Starting phenix.real_space_refine on Sat Aug 8 15:38:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vln_65161/08_2026/9vln_65161.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vln_65161/08_2026/9vln_65161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vln_65161/08_2026/9vln_65161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vln_65161/08_2026/9vln_65161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vln_65161/08_2026/9vln_65161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vln_65161/08_2026/9vln_65161.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 2 5.21 5 S 151 5.16 5 C 17665 2.51 5 N 4939 2.21 5 O 5432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 28206 Number of models: 1 Model: "" Number of chains: 11 Chain: "2" Number of atoms: 5340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5340 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 29, 'TRANS': 667} Chain breaks: 1 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 176 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 3, 'ARG:plan': 8, 'GLU:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 112 Chain: "3" Number of atoms: 4043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4043 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 19, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 128 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 3, 'PHE:plan': 1, 'HIS:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 112 Chain: "4" Number of atoms: 4919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 4919 Classifications: {'peptide': 663} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 25, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 462 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PHE:plan': 7, 'ARG:plan': 19, 'GLN:plan1': 5, 'GLU:plan': 10, 'ASP:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 225 Chain: "5" Number of atoms: 4231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4231 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 21, 'TRANS': 538} Chain breaks: 6 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 15, 'GLU:plan': 3, 'HIS:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 119 Chain: "6" Number of atoms: 5260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5260 Classifications: {'peptide': 666} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 21, 'TRANS': 644} Chain breaks: 3 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 5, 'PHE:plan': 1, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "7" Number of atoms: 4260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4260 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 25, 'TRANS': 538} Chain breaks: 3 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 4, 'PHE:plan': 1, 'ARG:plan': 13, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 121 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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 1129 SG CYS 2 329 91.441 72.551 73.146 1.00121.91 S ATOM 1152 SG CYS 2 332 93.500 75.059 75.151 1.00121.71 S ATOM 1303 SG CYS 2 352 90.128 74.137 76.446 1.00118.07 S ATOM 1325 SG CYS 2 355 90.324 76.193 73.339 1.00124.78 S ATOM 10413 SG CYS 4 306 111.962 77.784 88.666 1.00102.97 S ATOM 10435 SG CYS 4 309 115.245 79.265 89.794 1.00101.32 S ATOM 10569 SG CYS 4 328 113.176 81.084 87.164 1.00119.16 S ATOM 10584 SG CYS 4 331 114.731 77.700 86.257 1.00135.17 S ATOM 19669 SG CYS 6 158 107.537 61.195 80.826 1.00126.95 S ATOM 19691 SG CYS 6 161 110.872 60.368 81.307 1.00126.96 S ATOM 19852 SG CYS 6 180 109.987 64.214 81.544 1.00127.84 S ATOM 19891 SG CYS 6 185 110.145 62.380 78.223 1.00133.97 S ATOM 24868 SG CYS 7 184 105.820 103.046 72.156 1.00133.12 S ATOM 24891 SG CYS 7 187 107.430 105.938 70.693 1.00137.10 S ATOM 25034 SG CYS 7 206 105.615 103.570 68.381 1.00129.27 S ATOM 25071 SG CYS 7 211 108.892 102.364 69.940 1.00143.28 S Time building chain proxies: 5.66, per 1000 atoms: 0.20 Number of scatterers: 28206 At special positions: 0 Unit cell: (126.14, 142.04, 173.84, 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 151 16.00 P 13 15.00 Mg 2 11.99 O 5432 8.00 N 4939 7.00 C 17665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21003 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 352 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 332 " pdb="ZN ZN 21003 " - pdb=" SG CYS 2 355 " pdb="ZN ZN 21003 " - 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 4 331 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 328 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 309 " pdb=" ZN 6 902 " pdb="ZN ZN 6 902 " - pdb=" SG CYS 6 161 " pdb="ZN ZN 6 902 " - pdb=" SG CYS 6 158 " pdb="ZN ZN 6 902 " - pdb=" SG CYS 6 185 " pdb="ZN ZN 6 902 " - 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 7 187 " pdb="ZN ZN 7 802 " - pdb=" SG CYS 7 206 " pdb="ZN ZN 7 802 " - pdb=" SG CYS 7 211 " Number of angles added : 24 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7014 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 37 sheets defined 44.4% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain '2' and resid 191 through 206 Processing helix chain '2' and resid 213 through 225 removed outlier: 4.184A pdb=" N MET 2 222 " --> pdb=" O ARG 2 218 " (cutoff:3.500A) Processing helix chain '2' and resid 234 through 239 removed outlier: 3.650A pdb=" N ALA 2 239 " --> pdb=" O GLU 2 235 " (cutoff:3.500A) Processing helix chain '2' and resid 241 through 247 removed outlier: 3.605A pdb=" N PHE 2 247 " --> pdb=" O VAL 2 243 " (cutoff:3.500A) Processing helix chain '2' and resid 251 through 271 removed outlier: 3.534A pdb=" N ILE 2 258 " --> pdb=" O GLU 2 254 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU 2 261 " --> pdb=" O GLN 2 257 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA 2 263 " --> pdb=" O PHE 2 259 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU 2 264 " --> pdb=" O ASP 2 260 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU 2 265 " --> pdb=" O GLU 2 261 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL 2 266 " --> pdb=" O ALA 2 262 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL 2 267 " --> pdb=" O ALA 2 263 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU 2 268 " --> pdb=" O LEU 2 264 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR 2 271 " --> pdb=" O VAL 2 267 " (cutoff:3.500A) Processing helix chain '2' and resid 272 through 276 removed outlier: 4.158A pdb=" N ARG 2 276 " --> pdb=" O LYS 2 273 " (cutoff:3.500A) Processing helix chain '2' and resid 298 through 302 Processing helix chain '2' and resid 399 through 403 removed outlier: 3.621A pdb=" N VAL 2 403 " --> pdb=" O ALA 2 400 " (cutoff:3.500A) Processing helix chain '2' and resid 446 through 451 removed outlier: 3.786A pdb=" N LYS 2 450 " --> pdb=" O LYS 2 447 " (cutoff:3.500A) Processing helix chain '2' and resid 459 through 470 Processing helix chain '2' and resid 472 through 480 Processing helix chain '2' and resid 488 through 501 Processing helix chain '2' and resid 505 through 512 removed outlier: 3.646A pdb=" N GLY 2 509 " --> pdb=" O ASN 2 506 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS 2 510 " --> pdb=" O PRO 2 507 " (cutoff:3.500A) Processing helix chain '2' and resid 528 through 538 removed outlier: 3.502A pdb=" N PHE 2 532 " --> pdb=" O ALA 2 528 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU 2 533 " --> pdb=" O LYS 2 529 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS 2 538 " --> pdb=" O LYS 2 534 " (cutoff:3.500A) Processing helix chain '2' and resid 574 through 579 Processing helix chain '2' and resid 588 through 592 removed outlier: 3.697A pdb=" N MET 2 592 " --> pdb=" O PHE 2 589 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 606 removed outlier: 3.894A pdb=" N THR 2 598 " --> pdb=" O ASP 2 594 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER 2 599 " --> pdb=" O GLN 2 595 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N HIS 2 601 " --> pdb=" O ARG 2 597 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU 2 602 " --> pdb=" O THR 2 598 " (cutoff:3.500A) Processing helix chain '2' and resid 632 through 636 removed outlier: 4.174A pdb=" N ARG 2 636 " --> pdb=" O ILE 2 633 " (cutoff:3.500A) Processing helix chain '2' and resid 642 through 647 removed outlier: 3.504A pdb=" N VAL 2 647 " --> pdb=" O PHE 2 643 " (cutoff:3.500A) Processing helix chain '2' and resid 650 through 657 removed outlier: 3.526A pdb=" N ARG 2 656 " --> pdb=" O PRO 2 652 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE 2 657 " --> pdb=" O ILE 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 668 through 686 Processing helix chain '2' and resid 719 through 728 removed outlier: 3.894A pdb=" N ILE 2 725 " --> pdb=" O LYS 2 721 " (cutoff:3.500A) Processing helix chain '2' and resid 739 through 758 Processing helix chain '2' and resid 763 through 781 removed outlier: 3.565A pdb=" N ARG 2 772 " --> pdb=" O GLU 2 768 " (cutoff:3.500A) removed outlier: 3.558A 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 818 removed outlier: 4.287A pdb=" N SER 2 813 " --> pdb=" O SER 2 809 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE 2 818 " --> pdb=" O MET 2 814 " (cutoff:3.500A) Processing helix chain '2' and resid 818 through 823 Processing helix chain '2' and resid 827 through 851 removed outlier: 3.643A pdb=" N GLN 2 838 " --> pdb=" O PHE 2 834 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU 2 839 " --> pdb=" O ILE 2 835 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN 2 849 " --> pdb=" O THR 2 845 " (cutoff:3.500A) Processing helix chain '2' and resid 862 through 867 removed outlier: 3.925A pdb=" N ASP 2 867 " --> pdb=" O LYS 2 863 " (cutoff:3.500A) Processing helix chain '2' and resid 868 through 870 No H-bonds generated for 'chain '2' and resid 868 through 870' Processing helix chain '2' and resid 876 through 883 removed outlier: 3.557A pdb=" N PHE 2 880 " --> pdb=" O ASN 2 876 " (cutoff:3.500A) Processing helix chain '2' and resid 883 through 889 removed outlier: 4.022A pdb=" N ARG 2 887 " --> pdb=" O SER 2 883 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 24 removed outlier: 3.538A pdb=" N ASP 3 24 " --> pdb=" O LEU 3 20 " (cutoff:3.500A) Processing helix chain '3' and resid 30 through 42 Processing helix chain '3' and resid 51 through 57 Processing helix chain '3' and resid 58 through 66 removed outlier: 3.698A pdb=" N ARG 3 64 " --> pdb=" O LYS 3 60 " (cutoff:3.500A) Processing helix chain '3' and resid 72 through 88 removed outlier: 3.572A pdb=" N ILE 3 87 " --> pdb=" O PHE 3 83 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 95 removed outlier: 3.605A pdb=" N ALA 3 92 " --> pdb=" O ASP 3 88 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN 3 94 " --> pdb=" O THR 3 90 " (cutoff:3.500A) Processing helix chain '3' and resid 106 through 110 Processing helix chain '3' and resid 117 through 121 Processing helix chain '3' and resid 225 through 229 removed outlier: 4.235A pdb=" N ALA 3 229 " --> pdb=" O VAL 3 226 " (cutoff:3.500A) Processing helix chain '3' and resid 280 through 291 Processing helix chain '3' and resid 295 through 302 Processing helix chain '3' and resid 310 through 323 Processing helix chain '3' and resid 350 through 359 removed outlier: 3.659A pdb=" N LEU 3 354 " --> pdb=" O ALA 3 350 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU 3 355 " --> pdb=" O LYS 3 351 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU 3 359 " --> pdb=" O LEU 3 355 " (cutoff:3.500A) Processing helix chain '3' and resid 360 through 362 No H-bonds generated for 'chain '3' and resid 360 through 362' Processing helix chain '3' and resid 411 through 414 Processing helix chain '3' and resid 415 through 427 removed outlier: 3.600A pdb=" N THR 3 420 " --> pdb=" O ASP 3 416 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA 3 421 " --> pdb=" O MET 3 417 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS 3 423 " --> pdb=" O ARG 3 419 " (cutoff:3.500A) removed outlier: 4.066A 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 474 through 478 Processing helix chain '3' and resid 490 through 506 removed outlier: 3.570A pdb=" N ARG 3 495 " --> pdb=" O PRO 3 491 " (cutoff:3.500A) Processing helix chain '3' and resid 564 through 577 removed outlier: 3.545A pdb=" N MET 3 568 " --> pdb=" O SER 3 564 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS 3 569 " --> pdb=" O ALA 3 565 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS 3 570 " --> pdb=" O ALA 3 566 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE 3 577 " --> pdb=" O HIS 3 573 " (cutoff:3.500A) Processing helix chain '3' and resid 583 through 599 removed outlier: 4.037A pdb=" N TYR 3 589 " --> pdb=" O GLU 3 585 " (cutoff:3.500A) Processing helix chain '3' and resid 599 through 604 Processing helix chain '3' and resid 614 through 629 removed outlier: 3.937A pdb=" N LEU 3 618 " --> pdb=" O THR 3 614 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU 3 619 " --> pdb=" O ALA 3 615 " (cutoff:3.500A) Processing helix chain '3' and resid 630 through 632 No H-bonds generated for 'chain '3' and resid 630 through 632' Processing helix chain '3' and resid 638 through 654 removed outlier: 3.926A pdb=" N GLU 3 644 " --> pdb=" O GLN 3 640 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA 3 645 " --> pdb=" O ASP 3 641 " (cutoff:3.500A) Processing helix chain '4' and resid 161 through 166 Processing helix chain '4' and resid 192 through 204 removed outlier: 4.328A pdb=" N GLY 4 198 " --> pdb=" O MET 4 194 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN 4 201 " --> pdb=" O LEU 4 197 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL 4 202 " --> pdb=" O GLY 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 211 through 219 removed outlier: 3.756A pdb=" N ILE 4 215 " --> pdb=" O ASN 4 211 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE 4 218 " --> pdb=" O HIS 4 214 " (cutoff:3.500A) Processing helix chain '4' and resid 219 through 229 removed outlier: 4.032A pdb=" N TYR 4 223 " --> pdb=" O ASP 4 219 " (cutoff:3.500A) Processing helix chain '4' and resid 229 through 248 Proline residue: 4 235 - end of helix removed outlier: 4.007A pdb=" N PHE 4 246 " --> pdb=" O ASN 4 242 " (cutoff:3.500A) Processing helix chain '4' and resid 275 through 279 removed outlier: 3.848A pdb=" N ILE 4 279 " --> pdb=" O PRO 4 276 " (cutoff:3.500A) 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 445 through 455 removed outlier: 3.784A pdb=" N GLU 4 451 " --> pdb=" O GLU 4 447 " (cutoff:3.500A) Processing helix chain '4' and resid 457 through 467 removed outlier: 4.032A pdb=" N ALA 4 467 " --> pdb=" O ALA 4 463 " (cutoff:3.500A) Processing helix chain '4' and resid 473 through 486 Processing helix chain '4' and resid 516 through 527 removed outlier: 3.639A pdb=" N LEU 4 520 " --> pdb=" O LYS 4 516 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN 4 521 " --> pdb=" O SER 4 517 " (cutoff:3.500A) Processing helix chain '4' and resid 561 through 566 Processing helix chain '4' and resid 580 through 591 Processing helix chain '4' and resid 637 through 643 removed outlier: 3.809A pdb=" N ARG 4 643 " --> pdb=" O THR 4 639 " (cutoff:3.500A) Processing helix chain '4' and resid 655 through 671 Processing helix chain '4' and resid 676 through 698 removed outlier: 3.917A pdb=" N GLU 4 680 " --> pdb=" O GLN 4 676 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA 4 692 " --> pdb=" O LYS 4 688 " (cutoff:3.500A) Processing helix chain '4' and resid 703 through 723 removed outlier: 4.389A pdb=" N GLY 4 721 " --> pdb=" O MET 4 717 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER 4 723 " --> pdb=" O LYS 4 719 " (cutoff:3.500A) Processing helix chain '4' and resid 730 through 748 removed outlier: 3.574A pdb=" N LEU 4 734 " --> pdb=" O TYR 4 730 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU 4 735 " --> pdb=" O PRO 4 731 " (cutoff:3.500A) Processing helix chain '4' and resid 754 through 773 removed outlier: 3.686A pdb=" N VAL 4 758 " --> pdb=" O GLU 4 754 " (cutoff:3.500A) Processing helix chain '4' and resid 783 through 789 Processing helix chain '4' and resid 800 through 805 Processing helix chain '4' and resid 805 through 813 Processing helix chain '4' and resid 819 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 '5' and resid 30 through 40 removed outlier: 3.552A pdb=" N PHE 5 35 " --> pdb=" O LEU 5 31 " (cutoff:3.500A) Processing helix chain '5' and resid 53 through 60 removed outlier: 3.593A pdb=" N GLU 5 58 " --> pdb=" O LYS 5 54 " (cutoff:3.500A) Processing helix chain '5' and resid 61 through 66 Processing helix chain '5' and resid 73 through 79 removed outlier: 4.157A pdb=" N LEU 5 77 " --> pdb=" O GLU 5 73 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER 5 79 " --> pdb=" O GLU 5 75 " (cutoff:3.500A) Processing helix chain '5' and resid 81 through 91 removed outlier: 3.619A pdb=" N LEU 5 88 " --> pdb=" O LEU 5 84 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR 5 89 " --> pdb=" O ALA 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 107 removed outlier: 4.336A pdb=" N HIS 5 95 " --> pdb=" O GLN 5 91 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU 5 105 " --> pdb=" O GLU 5 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA 5 107 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 316 through 328 removed outlier: 4.163A pdb=" N GLU 5 321 " --> pdb=" O GLN 5 317 " (cutoff:3.500A) Processing helix chain '5' and resid 330 through 339 removed outlier: 4.029A pdb=" N VAL 5 334 " --> pdb=" O ASN 5 330 " (cutoff:3.500A) Processing helix chain '5' and resid 346 through 359 Processing helix chain '5' and resid 383 through 388 removed outlier: 4.332A pdb=" N LYS 5 387 " --> pdb=" O PRO 5 383 " (cutoff:3.500A) Processing helix chain '5' and resid 389 through 398 removed outlier: 3.739A pdb=" N GLU 5 395 " --> pdb=" O LEU 5 391 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS 5 396 " --> pdb=" O LYS 5 392 " (cutoff:3.500A) Processing helix chain '5' and resid 432 through 437 Processing helix chain '5' and resid 446 through 450 removed outlier: 3.809A pdb=" N LYS 5 449 " --> pdb=" O GLU 5 446 " (cutoff:3.500A) Processing helix chain '5' and resid 451 through 456 removed outlier: 3.942A pdb=" N VAL 5 456 " --> pdb=" O GLU 5 452 " (cutoff:3.500A) Processing helix chain '5' and resid 457 through 462 removed outlier: 3.972A pdb=" N MET 5 462 " --> pdb=" O ILE 5 458 " (cutoff:3.500A) Processing helix chain '5' and resid 555 through 570 removed outlier: 3.728A pdb=" N VAL 5 568 " --> pdb=" O ALA 5 564 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N CYS 5 570 " --> pdb=" O CYS 5 566 " (cutoff:3.500A) Processing helix chain '5' and resid 575 through 592 removed outlier: 3.824A pdb=" N ILE 5 588 " --> pdb=" O ASN 5 584 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER 5 591 " --> pdb=" O ILE 5 587 " (cutoff:3.500A) Processing helix chain '5' and resid 594 through 598 Processing helix chain '5' and resid 609 through 627 removed outlier: 3.936A pdb=" N LYS 5 627 " --> pdb=" O LEU 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 633 through 642 removed outlier: 3.597A pdb=" N GLU 5 639 " --> pdb=" O ALA 5 635 " (cutoff:3.500A) Processing helix chain '5' and resid 647 through 652 Processing helix chain '5' and resid 653 through 658 removed outlier: 3.961A pdb=" N LEU 5 657 " --> pdb=" O LEU 5 653 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER 5 658 " --> pdb=" O SER 5 654 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 653 through 658' Processing helix chain '5' and resid 668 through 683 Processing helix chain '5' and resid 690 through 701 removed outlier: 3.605A pdb=" N GLN 5 701 " --> pdb=" O ASP 5 697 " (cutoff:3.500A) Processing helix chain '5' and resid 704 through 719 Processing helix chain '6' and resid 21 through 36 removed outlier: 3.653A pdb=" N GLU 6 35 " --> pdb=" O LEU 6 31 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 50 removed outlier: 3.696A pdb=" N GLN 6 48 " --> pdb=" O ILE 6 44 " (cutoff:3.500A) Processing helix chain '6' and resid 51 through 55 Processing helix chain '6' and resid 65 through 70 Processing helix chain '6' and resid 72 through 82 removed outlier: 3.551A pdb=" N GLU 6 81 " --> pdb=" O THR 6 77 " (cutoff:3.500A) Processing helix chain '6' and resid 82 through 100 Proline residue: 6 88 - end of helix removed outlier: 3.867A pdb=" N ARG 6 92 " --> pdb=" O PRO 6 88 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA 6 93 " --> pdb=" O TYR 6 89 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL 6 98 " --> pdb=" O LEU 6 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP 6 100 " --> pdb=" O THR 6 96 " (cutoff:3.500A) Processing helix chain '6' and resid 186 through 189 removed outlier: 4.172A 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 211 through 215 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 removed outlier: 3.687A pdb=" N ILE 6 325 " --> pdb=" O THR 6 321 " (cutoff:3.500A) Processing helix chain '6' and resid 330 through 343 removed outlier: 3.549A pdb=" N LYS 6 336 " --> pdb=" O LYS 6 332 " (cutoff:3.500A) Processing helix chain '6' and resid 345 through 355 removed outlier: 4.108A pdb=" N CYS 6 351 " --> pdb=" O TYR 6 347 " (cutoff:3.500A) Processing helix chain '6' and resid 361 through 374 removed outlier: 3.614A pdb=" N LEU 6 372 " --> pdb=" O VAL 6 368 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE 6 373 " --> pdb=" O LEU 6 369 " (cutoff:3.500A) Processing helix chain '6' and resid 401 through 413 removed outlier: 3.707A pdb=" N LEU 6 406 " --> pdb=" O LYS 6 402 " (cutoff:3.500A) Processing helix chain '6' and resid 461 through 465 removed outlier: 3.907A pdb=" N MET 6 465 " --> pdb=" O PHE 6 462 " (cutoff:3.500A) Processing helix chain '6' and resid 466 through 479 removed outlier: 4.065A pdb=" N VAL 6 471 " --> pdb=" O VAL 6 467 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA 6 472 " --> pdb=" O ARG 6 468 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU 6 475 " --> pdb=" O VAL 6 471 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN 6 479 " --> pdb=" O GLU 6 475 " (cutoff:3.500A) Processing helix chain '6' and resid 515 through 519 Processing helix chain '6' and resid 523 through 529 removed outlier: 3.530A pdb=" N ARG 6 529 " --> pdb=" O PRO 6 525 " (cutoff:3.500A) Processing helix chain '6' and resid 542 through 558 Processing helix chain '6' and resid 571 through 580 Processing helix chain '6' and resid 587 through 604 removed outlier: 3.605A pdb=" N ASP 6 592 " --> pdb=" O LYS 6 588 " (cutoff:3.500A) Processing helix chain '6' and resid 617 through 635 removed outlier: 4.084A pdb=" N LEU 6 621 " --> pdb=" O THR 6 617 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 656 removed outlier: 3.517A pdb=" N VAL 6 645 " --> pdb=" O GLN 6 641 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU 6 647 " --> pdb=" O LYS 6 643 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU 6 652 " --> pdb=" O ALA 6 648 " (cutoff:3.500A) Processing helix chain '6' and resid 721 through 739 removed outlier: 3.723A pdb=" N GLU 6 735 " --> pdb=" O LEU 6 731 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU 6 736 " --> pdb=" O ARG 6 732 " (cutoff:3.500A) Processing helix chain '6' and resid 750 through 757 Processing helix chain '6' and resid 765 through 777 removed outlier: 4.261A pdb=" N ARG 6 771 " --> pdb=" O ILE 6 767 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE 6 773 " --> pdb=" O LYS 6 769 " (cutoff:3.500A) Processing helix chain '7' and resid 31 through 42 removed outlier: 3.607A pdb=" N ARG 7 39 " --> pdb=" O ASN 7 35 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 56 removed outlier: 3.783A pdb=" N ALA 7 56 " --> pdb=" O LEU 7 52 " (cutoff:3.500A) Processing helix chain '7' and resid 59 through 69 removed outlier: 3.850A pdb=" N VAL 7 63 " --> pdb=" O ASP 7 59 " (cutoff:3.500A) Processing helix chain '7' and resid 69 through 84 removed outlier: 3.544A pdb=" N TYR 7 73 " --> pdb=" O ASN 7 69 " (cutoff:3.500A) Processing helix chain '7' and resid 128 through 132 Processing helix chain '7' and resid 148 through 153 removed outlier: 4.522A pdb=" N ARG 7 153 " --> pdb=" O ILE 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 213 removed outlier: 3.776A pdb=" N THR 7 213 " --> pdb=" O GLN 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 326 through 330 Processing helix chain '7' and resid 332 through 340 removed outlier: 3.599A pdb=" N ALA 7 338 " --> pdb=" O GLU 7 334 " (cutoff:3.500A) Processing helix chain '7' and resid 347 through 360 removed outlier: 3.743A pdb=" N ALA 7 353 " --> pdb=" O ASP 7 349 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL 7 359 " --> pdb=" O LEU 7 355 " (cutoff:3.500A) Processing helix chain '7' and resid 386 through 398 removed outlier: 3.549A pdb=" N ALA 7 398 " --> pdb=" O ILE 7 394 " (cutoff:3.500A) Processing helix chain '7' and resid 405 through 410 removed outlier: 3.605A pdb=" N SER 7 409 " --> pdb=" O GLY 7 406 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER 7 410 " --> pdb=" O ARG 7 407 " (cutoff:3.500A) Processing helix chain '7' and resid 454 through 464 removed outlier: 3.508A pdb=" N MET 7 462 " --> pdb=" O ILE 7 458 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU 7 463 " --> pdb=" O HIS 7 459 " (cutoff:3.500A) Processing helix chain '7' and resid 500 through 505 Processing helix chain '7' and resid 508 through 515 removed outlier: 3.513A pdb=" N LEU 7 512 " --> pdb=" O PRO 7 508 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER 7 513 " --> pdb=" O ALA 7 509 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG 7 514 " --> pdb=" O ALA 7 510 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE 7 515 " --> pdb=" O LEU 7 511 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 508 through 515' Processing helix chain '7' and resid 526 through 544 removed outlier: 4.024A pdb=" N HIS 7 543 " --> pdb=" O TYR 7 539 " (cutoff:3.500A) Processing helix chain '7' and resid 555 through 569 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 Processing helix chain '7' and resid 602 through 620 removed outlier: 3.965A pdb=" N LEU 7 606 " --> pdb=" O SER 7 602 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU 7 607 " --> pdb=" O ALA 7 603 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 7 615 " --> pdb=" O ARG 7 611 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 641 Processing sheet with id=AA1, first strand: chain '2' and resid 229 through 233 Processing sheet with id=AA2, first strand: chain '2' and resid 304 through 305 removed outlier: 3.768A pdb=" N GLN 2 304 " --> pdb=" O TYR 2 418 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 314 through 315 removed outlier: 3.840A pdb=" N GLU 2 568 " --> pdb=" O HIS 2 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 339 through 340 removed outlier: 7.114A pdb=" N MET 2 324 " --> pdb=" O THR 2 368 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR 2 368 " --> pdb=" O MET 2 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 334 through 335 removed outlier: 3.612A pdb=" N PHE 2 334 " --> pdb=" O CYS 2 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 421 through 422 removed outlier: 3.863A pdb=" N ASN 2 421 " --> pdb=" O ALA 2 436 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA 2 436 " --> pdb=" O ASN 2 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '2' and resid 520 through 522 removed outlier: 6.588A pdb=" N LEU 2 521 " --> pdb=" O ALA 2 630 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N CYS 2 584 " --> pdb=" O ILE 2 627 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ALA 2 629 " --> pdb=" O CYS 2 584 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE 2 586 " --> pdb=" O ALA 2 629 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 608 through 613 Processing sheet with id=AA9, first strand: chain '3' and resid 46 through 50 Processing sheet with id=AB1, first strand: chain '3' and resid 234 through 240 removed outlier: 6.872A pdb=" N THR 3 200 " --> pdb=" O THR 3 132 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N CYS 3 134 " --> pdb=" O THR 3 198 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR 3 198 " --> pdb=" O CYS 3 134 " (cutoff:3.500A) removed outlier: 7.127A 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 240 removed outlier: 3.678A pdb=" N CYS 3 134 " --> pdb=" O LEU 3 393 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 368 through 369 removed outlier: 6.512A pdb=" N THR 3 368 " --> pdb=" O ASP 3 409 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE 3 341 " --> pdb=" O ALA 3 450 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N ALA 3 452 " --> pdb=" O ILE 3 341 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU 3 343 " --> pdb=" O ALA 3 452 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU 3 342 " --> pdb=" O PHE 3 483 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N MET 3 485 " --> pdb=" O LEU 3 342 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE 3 344 " --> pdb=" O MET 3 485 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 430 through 432 Processing sheet with id=AB5, first strand: chain '4' and resid 207 through 208 removed outlier: 3.688A pdb=" N LEU 4 208 " --> pdb=" O GLN 4 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '4' and resid 281 through 283 removed outlier: 3.727A pdb=" N GLN 4 281 " --> pdb=" O TYR 4 394 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE 4 393 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL 4 418 " --> pdb=" O ILE 4 393 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ARG 4 395 " --> pdb=" O ILE 4 416 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE 4 416 " --> pdb=" O ARG 4 395 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL 4 397 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR 4 414 " --> pdb=" O VAL 4 397 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE 4 371 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N HIS 4 375 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N HIS 4 420 " --> pdb=" O HIS 4 375 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU 4 345 " --> pdb=" O GLU 4 301 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU 4 301 " --> pdb=" O LEU 4 345 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '4' and resid 312 through 313 Processing sheet with id=AB8, first strand: chain '4' and resid 408 through 409 removed outlier: 3.814A pdb=" N PHE 7 200 " --> pdb=" O VAL 4 408 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 531 through 534 removed outlier: 6.403A pdb=" N GLN 4 531 " --> pdb=" O CYS 4 572 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASP 4 574 " --> pdb=" O GLN 4 531 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR 4 533 " --> pdb=" O ASP 4 574 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE 4 506 " --> pdb=" O ALA 4 615 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ALA 4 617 " --> pdb=" O ILE 4 506 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU 4 508 " --> pdb=" O ALA 4 617 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU 4 507 " --> pdb=" O PHE 4 648 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 546 through 550 removed outlier: 3.672A pdb=" N GLN 4 555 " --> pdb=" O ASP 4 550 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 599 through 600 removed outlier: 3.517A pdb=" N LYS 4 600 " --> pdb=" O ILE 4 603 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '4' and resid 701 through 702 removed outlier: 6.586A pdb=" N ARG 4 701 " --> pdb=" O VAL 4 753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '5' and resid 244 through 245 removed outlier: 3.556A pdb=" N VAL 5 263 " --> pdb=" O GLY 5 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '5' and resid 363 through 364 Processing sheet with id=AC6, first strand: chain '5' and resid 377 through 380 removed outlier: 4.166A pdb=" N LEU 5 378 " --> pdb=" O MET 5 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 401 through 403 removed outlier: 6.401A pdb=" N VAL 5 402 " --> pdb=" O CYS 5 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '5' and resid 573 through 574 removed outlier: 8.107A pdb=" N ARG 5 573 " --> pdb=" O ALA 5 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '6' and resid 60 through 64 removed outlier: 5.991A pdb=" N LEU 6 61 " --> pdb=" O ALA 6 113 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLN 6 115 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL 6 63 " --> pdb=" O GLN 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain '6' and resid 134 through 138 removed outlier: 3.637A pdb=" N THR 6 245 " --> pdb=" O CYS 6 302 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS 6 302 " --> pdb=" O THR 6 245 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR 6 247 " --> pdb=" O ALA 6 300 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA 6 300 " --> pdb=" O THR 6 247 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE 6 249 " --> pdb=" O PHE 6 298 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE 6 298 " --> pdb=" O ILE 6 249 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL 6 251 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LEU 6 296 " --> pdb=" O VAL 6 251 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N SER 6 223 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N PHE 6 298 " --> pdb=" O SER 6 223 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU 6 225 " --> pdb=" O PHE 6 298 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA 6 300 " --> pdb=" O GLU 6 225 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE 6 227 " --> pdb=" O ALA 6 300 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N CYS 6 302 " --> pdb=" O ILE 6 227 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ARG 6 229 " --> pdb=" O CYS 6 302 " (cutoff:3.500A) removed outlier: 10.801A pdb=" N ALA 6 304 " --> pdb=" O ARG 6 229 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER 6 153 " --> pdb=" O ARG 6 199 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL 6 201 " --> pdb=" O LEU 6 151 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU 6 151 " --> pdb=" O VAL 6 201 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE 6 203 " --> pdb=" O PRO 6 149 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL 6 152 " --> pdb=" O GLU 6 169 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU 6 169 " --> pdb=" O VAL 6 152 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY 6 154 " --> pdb=" O ASP 6 167 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 140 through 144 removed outlier: 6.501A pdb=" N ARG 6 207 " --> pdb=" O VAL 6 142 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N THR 6 144 " --> pdb=" O LYS 6 205 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LYS 6 205 " --> pdb=" O THR 6 144 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER 6 153 " --> pdb=" O ARG 6 199 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL 6 201 " --> pdb=" O LEU 6 151 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU 6 151 " --> pdb=" O VAL 6 201 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE 6 203 " --> pdb=" O PRO 6 149 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 417 through 420 removed outlier: 3.760A pdb=" N VAL 6 417 " --> pdb=" O VAL 6 456 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL 6 392 " --> pdb=" O ALA 6 501 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 433 through 435 Processing sheet with id=AD5, first strand: chain '6' and resid 481 through 484 Processing sheet with id=AD6, first strand: chain '6' and resid 585 through 586 removed outlier: 7.471A pdb=" N LYS 6 585 " --> pdb=" O VAL 6 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain '7' and resid 48 through 50 removed outlier: 6.805A pdb=" N LEU 7 48 " --> pdb=" O TYR 7 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain '7' and resid 192 through 193 removed outlier: 3.844A pdb=" N LYS 7 174 " --> pdb=" O PHE 7 232 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ARG 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '7' and resid 220 through 222 removed outlier: 3.844A pdb=" N LYS 7 174 " --> pdb=" O PHE 7 232 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ARG 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG 7 169 " --> pdb=" O LYS 7 236 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLN 7 238 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL 7 167 " --> pdb=" O GLN 7 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET 7 306 " --> pdb=" O SER 7 272 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '7' and resid 485 through 487 removed outlier: 6.144A pdb=" N ILE 7 377 " --> pdb=" O ALA 7 486 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET 7 380 " --> pdb=" O TRP 7 519 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3021 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: 5.97 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9592 1.34 - 1.46: 5021 1.46 - 1.58: 13778 1.58 - 1.69: 21 1.69 - 1.81: 234 Bond restraints: 28646 Sorted by residual: bond pdb=" C4 ADP 3 901 " pdb=" C5 ADP 3 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C5 ADP 3 901 " pdb=" C6 ADP 3 901 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" N SER 7 549 " pdb=" CA SER 7 549 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.16e-02 7.43e+03 7.94e+00 bond pdb=" N ASP 7 555 " pdb=" CA ASP 7 555 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.18e-02 7.18e+03 7.39e+00 bond pdb=" N ARG 7 545 " pdb=" CA ARG 7 545 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.34e+00 ... (remaining 28641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 38395 2.17 - 4.34: 393 4.34 - 6.50: 52 6.50 - 8.67: 9 8.67 - 10.84: 5 Bond angle restraints: 38854 Sorted by residual: angle pdb=" PB ATP 4 902 " pdb=" O3B ATP 4 902 " pdb=" PG ATP 4 902 " ideal model delta sigma weight residual 139.87 129.03 10.84 1.00e+00 1.00e+00 1.18e+02 angle pdb=" PB ATP 6 901 " pdb=" O3B ATP 6 901 " pdb=" PG ATP 6 901 " ideal model delta sigma weight residual 139.87 129.21 10.66 1.00e+00 1.00e+00 1.14e+02 angle pdb=" PA ATP 6 901 " pdb=" O3A ATP 6 901 " pdb=" PB ATP 6 901 " ideal model delta sigma weight residual 136.83 128.44 8.39 1.00e+00 1.00e+00 7.04e+01 angle pdb=" PA ATP 4 902 " pdb=" O3A ATP 4 902 " pdb=" PB ATP 4 902 " ideal model delta sigma weight residual 136.83 130.82 6.01 1.00e+00 1.00e+00 3.61e+01 angle pdb=" N VAL 7 178 " pdb=" CA VAL 7 178 " pdb=" C VAL 7 178 " ideal model delta sigma weight residual 112.96 107.79 5.17 1.00e+00 1.00e+00 2.68e+01 ... (remaining 38849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.88: 16620 23.88 - 47.75: 789 47.75 - 71.63: 179 71.63 - 95.50: 16 95.50 - 119.38: 2 Dihedral angle restraints: 17606 sinusoidal: 6829 harmonic: 10777 Sorted by residual: dihedral pdb=" O2A ADP 3 901 " pdb=" O3A ADP 3 901 " pdb=" PA ADP 3 901 " pdb=" PB ADP 3 901 " ideal model delta sinusoidal sigma weight residual -60.00 59.38 -119.38 1 2.00e+01 2.50e-03 3.58e+01 dihedral pdb=" O2A ADP 7 801 " pdb=" O3A ADP 7 801 " pdb=" PA ADP 7 801 " pdb=" PB ADP 7 801 " ideal model delta sinusoidal sigma weight residual -60.00 52.35 -112.35 1 2.00e+01 2.50e-03 3.31e+01 dihedral pdb=" CA ARG 2 218 " pdb=" C ARG 2 218 " pdb=" N ILE 2 219 " pdb=" CA ILE 2 219 " ideal model delta harmonic sigma weight residual 180.00 159.41 20.59 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 17603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3331 0.040 - 0.081: 870 0.081 - 0.121: 320 0.121 - 0.161: 16 0.161 - 0.202: 3 Chirality restraints: 4540 Sorted by residual: chirality pdb=" CA MET 7 556 " pdb=" N MET 7 556 " pdb=" C MET 7 556 " pdb=" CB MET 7 556 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB THR 7 405 " pdb=" CA THR 7 405 " pdb=" OG1 THR 7 405 " pdb=" CG2 THR 7 405 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CA GLN 7 550 " pdb=" N GLN 7 550 " pdb=" C GLN 7 550 " pdb=" CB GLN 7 550 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 4537 not shown) Planarity restraints: 5050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 6 104 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO 6 105 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO 6 105 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO 6 105 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 2 668 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO 2 669 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO 2 669 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO 2 669 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 7 85 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO 7 86 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO 7 86 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO 7 86 " 0.021 5.00e-02 4.00e+02 ... (remaining 5047 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 31 2.64 - 3.20: 27191 3.20 - 3.77: 42976 3.77 - 4.33: 59267 4.33 - 4.90: 93672 Nonbonded interactions: 223137 Sorted by model distance: nonbonded pdb="MG MG 21001 " pdb=" O2B ATP 21002 " model vdw 2.071 2.170 nonbonded pdb=" OG SER 2 530 " pdb="MG MG 21001 " model vdw 2.097 2.170 nonbonded pdb=" O1G ATP 4 902 " pdb="MG MG 4 903 " model vdw 2.107 2.170 nonbonded pdb=" O1B ATP 4 902 " pdb="MG MG 4 903 " model vdw 2.206 2.170 nonbonded pdb="MG MG 21001 " pdb=" O2G ATP 21002 " model vdw 2.219 2.170 ... (remaining 223132 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: 5.330 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 28.160 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 28662 Z= 0.138 Angle : 0.576 13.069 38878 Z= 0.306 Chirality : 0.041 0.202 4540 Planarity : 0.004 0.057 5050 Dihedral : 14.095 119.381 10592 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -1.51 (0.14), residues: 3636 helix: -0.60 (0.14), residues: 1394 sheet: -1.54 (0.24), residues: 458 loop : -1.08 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 3 445 TYR 0.011 0.001 TYR 5 731 PHE 0.011 0.001 PHE 5 358 TRP 0.007 0.001 TRP 6 334 HIS 0.006 0.001 HIS 7 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (28646) covalent geometry : angle 0.56652 / 0.31 (38854) hydrogen bonds : bond 0.26335 / 17.92 ( 1057) hydrogen bonds : angle 8.61627 / 6.05 ( 3021) metal coordination : bond 0.00469 / 0.27 ( 16) metal coordination : angle 4.25035 / 3.24 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.112 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: 3 259 VAL cc_start: 0.8467 (t) cc_final: 0.8190 (m) REVERT: 3 518 MET cc_start: 0.7234 (ptm) cc_final: 0.6924 (ptp) REVERT: 5 733 LEU cc_start: 0.8217 (tp) cc_final: 0.7870 (tt) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.1562 time to fit residues: 79.3034 Evaluate side-chains 165 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 0.0470 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 40.0000 chunk 298 optimal weight: 5.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 264 ASN 3 423 HIS 3 443 ASN ** 3 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 494 HIS 4 672 GLN ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.063564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.045049 restraints weight = 154118.788| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 5.08 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28662 Z= 0.186 Angle : 0.651 12.827 38878 Z= 0.326 Chirality : 0.043 0.180 4540 Planarity : 0.004 0.046 5050 Dihedral : 7.047 116.202 4094 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.64 % Allowed : 7.84 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3636 helix: 0.06 (0.14), residues: 1414 sheet: -1.51 (0.22), residues: 510 loop : -1.06 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 3 445 TYR 0.024 0.001 TYR 7 562 PHE 0.020 0.001 PHE 7 200 TRP 0.015 0.002 TRP 5 69 HIS 0.019 0.001 HIS 2 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (28646) covalent geometry : angle 0.64024 / 0.33 (38854) hydrogen bonds : bond 0.04789 / 3.25 ( 1057) hydrogen bonds : angle 5.88929 / 4.15 ( 3021) metal coordination : bond 0.00646 / 0.35 ( 16) metal coordination : angle 4.75753 / 3.44 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.053 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: 2 270 MET cc_start: 0.7919 (mmm) cc_final: 0.7391 (mtt) REVERT: 2 674 MET cc_start: 0.8932 (mmm) cc_final: 0.8708 (mmm) REVERT: 2 770 MET cc_start: 0.9332 (mmt) cc_final: 0.9130 (mmt) REVERT: 2 773 MET cc_start: 0.9178 (mtt) cc_final: 0.8197 (mtm) REVERT: 2 798 MET cc_start: 0.9253 (tpp) cc_final: 0.8882 (tpp) REVERT: 2 814 MET cc_start: 0.9056 (ptm) cc_final: 0.8601 (ptt) REVERT: 3 65 LEU cc_start: 0.9731 (tp) cc_final: 0.9436 (mt) REVERT: 3 102 LEU cc_start: 0.9508 (tp) cc_final: 0.9283 (tp) REVERT: 3 398 MET cc_start: 0.9239 (mmm) cc_final: 0.8812 (mmm) REVERT: 3 424 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: 4 256 HIS cc_start: 0.7888 (t-90) cc_final: 0.7548 (t70) REVERT: 4 684 MET cc_start: 0.9216 (ttt) cc_final: 0.8877 (tpp) REVERT: 5 69 TRP cc_start: 0.9419 (p-90) cc_final: 0.9002 (p-90) REVERT: 5 349 MET cc_start: 0.8969 (mmt) cc_final: 0.8450 (mmp) REVERT: 5 516 MET cc_start: 0.6990 (tpp) cc_final: 0.6774 (tpt) REVERT: 6 527 MET cc_start: 0.8717 (mtm) cc_final: 0.8201 (mtm) REVERT: 7 131 MET cc_start: 0.9044 (mmt) cc_final: 0.8773 (mmm) REVERT: 7 237 MET cc_start: 0.8168 (tmm) cc_final: 0.7274 (tmm) REVERT: 7 405 THR cc_start: 0.8898 (p) cc_final: 0.8595 (t) REVERT: 7 446 GLU cc_start: 0.6145 (tt0) cc_final: 0.5803 (tt0) REVERT: 7 559 MET cc_start: 0.9437 (tpp) cc_final: 0.8912 (mmp) outliers start: 19 outliers final: 10 residues processed: 196 average time/residue: 0.1704 time to fit residues: 56.7898 Evaluate side-chains 169 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 232 VAL Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 4 residue 613 VAL Chi-restraints excluded: chain 5 residue 692 HIS Chi-restraints excluded: chain 5 residue 722 GLN Chi-restraints excluded: chain 6 residue 371 MET Chi-restraints excluded: chain 6 residue 471 VAL Chi-restraints excluded: chain 6 residue 729 LEU Chi-restraints excluded: chain 7 residue 273 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 291 optimal weight: 0.0670 chunk 110 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 269 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 187 optimal weight: 30.0000 chunk 311 optimal weight: 6.9990 chunk 325 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 419 HIS 3 33 GLN 3 110 HIS ** 3 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 612 GLN 6 778 HIS 7 240 HIS 7 243 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.061671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.042845 restraints weight = 160449.948| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 5.09 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 28662 Z= 0.260 Angle : 0.666 14.237 38878 Z= 0.336 Chirality : 0.043 0.160 4540 Planarity : 0.004 0.043 5050 Dihedral : 7.144 117.890 4094 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.09 % Allowed : 9.64 % Favored : 89.27 % 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: -1.09 (0.14), residues: 3636 helix: 0.17 (0.14), residues: 1437 sheet: -1.64 (0.22), residues: 525 loop : -1.11 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 5 717 TYR 0.021 0.002 TYR 4 412 PHE 0.033 0.002 PHE 7 200 TRP 0.011 0.002 TRP 2 569 HIS 0.012 0.001 HIS 2 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.26 (28646) covalent geometry : angle 0.65288 / 0.34 (38854) hydrogen bonds : bond 0.04279 / 2.90 ( 1057) hydrogen bonds : angle 5.52185 / 3.90 ( 3021) metal coordination : bond 0.01070 / 0.61 ( 16) metal coordination : angle 5.40979 / 3.86 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 255 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7397 (mp) REVERT: 2 270 MET cc_start: 0.8108 (mmm) cc_final: 0.7646 (mtt) REVERT: 2 324 MET cc_start: 0.8488 (mmm) cc_final: 0.7798 (mmm) REVERT: 2 592 MET cc_start: 0.8484 (mmm) cc_final: 0.8006 (mmm) REVERT: 2 674 MET cc_start: 0.8954 (mmm) cc_final: 0.8753 (mmm) REVERT: 2 770 MET cc_start: 0.9407 (mmt) cc_final: 0.9107 (mmm) REVERT: 3 65 LEU cc_start: 0.9764 (tp) cc_final: 0.9461 (mt) REVERT: 3 102 LEU cc_start: 0.9476 (tp) cc_final: 0.9276 (tp) REVERT: 3 204 MET cc_start: 0.8626 (mmm) cc_final: 0.8309 (mmt) REVERT: 3 398 MET cc_start: 0.9305 (mmm) cc_final: 0.8656 (mmm) REVERT: 3 424 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: 4 256 HIS cc_start: 0.7922 (t-90) cc_final: 0.7564 (t70) REVERT: 5 69 TRP cc_start: 0.9498 (p-90) cc_final: 0.8897 (p-90) REVERT: 5 436 LEU cc_start: 0.9613 (mt) cc_final: 0.9385 (mt) REVERT: 6 234 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8396 (tp30) REVERT: 7 131 MET cc_start: 0.9106 (mmt) cc_final: 0.8654 (mmt) REVERT: 7 201 MET cc_start: 0.9403 (ttm) cc_final: 0.8938 (tpt) REVERT: 7 237 MET cc_start: 0.8187 (tmm) cc_final: 0.7271 (tmm) REVERT: 7 258 GLU cc_start: 0.9050 (pm20) cc_final: 0.8834 (pm20) REVERT: 7 356 LEU cc_start: 0.9235 (pp) cc_final: 0.9009 (tp) REVERT: 7 405 THR cc_start: 0.8928 (p) cc_final: 0.8393 (t) REVERT: 7 446 GLU cc_start: 0.6381 (tt0) cc_final: 0.5838 (tt0) REVERT: 7 559 MET cc_start: 0.9477 (tpp) cc_final: 0.8983 (mmp) outliers start: 32 outliers final: 18 residues processed: 189 average time/residue: 0.1624 time to fit residues: 53.6135 Evaluate side-chains 168 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 232 VAL Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 2 residue 626 VAL Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 613 VAL Chi-restraints excluded: chain 4 residue 289 VAL Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 613 VAL Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 692 HIS Chi-restraints excluded: chain 6 residue 371 MET Chi-restraints excluded: chain 6 residue 471 VAL Chi-restraints excluded: chain 6 residue 729 LEU Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 516 ASP Chi-restraints excluded: chain 7 residue 634 ILE Chi-restraints excluded: chain 7 residue 636 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 204 optimal weight: 0.0970 chunk 51 optimal weight: 0.0970 chunk 92 optimal weight: 0.2980 chunk 285 optimal weight: 0.9980 chunk 192 optimal weight: 20.0000 chunk 345 optimal weight: 0.0060 chunk 237 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 328 optimal weight: 8.9990 chunk 146 optimal weight: 0.5980 overall best weight: 0.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 646 ASN 2 889 ASN 3 110 HIS ** 3 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 500 HIS ** 3 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 368 HIS 4 695 HIS ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 595 GLN 5 612 GLN 7 389 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.063489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.045097 restraints weight = 152430.978| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 5.04 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 28662 Z= 0.107 Angle : 0.581 11.322 38878 Z= 0.283 Chirality : 0.042 0.145 4540 Planarity : 0.003 0.043 5050 Dihedral : 6.846 113.300 4094 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.88 % Allowed : 11.03 % Favored : 88.09 % 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: -0.77 (0.14), residues: 3636 helix: 0.55 (0.14), residues: 1420 sheet: -1.68 (0.22), residues: 507 loop : -0.96 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 815 TYR 0.013 0.001 TYR 4 690 PHE 0.011 0.001 PHE 2 808 TRP 0.008 0.001 TRP 5 69 HIS 0.010 0.001 HIS 5 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (28646) covalent geometry : angle 0.57309 / 0.28 (38854) hydrogen bonds : bond 0.03455 / 2.33 ( 1057) hydrogen bonds : angle 5.02678 / 3.54 ( 3021) metal coordination : bond 0.00471 / 0.28 ( 16) metal coordination : angle 3.90689 / 2.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 1.104 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: 2 270 MET cc_start: 0.8004 (mmm) cc_final: 0.7710 (mtt) REVERT: 2 592 MET cc_start: 0.8434 (mmm) cc_final: 0.8012 (tpp) REVERT: 2 738 MET cc_start: 0.9347 (mmp) cc_final: 0.8715 (mpp) REVERT: 2 773 MET cc_start: 0.9253 (mtm) cc_final: 0.8180 (mtm) REVERT: 2 798 MET cc_start: 0.9155 (tpp) cc_final: 0.8814 (tpp) REVERT: 3 204 MET cc_start: 0.8681 (mmm) cc_final: 0.8313 (mmt) REVERT: 3 398 MET cc_start: 0.9177 (mmm) cc_final: 0.8610 (mmm) REVERT: 3 424 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: 3 603 MET cc_start: 0.6646 (ppp) cc_final: 0.6270 (ppp) REVERT: 4 256 HIS cc_start: 0.7821 (t-90) cc_final: 0.7548 (t70) REVERT: 5 69 TRP cc_start: 0.9440 (p-90) cc_final: 0.8855 (p-90) REVERT: 5 100 GLU cc_start: 0.8639 (pt0) cc_final: 0.8327 (mt-10) REVERT: 5 436 LEU cc_start: 0.9632 (mt) cc_final: 0.9406 (mt) REVERT: 5 516 MET cc_start: 0.7074 (tpp) cc_final: 0.6333 (tpt) REVERT: 6 234 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8279 (tp30) REVERT: 6 329 MET cc_start: 0.9246 (ptp) cc_final: 0.8995 (ppp) REVERT: 7 131 MET cc_start: 0.9062 (mmt) cc_final: 0.8632 (mmt) REVERT: 7 405 THR cc_start: 0.8951 (p) cc_final: 0.8342 (t) REVERT: 7 446 GLU cc_start: 0.6304 (tt0) cc_final: 0.5722 (tt0) REVERT: 7 559 MET cc_start: 0.9439 (tpp) cc_final: 0.9110 (mmp) outliers start: 26 outliers final: 15 residues processed: 188 average time/residue: 0.1579 time to fit residues: 52.0779 Evaluate side-chains 168 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 232 VAL Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 4 residue 289 VAL Chi-restraints excluded: chain 4 residue 613 VAL Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 5 residue 395 GLU Chi-restraints excluded: chain 5 residue 692 HIS Chi-restraints excluded: chain 6 residue 371 MET Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 471 VAL Chi-restraints excluded: chain 6 residue 729 LEU Chi-restraints excluded: chain 7 residue 256 LEU Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 516 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 65 optimal weight: 30.0000 chunk 21 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 299 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 250 optimal weight: 0.5980 chunk 329 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 280 HIS 3 110 HIS ** 3 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 635 GLN 4 695 HIS ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 238 HIS ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 612 GLN 7 465 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.061884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.043385 restraints weight = 158956.456| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 5.08 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28662 Z= 0.182 Angle : 0.596 13.107 38878 Z= 0.293 Chirality : 0.042 0.174 4540 Planarity : 0.003 0.039 5050 Dihedral : 6.855 115.857 4094 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.22 % Allowed : 12.22 % Favored : 86.56 % 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: -0.72 (0.14), residues: 3636 helix: 0.62 (0.14), residues: 1433 sheet: -1.54 (0.22), residues: 513 loop : -1.02 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 618 TYR 0.016 0.001 TYR 6 347 PHE 0.012 0.001 PHE 4 485 TRP 0.009 0.001 TRP 2 569 HIS 0.009 0.001 HIS 5 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (28646) covalent geometry : angle 0.58526 / 0.29 (38854) hydrogen bonds : bond 0.03424 / 2.32 ( 1057) hydrogen bonds : angle 4.99453 / 3.52 ( 3021) metal coordination : bond 0.00759 / 0.43 ( 16) metal coordination : angle 4.63650 / 3.34 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 1.170 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: 2 255 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7477 (mp) REVERT: 2 270 MET cc_start: 0.7842 (mmm) cc_final: 0.7634 (mtt) REVERT: 2 395 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7614 (p0) REVERT: 2 592 MET cc_start: 0.8480 (mmm) cc_final: 0.8115 (mmm) REVERT: 2 738 MET cc_start: 0.9348 (mmp) cc_final: 0.8759 (mpp) REVERT: 2 770 MET cc_start: 0.9402 (mmt) cc_final: 0.9155 (mmm) REVERT: 2 773 MET cc_start: 0.9322 (mtm) cc_final: 0.8235 (mtm) REVERT: 2 798 MET cc_start: 0.9151 (tpp) cc_final: 0.8891 (tpp) REVERT: 2 804 ASP cc_start: 0.8278 (t0) cc_final: 0.8030 (t0) REVERT: 3 369 THR cc_start: 0.9630 (OUTLIER) cc_final: 0.9248 (t) REVERT: 3 398 MET cc_start: 0.9293 (mmm) cc_final: 0.8752 (mmm) REVERT: 3 424 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: 3 603 MET cc_start: 0.7097 (ppp) cc_final: 0.6801 (ppp) REVERT: 4 256 HIS cc_start: 0.7847 (t-90) cc_final: 0.7553 (t70) REVERT: 5 69 TRP cc_start: 0.9489 (p-90) cc_final: 0.8892 (p-90) REVERT: 5 255 ASP cc_start: 0.8821 (p0) cc_final: 0.8010 (t0) REVERT: 5 436 LEU cc_start: 0.9679 (mt) cc_final: 0.9472 (mt) REVERT: 5 516 MET cc_start: 0.7121 (tpp) cc_final: 0.6909 (tpt) REVERT: 6 234 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8409 (tp30) REVERT: 7 131 MET cc_start: 0.9086 (mmt) cc_final: 0.8634 (mmt) REVERT: 7 258 GLU cc_start: 0.8843 (pm20) cc_final: 0.8602 (mp0) REVERT: 7 356 LEU cc_start: 0.9231 (pp) cc_final: 0.8988 (tp) REVERT: 7 405 THR cc_start: 0.8969 (p) cc_final: 0.8455 (t) REVERT: 7 446 GLU cc_start: 0.6489 (tt0) cc_final: 0.5983 (tt0) REVERT: 7 559 MET cc_start: 0.9466 (tpp) cc_final: 0.9261 (mmp) outliers start: 36 outliers final: 22 residues processed: 188 average time/residue: 0.1622 time to fit residues: 53.3369 Evaluate side-chains 173 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 232 VAL Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 395 ASP Chi-restraints excluded: chain 2 residue 769 SER Chi-restraints excluded: chain 3 residue 339 ILE Chi-restraints excluded: chain 3 residue 369 THR Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 427 GLU Chi-restraints excluded: chain 3 residue 613 VAL Chi-restraints excluded: chain 4 residue 289 VAL Chi-restraints excluded: chain 4 residue 613 VAL Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 4 residue 695 HIS Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 395 GLU Chi-restraints excluded: chain 5 residue 484 VAL Chi-restraints excluded: chain 5 residue 692 HIS Chi-restraints excluded: chain 6 residue 371 MET Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 471 VAL Chi-restraints excluded: chain 6 residue 729 LEU Chi-restraints excluded: chain 7 residue 256 LEU Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 516 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 282 optimal weight: 0.7980 chunk 309 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 646 ASN ** 3 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 695 HIS ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** 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 = 0.3674 r_free = 0.3674 target = 0.062199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.043771 restraints weight = 158335.255| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 5.01 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28662 Z= 0.137 Angle : 0.580 15.193 38878 Z= 0.281 Chirality : 0.041 0.168 4540 Planarity : 0.003 0.039 5050 Dihedral : 6.789 114.173 4094 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.56 % Allowed : 12.66 % Favored : 85.78 % 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: -0.60 (0.14), residues: 3636 helix: 0.72 (0.14), residues: 1435 sheet: -1.37 (0.22), residues: 511 loop : -1.00 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 5 455 TYR 0.013 0.001 TYR 6 347 PHE 0.025 0.001 PHE 7 16 TRP 0.007 0.001 TRP 2 569 HIS 0.012 0.001 HIS 4 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (28646) covalent geometry : angle 0.57044 / 0.28 (38854) hydrogen bonds : bond 0.03235 / 2.19 ( 1057) hydrogen bonds : angle 4.85979 / 3.42 ( 3021) metal coordination : bond 0.00664 / 0.39 ( 16) metal coordination : angle 4.23721 / 3.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 1.126 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: 2 255 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7535 (mp) REVERT: 2 395 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7524 (p0) REVERT: 2 592 MET cc_start: 0.8465 (mmm) cc_final: 0.8120 (tpp) REVERT: 2 738 MET cc_start: 0.9343 (mmp) cc_final: 0.8739 (mpp) REVERT: 2 773 MET cc_start: 0.9342 (mtm) cc_final: 0.8284 (mtm) REVERT: 2 798 MET cc_start: 0.9084 (tpp) cc_final: 0.8860 (tpp) REVERT: 2 804 ASP cc_start: 0.8284 (t0) cc_final: 0.8009 (t0) REVERT: 3 204 MET cc_start: 0.8695 (mmm) cc_final: 0.8382 (mmt) REVERT: 3 369 THR cc_start: 0.9657 (OUTLIER) cc_final: 0.9281 (t) REVERT: 3 398 MET cc_start: 0.9292 (mmm) cc_final: 0.8710 (mmm) REVERT: 3 424 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: 3 603 MET cc_start: 0.7180 (ppp) cc_final: 0.6891 (ppp) REVERT: 4 256 HIS cc_start: 0.7848 (t-90) cc_final: 0.7593 (t70) REVERT: 4 271 MET cc_start: 0.8120 (mtm) cc_final: 0.7882 (mpp) REVERT: 4 506 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9113 (mt) REVERT: 5 69 TRP cc_start: 0.9539 (p-90) cc_final: 0.8974 (p-90) REVERT: 5 255 ASP cc_start: 0.8826 (p0) cc_final: 0.7966 (t0) REVERT: 5 436 LEU cc_start: 0.9701 (mt) cc_final: 0.9496 (mt) REVERT: 5 516 MET cc_start: 0.7232 (tpp) cc_final: 0.6964 (tpt) REVERT: 6 234 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8418 (tp30) REVERT: 7 131 MET cc_start: 0.9109 (mmt) cc_final: 0.8659 (mmt) REVERT: 7 201 MET cc_start: 0.9475 (ttm) cc_final: 0.9090 (mmm) REVERT: 7 258 GLU cc_start: 0.8830 (pm20) cc_final: 0.8615 (mp0) REVERT: 7 356 LEU cc_start: 0.9190 (pp) cc_final: 0.8986 (tp) REVERT: 7 405 THR cc_start: 0.8982 (p) cc_final: 0.8389 (t) REVERT: 7 446 GLU cc_start: 0.6372 (tt0) cc_final: 0.5813 (tt0) REVERT: 7 559 MET cc_start: 0.9447 (tpp) cc_final: 0.9060 (mmp) REVERT: 7 565 MET cc_start: 0.8895 (pmm) cc_final: 0.8444 (ppp) REVERT: 7 621 MET cc_start: 0.8870 (mmm) cc_final: 0.7227 (mmm) outliers start: 46 outliers final: 26 residues processed: 193 average time/residue: 0.1651 time to fit residues: 54.6906 Evaluate side-chains 179 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 232 VAL Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 395 ASP Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 2 residue 626 VAL Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 3 residue 339 ILE Chi-restraints excluded: chain 3 residue 369 THR Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 427 GLU Chi-restraints excluded: chain 3 residue 613 VAL Chi-restraints excluded: chain 4 residue 289 VAL Chi-restraints excluded: chain 4 residue 506 ILE Chi-restraints excluded: chain 4 residue 613 VAL Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 4 residue 695 HIS Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 70 ILE Chi-restraints excluded: chain 5 residue 484 VAL Chi-restraints excluded: chain 5 residue 692 HIS Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 329 MET Chi-restraints excluded: chain 6 residue 371 MET Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 471 VAL Chi-restraints excluded: chain 6 residue 729 LEU Chi-restraints excluded: chain 7 residue 256 LEU Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 516 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 234 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 297 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 334 optimal weight: 1.9990 chunk 293 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 646 ASN ** 3 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 695 HIS ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** 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 = 0.3673 r_free = 0.3673 target = 0.062088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.043783 restraints weight = 157377.266| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 5.00 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28662 Z= 0.134 Angle : 0.580 16.834 38878 Z= 0.281 Chirality : 0.041 0.172 4540 Planarity : 0.003 0.039 5050 Dihedral : 6.742 113.300 4094 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.46 % Allowed : 13.31 % Favored : 85.23 % 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: -0.56 (0.14), residues: 3636 helix: 0.77 (0.14), residues: 1447 sheet: -1.32 (0.22), residues: 511 loop : -1.02 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 6 619 TYR 0.012 0.001 TYR 4 671 PHE 0.029 0.001 PHE 7 16 TRP 0.007 0.001 TRP 2 569 HIS 0.013 0.001 HIS 4 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (28646) covalent geometry : angle 0.57082 / 0.28 (38854) hydrogen bonds : bond 0.03147 / 2.13 ( 1057) hydrogen bonds : angle 4.78303 / 3.37 ( 3021) metal coordination : bond 0.00674 / 0.39 ( 16) metal coordination : angle 4.11511 / 3.02 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 1.159 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: 2 270 MET cc_start: 0.6950 (mtt) cc_final: 0.6133 (mtt) REVERT: 2 365 MET cc_start: 0.5788 (tpt) cc_final: 0.5538 (tpt) REVERT: 2 395 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7517 (p0) REVERT: 2 592 MET cc_start: 0.8518 (mmm) cc_final: 0.8152 (tpp) REVERT: 2 738 MET cc_start: 0.9351 (mmp) cc_final: 0.8728 (mpp) REVERT: 2 773 MET cc_start: 0.9316 (mtm) cc_final: 0.8277 (mtm) REVERT: 2 798 MET cc_start: 0.9098 (tpp) cc_final: 0.8850 (tpp) REVERT: 2 804 ASP cc_start: 0.8243 (t0) cc_final: 0.7969 (t0) REVERT: 3 204 MET cc_start: 0.8769 (mmm) cc_final: 0.8450 (mmt) REVERT: 3 369 THR cc_start: 0.9630 (OUTLIER) cc_final: 0.9240 (t) REVERT: 3 398 MET cc_start: 0.9275 (mmm) cc_final: 0.8698 (mmm) REVERT: 3 424 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: 3 603 MET cc_start: 0.7239 (ppp) cc_final: 0.6952 (ppp) REVERT: 4 256 HIS cc_start: 0.7904 (t-90) cc_final: 0.7606 (t70) REVERT: 4 351 MET cc_start: 0.8527 (tpp) cc_final: 0.8063 (tpp) REVERT: 4 506 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9111 (mt) REVERT: 5 69 TRP cc_start: 0.9533 (p-90) cc_final: 0.8947 (p-90) REVERT: 5 255 ASP cc_start: 0.8794 (p0) cc_final: 0.7980 (t0) REVERT: 5 436 LEU cc_start: 0.9694 (mt) cc_final: 0.9490 (mt) REVERT: 5 516 MET cc_start: 0.7193 (tpp) cc_final: 0.6903 (tpt) REVERT: 6 234 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8396 (tp30) REVERT: 7 131 MET cc_start: 0.9108 (mmt) cc_final: 0.8661 (mmt) REVERT: 7 201 MET cc_start: 0.9466 (ttm) cc_final: 0.9079 (mmm) REVERT: 7 258 GLU cc_start: 0.8852 (pm20) cc_final: 0.8651 (mp0) REVERT: 7 405 THR cc_start: 0.8972 (p) cc_final: 0.8425 (t) REVERT: 7 446 GLU cc_start: 0.6383 (tt0) cc_final: 0.5819 (tt0) REVERT: 7 462 MET cc_start: 0.9260 (mmm) cc_final: 0.9017 (mmm) REVERT: 7 559 MET cc_start: 0.9437 (tpp) cc_final: 0.9065 (mmp) REVERT: 7 565 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8572 (ppp) outliers start: 43 outliers final: 29 residues processed: 188 average time/residue: 0.1596 time to fit residues: 51.7115 Evaluate side-chains 182 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 232 VAL Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 395 ASP Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 2 residue 626 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 3 residue 339 ILE Chi-restraints excluded: chain 3 residue 369 THR Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 427 GLU Chi-restraints excluded: chain 3 residue 613 VAL Chi-restraints excluded: chain 4 residue 289 VAL Chi-restraints excluded: chain 4 residue 506 ILE Chi-restraints excluded: chain 4 residue 613 VAL Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 4 residue 695 HIS Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 70 ILE Chi-restraints excluded: chain 5 residue 428 ILE Chi-restraints excluded: chain 5 residue 484 VAL Chi-restraints excluded: chain 5 residue 692 HIS Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 329 MET Chi-restraints excluded: chain 6 residue 371 MET Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 471 VAL Chi-restraints excluded: chain 6 residue 729 LEU Chi-restraints excluded: chain 7 residue 256 LEU Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 516 ASP Chi-restraints excluded: chain 7 residue 551 PHE Chi-restraints excluded: chain 7 residue 565 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 109 optimal weight: 0.8980 chunk 24 optimal weight: 0.0070 chunk 127 optimal weight: 0.7980 chunk 315 optimal weight: 0.0070 chunk 65 optimal weight: 0.8980 chunk 223 optimal weight: 20.0000 chunk 205 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 183 optimal weight: 50.0000 chunk 232 optimal weight: 0.6980 chunk 335 optimal weight: 3.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 635 GLN 4 695 HIS ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** 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 = 0.3689 r_free = 0.3689 target = 0.062788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.044377 restraints weight = 155174.785| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 5.05 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 28662 Z= 0.099 Angle : 0.585 17.591 38878 Z= 0.279 Chirality : 0.041 0.194 4540 Planarity : 0.003 0.039 5050 Dihedral : 6.627 110.302 4094 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.32 % Allowed : 14.02 % Favored : 84.66 % 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: -0.43 (0.14), residues: 3636 helix: 0.87 (0.14), residues: 1439 sheet: -1.15 (0.23), residues: 488 loop : -0.98 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 6 619 TYR 0.013 0.001 TYR 4 690 PHE 0.010 0.001 PHE 2 808 TRP 0.006 0.001 TRP 5 69 HIS 0.011 0.001 HIS 5 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (28646) covalent geometry : angle 0.57767 / 0.28 (38854) hydrogen bonds : bond 0.03009 / 2.04 ( 1057) hydrogen bonds : angle 4.59446 / 3.24 ( 3021) metal coordination : bond 0.00480 / 0.29 ( 16) metal coordination : angle 3.74540 / 2.79 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.136 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: 2 255 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7661 (mp) REVERT: 2 270 MET cc_start: 0.6941 (mtt) cc_final: 0.6145 (mtt) REVERT: 2 395 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7497 (p0) REVERT: 2 592 MET cc_start: 0.8446 (mmm) cc_final: 0.8111 (tpp) REVERT: 2 604 MET cc_start: 0.9190 (ttm) cc_final: 0.8769 (ttp) REVERT: 2 674 MET cc_start: 0.8718 (mmm) cc_final: 0.8257 (mmm) REVERT: 2 738 MET cc_start: 0.9477 (mmp) cc_final: 0.8888 (mpp) REVERT: 2 773 MET cc_start: 0.9301 (mtm) cc_final: 0.8332 (mtm) REVERT: 2 814 MET cc_start: 0.8145 (ptt) cc_final: 0.7719 (ppp) REVERT: 3 259 VAL cc_start: 0.8954 (t) cc_final: 0.8623 (m) REVERT: 3 369 THR cc_start: 0.9587 (OUTLIER) cc_final: 0.9186 (t) REVERT: 3 398 MET cc_start: 0.9319 (mmm) cc_final: 0.8723 (mmm) REVERT: 3 424 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: 3 603 MET cc_start: 0.7173 (ppp) cc_final: 0.6952 (ppp) REVERT: 4 256 HIS cc_start: 0.7847 (t-90) cc_final: 0.7552 (t70) REVERT: 5 69 TRP cc_start: 0.9514 (p-90) cc_final: 0.8925 (p-90) REVERT: 5 255 ASP cc_start: 0.8780 (p0) cc_final: 0.7941 (t0) REVERT: 5 516 MET cc_start: 0.7121 (tpp) cc_final: 0.6826 (tpt) REVERT: 6 234 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8387 (tp30) REVERT: 7 131 MET cc_start: 0.9094 (mmt) cc_final: 0.8667 (mmt) REVERT: 7 201 MET cc_start: 0.9471 (ttm) cc_final: 0.9087 (mmm) REVERT: 7 258 GLU cc_start: 0.8855 (pm20) cc_final: 0.8600 (mp0) REVERT: 7 378 CYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8576 (m) REVERT: 7 405 THR cc_start: 0.8983 (p) cc_final: 0.8318 (t) REVERT: 7 446 GLU cc_start: 0.6409 (tt0) cc_final: 0.5845 (tt0) REVERT: 7 559 MET cc_start: 0.9422 (tpp) cc_final: 0.9072 (mmp) REVERT: 7 565 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8603 (ppp) outliers start: 39 outliers final: 25 residues processed: 186 average time/residue: 0.1603 time to fit residues: 52.2023 Evaluate side-chains 180 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 232 VAL Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 395 ASP Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 2 residue 626 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 3 residue 369 THR Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 427 GLU Chi-restraints excluded: chain 3 residue 613 VAL Chi-restraints excluded: chain 4 residue 289 VAL Chi-restraints excluded: chain 4 residue 613 VAL Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 70 ILE Chi-restraints excluded: chain 5 residue 484 VAL Chi-restraints excluded: chain 5 residue 692 HIS Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 329 MET Chi-restraints excluded: chain 6 residue 371 MET Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 471 VAL Chi-restraints excluded: chain 7 residue 256 LEU Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 378 CYS Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 516 ASP Chi-restraints excluded: chain 7 residue 551 PHE Chi-restraints excluded: chain 7 residue 565 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 98 optimal weight: 1.9990 chunk 168 optimal weight: 0.0060 chunk 31 optimal weight: 0.7980 chunk 220 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 184 optimal weight: 50.0000 chunk 7 optimal weight: 1.9990 chunk 344 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 317 optimal weight: 9.9990 chunk 356 optimal weight: 8.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 672 GLN 4 695 HIS ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** 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 = 0.3683 r_free = 0.3683 target = 0.062483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.044187 restraints weight = 156669.358| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 5.04 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 28662 Z= 0.113 Angle : 0.587 18.759 38878 Z= 0.281 Chirality : 0.041 0.203 4540 Planarity : 0.003 0.039 5050 Dihedral : 6.570 109.842 4094 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.32 % Allowed : 14.02 % Favored : 84.66 % 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: -0.38 (0.14), residues: 3636 helix: 0.91 (0.14), residues: 1444 sheet: -1.15 (0.23), residues: 488 loop : -0.95 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 6 619 TYR 0.012 0.001 TYR 4 690 PHE 0.012 0.001 PHE 2 808 TRP 0.006 0.001 TRP 2 569 HIS 0.010 0.001 HIS 5 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (28646) covalent geometry : angle 0.57975 / 0.28 (38854) hydrogen bonds : bond 0.02987 / 2.03 ( 1057) hydrogen bonds : angle 4.57907 / 3.23 ( 3021) metal coordination : bond 0.00538 / 0.32 ( 16) metal coordination : angle 3.81641 / 2.84 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.177 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: 2 255 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7576 (mp) REVERT: 2 270 MET cc_start: 0.6870 (mtt) cc_final: 0.6073 (mtt) REVERT: 2 395 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7491 (p0) REVERT: 2 592 MET cc_start: 0.8491 (mmm) cc_final: 0.8166 (tpp) REVERT: 2 674 MET cc_start: 0.8764 (mmm) cc_final: 0.8306 (mmm) REVERT: 2 738 MET cc_start: 0.9480 (mmp) cc_final: 0.8868 (mpp) REVERT: 2 773 MET cc_start: 0.9166 (mtm) cc_final: 0.8661 (mtp) REVERT: 2 798 MET cc_start: 0.8279 (tpp) cc_final: 0.8075 (mmp) REVERT: 2 814 MET cc_start: 0.8163 (ptt) cc_final: 0.7728 (ppp) REVERT: 3 259 VAL cc_start: 0.8963 (t) cc_final: 0.8627 (m) REVERT: 3 369 THR cc_start: 0.9580 (OUTLIER) cc_final: 0.9187 (t) REVERT: 3 398 MET cc_start: 0.9302 (mmm) cc_final: 0.8706 (mmm) REVERT: 3 424 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8249 (tm-30) REVERT: 3 603 MET cc_start: 0.7302 (ppp) cc_final: 0.7076 (ppp) REVERT: 4 256 HIS cc_start: 0.7906 (t-90) cc_final: 0.7617 (t70) REVERT: 5 69 TRP cc_start: 0.9500 (p-90) cc_final: 0.8919 (p-90) REVERT: 5 255 ASP cc_start: 0.8760 (p0) cc_final: 0.7962 (t0) REVERT: 5 516 MET cc_start: 0.7131 (tpp) cc_final: 0.6812 (tpt) REVERT: 5 626 MET cc_start: 0.8586 (mmt) cc_final: 0.8077 (tmm) REVERT: 6 234 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8385 (tp30) REVERT: 7 131 MET cc_start: 0.9095 (mmt) cc_final: 0.8674 (mmt) REVERT: 7 201 MET cc_start: 0.9484 (ttm) cc_final: 0.9092 (mmm) REVERT: 7 258 GLU cc_start: 0.8849 (pm20) cc_final: 0.8556 (mp0) REVERT: 7 378 CYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8557 (m) REVERT: 7 405 THR cc_start: 0.8984 (p) cc_final: 0.8390 (t) REVERT: 7 446 GLU cc_start: 0.6426 (tt0) cc_final: 0.5868 (tt0) REVERT: 7 559 MET cc_start: 0.9434 (tpp) cc_final: 0.9070 (mmp) REVERT: 7 565 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8616 (ppp) outliers start: 39 outliers final: 30 residues processed: 185 average time/residue: 0.1562 time to fit residues: 50.8043 Evaluate side-chains 180 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 223 CYS Chi-restraints excluded: chain 2 residue 230 LEU Chi-restraints excluded: chain 2 residue 232 VAL Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 395 ASP Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 2 residue 626 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 769 SER Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 3 residue 369 THR Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 427 GLU Chi-restraints excluded: chain 3 residue 613 VAL Chi-restraints excluded: chain 4 residue 289 VAL Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 613 VAL Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 4 residue 695 HIS Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 70 ILE Chi-restraints excluded: chain 5 residue 484 VAL Chi-restraints excluded: chain 5 residue 692 HIS Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 329 MET Chi-restraints excluded: chain 6 residue 371 MET Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 471 VAL Chi-restraints excluded: chain 7 residue 256 LEU Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 378 CYS Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 516 ASP Chi-restraints excluded: chain 7 residue 551 PHE Chi-restraints excluded: chain 7 residue 565 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 202 optimal weight: 3.9990 chunk 286 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 252 optimal weight: 3.9990 chunk 345 optimal weight: 0.4980 chunk 238 optimal weight: 10.0000 chunk 309 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 893 HIS 3 505 HIS ** 3 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 672 GLN 4 695 HIS ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.061056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.042821 restraints weight = 156773.263| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 4.96 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 28662 Z= 0.201 Angle : 0.643 20.310 38878 Z= 0.313 Chirality : 0.042 0.200 4540 Planarity : 0.004 0.038 5050 Dihedral : 6.710 111.138 4094 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.53 % Allowed : 14.05 % Favored : 84.42 % 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: 3636 helix: 0.89 (0.14), residues: 1450 sheet: -1.26 (0.22), residues: 511 loop : -0.97 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 6 619 TYR 0.018 0.001 TYR 4 690 PHE 0.012 0.001 PHE 5 38 TRP 0.012 0.001 TRP 2 569 HIS 0.028 0.001 HIS 4 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (28646) covalent geometry : angle 0.63374 / 0.31 (38854) hydrogen bonds : bond 0.03269 / 2.21 ( 1057) hydrogen bonds : angle 4.76353 / 3.38 ( 3021) metal coordination : bond 0.00924 / 0.53 ( 16) metal coordination : angle 4.49679 / 3.24 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7272 Ramachandran restraints generated. 3636 Oldfield, 0 Emsley, 3636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 1.937 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: 2 255 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7641 (mp) REVERT: 2 270 MET cc_start: 0.6847 (mtt) cc_final: 0.6144 (mtt) REVERT: 2 571 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9058 (pt) REVERT: 2 592 MET cc_start: 0.8519 (mmm) cc_final: 0.8191 (tpt) REVERT: 2 674 MET cc_start: 0.8784 (mmm) cc_final: 0.8317 (mmm) REVERT: 2 773 MET cc_start: 0.9134 (mtm) cc_final: 0.8839 (mtp) REVERT: 2 798 MET cc_start: 0.8503 (tpp) cc_final: 0.8157 (mmp) REVERT: 2 804 ASP cc_start: 0.8325 (t0) cc_final: 0.8061 (t0) REVERT: 3 369 THR cc_start: 0.9607 (OUTLIER) cc_final: 0.9225 (t) REVERT: 3 398 MET cc_start: 0.9312 (mmm) cc_final: 0.8777 (mmm) REVERT: 3 424 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8282 (tm-30) REVERT: 3 603 MET cc_start: 0.7447 (ppp) cc_final: 0.7188 (ppp) REVERT: 4 256 HIS cc_start: 0.8008 (t-90) cc_final: 0.7678 (t70) REVERT: 4 351 MET cc_start: 0.8380 (tpp) cc_final: 0.7831 (tpp) REVERT: 5 69 TRP cc_start: 0.9540 (p-90) cc_final: 0.8938 (p-90) REVERT: 5 516 MET cc_start: 0.7177 (tpp) cc_final: 0.6860 (tpt) REVERT: 5 626 MET cc_start: 0.8661 (mmt) cc_final: 0.8105 (tmm) REVERT: 6 234 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8433 (tp30) REVERT: 6 527 MET cc_start: 0.8711 (mtm) cc_final: 0.8202 (mtm) REVERT: 7 17 LEU cc_start: 0.9649 (tp) cc_final: 0.8960 (pt) REVERT: 7 131 MET cc_start: 0.9118 (mmt) cc_final: 0.8699 (mmt) REVERT: 7 201 MET cc_start: 0.9487 (ttm) cc_final: 0.9116 (mmm) REVERT: 7 258 GLU cc_start: 0.8859 (pm20) cc_final: 0.8570 (mp0) REVERT: 7 296 THR cc_start: 0.7933 (m) cc_final: 0.7697 (p) REVERT: 7 378 CYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8560 (m) REVERT: 7 405 THR cc_start: 0.8953 (p) cc_final: 0.8324 (t) REVERT: 7 446 GLU cc_start: 0.6505 (tt0) cc_final: 0.5879 (tt0) REVERT: 7 462 MET cc_start: 0.9118 (mmm) cc_final: 0.8881 (tmm) REVERT: 7 559 MET cc_start: 0.9413 (tpp) cc_final: 0.9119 (mmp) REVERT: 7 565 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8583 (ppp) REVERT: 7 572 MET cc_start: 0.8753 (tpp) cc_final: 0.8498 (tpp) outliers start: 45 outliers final: 33 residues processed: 188 average time/residue: 0.1609 time to fit residues: 52.7919 Evaluate side-chains 187 residues out of total 3223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 223 CYS Chi-restraints excluded: chain 2 residue 230 LEU Chi-restraints excluded: chain 2 residue 232 VAL Chi-restraints excluded: chain 2 residue 255 LEU Chi-restraints excluded: chain 2 residue 308 THR Chi-restraints excluded: chain 2 residue 434 VAL Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 2 residue 571 LEU Chi-restraints excluded: chain 2 residue 626 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 769 SER Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 3 residue 369 THR Chi-restraints excluded: chain 3 residue 424 GLU Chi-restraints excluded: chain 3 residue 427 GLU Chi-restraints excluded: chain 3 residue 613 VAL Chi-restraints excluded: chain 4 residue 289 VAL Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 613 VAL Chi-restraints excluded: chain 4 residue 629 THR Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 70 ILE Chi-restraints excluded: chain 5 residue 428 ILE Chi-restraints excluded: chain 5 residue 484 VAL Chi-restraints excluded: chain 5 residue 692 HIS Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 329 MET Chi-restraints excluded: chain 6 residue 371 MET Chi-restraints excluded: chain 6 residue 400 THR Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 6 residue 471 VAL Chi-restraints excluded: chain 7 residue 256 LEU Chi-restraints excluded: chain 7 residue 273 VAL Chi-restraints excluded: chain 7 residue 378 CYS Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 516 ASP Chi-restraints excluded: chain 7 residue 551 PHE Chi-restraints excluded: chain 7 residue 565 MET Chi-restraints excluded: chain 7 residue 607 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 325 optimal weight: 4.9990 chunk 266 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 195 optimal weight: 0.0980 chunk 209 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 646 ASN ** 3 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 341 HIS ** 5 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 722 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 = 0.3661 r_free = 0.3661 target = 0.061541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.043382 restraints weight = 156489.016| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 4.95 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28662 Z= 0.149 Angle : 0.614 18.379 38878 Z= 0.296 Chirality : 0.041 0.205 4540 Planarity : 0.003 0.052 5050 Dihedral : 6.689 108.615 4094 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.39 % Allowed : 14.49 % Favored : 84.11 % 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: -0.41 (0.14), residues: 3636 helix: 0.93 (0.14), residues: 1453 sheet: -1.29 (0.22), residues: 509 loop : -0.96 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 5 724 TYR 0.013 0.001 TYR 6 347 PHE 0.012 0.001 PHE 2 808 TRP 0.011 0.001 TRP 2 569 HIS 0.011 0.001 HIS 5 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (28646) covalent geometry : angle 0.60541 / 0.30 (38854) hydrogen bonds : bond 0.03084 / 2.08 ( 1057) hydrogen bonds : angle 4.65133 / 3.29 ( 3021) metal coordination : bond 0.00768 / 0.45 ( 16) metal coordination : angle 4.05759 / 2.93 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5642.45 seconds wall clock time: 98 minutes 9.38 seconds (5889.38 seconds total)