16) metal coordination : angle 3.35613 / 2.15 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6856.44 seconds wall clock time: 117 minutes 38.20 seconds (7058.20 seconds total)