Starting phenix.real_space_refine on Tue Nov 19 21:41:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouw_17204/11_2024/8ouw_17204.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouw_17204/11_2024/8ouw_17204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouw_17204/11_2024/8ouw_17204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouw_17204/11_2024/8ouw_17204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouw_17204/11_2024/8ouw_17204.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouw_17204/11_2024/8ouw_17204.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 79 5.49 5 Mg 4 5.21 5 S 330 5.16 5 C 33611 2.51 5 N 9396 2.21 5 O 10329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 417 residue(s): 0.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 53754 Number of models: 1 Model: "" Number of chains: 25 Chain: "2" Number of atoms: 5547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5547 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 671} Chain breaks: 7 Chain: "3" Number of atoms: 4872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4872 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 23, 'TRANS': 595} Chain breaks: 3 Chain: "4" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4906 Classifications: {'peptide': 619} Link IDs: {'PTRANS': 21, 'TRANS': 597} Chain breaks: 2 Chain: "5" Number of atoms: 4256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4256 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 514} Chain breaks: 9 Chain: "6" Number of atoms: 5595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5595 Classifications: {'peptide': 707} Link IDs: {'PTRANS': 19, 'TRANS': 687} Chain breaks: 5 Chain: "7" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 4963 Classifications: {'peptide': 632} Link IDs: {'PTRANS': 26, 'TRANS': 605} Chain breaks: 3 Chain: "A" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1534 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "B" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1423 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 171} Chain: "C" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1404 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "D" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1625 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 192} Chain: "E" Number of atoms: 4547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4547 Classifications: {'peptide': 563} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 543} Chain breaks: 1 Chain: "F" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2741 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 326} Chain breaks: 3 Chain: "G" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2564 Classifications: {'peptide': 326} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 306} Chain breaks: 2 Chain: "H" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 148 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "I" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "J" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 611 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "K" Number of atoms: 5446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5446 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 13, 'TRANS': 642} Chain breaks: 1 Chain: "L" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 681 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "M" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 578 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1410 SG CYS 2 305 112.452 122.683 106.619 1.00 88.05 S ATOM 1428 SG CYS 2 308 115.665 123.827 105.068 1.00 84.48 S ATOM 1587 SG CYS 2 328 114.133 125.625 107.991 1.00 84.41 S ATOM 1606 SG CYS 2 331 112.710 126.225 104.616 1.00 83.18 S ATOM 11771 SG CYS 4 269 79.092 148.202 123.311 1.00 89.97 S ATOM 11789 SG CYS 4 272 78.830 151.836 124.444 1.00 89.01 S ATOM 11933 SG CYS 4 291 76.783 150.508 121.444 1.00 85.09 S ATOM 11954 SG CYS 4 294 80.424 151.259 121.170 1.00 84.30 S ATOM 16531 SG CYS 5 172 93.368 112.682 93.360 1.00 84.67 S ATOM 16557 SG CYS 5 175 94.160 113.654 89.817 1.00 78.19 S ATOM 16723 SG CYS 5 197 96.363 114.983 92.443 1.00 77.52 S ATOM 16739 SG CYS 5 208 92.779 116.284 92.352 1.00 69.16 S ATOM 20855 SG CYS 6 157 96.547 141.931 119.586 1.00 87.90 S ATOM 20878 SG CYS 6 160 98.644 144.961 119.864 1.00 81.89 S ATOM 21035 SG CYS 6 179 94.870 145.144 120.528 1.00 79.00 S ATOM 21070 SG CYS 6 184 96.097 144.817 116.969 1.00 78.30 S ATOM 26678 SG CYS 7 197 60.009 136.556 103.125 1.00 88.61 S ATOM 26699 SG CYS 7 200 58.770 137.555 99.839 1.00 83.23 S ATOM 26843 SG CYS 7 219 61.360 134.868 100.198 1.00 81.22 S ATOM 26882 SG CYS 7 224 62.473 138.513 100.619 1.00 79.40 S Time building chain proxies: 28.46, per 1000 atoms: 0.53 Number of scatterers: 53754 At special positions: 0 Unit cell: (216.265, 217.56, 222.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 330 16.00 P 79 15.00 Mg 4 11.99 O 10329 8.00 N 9396 7.00 C 33611 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: 12.75 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 901 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 328 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 308 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 305 " pdb="ZN ZN 2 901 " - pdb=" SG CYS 2 331 " pdb=" ZN 41503 " pdb="ZN ZN 41503 " - pdb=" SG CYS 4 272 " pdb="ZN ZN 41503 " - pdb=" SG CYS 4 291 " pdb="ZN ZN 41503 " - pdb=" SG CYS 4 294 " pdb="ZN ZN 41503 " - pdb=" SG CYS 4 269 " pdb=" ZN 5 801 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 175 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 197 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 172 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 208 " pdb=" ZN 6 901 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 179 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 160 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 157 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 184 " pdb=" ZN 71502 " pdb="ZN ZN 71502 " - pdb=" SG CYS 7 219 " pdb="ZN ZN 71502 " - pdb=" SG CYS 7 200 " pdb="ZN ZN 71502 " - pdb=" SG CYS 7 197 " pdb="ZN ZN 71502 " - pdb=" SG CYS 7 224 " Number of angles added : 30 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12530 Finding SS restraints... Secondary structure from input PDB file: 302 helices and 58 sheets defined 51.8% alpha, 12.6% beta 29 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 17.73 Creating SS restraints... Processing helix chain '2' and resid 100 through 106 Processing helix chain '2' and resid 107 through 111 Processing helix chain '2' and resid 146 through 151 removed outlier: 3.654A pdb=" N ASN 2 149 " --> pdb=" O ILE 2 146 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG 2 151 " --> pdb=" O GLU 2 148 " (cutoff:3.500A) Processing helix chain '2' and resid 154 through 158 Processing helix chain '2' and resid 161 through 179 removed outlier: 3.644A pdb=" N GLU 2 167 " --> pdb=" O ALA 2 163 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS 2 173 " --> pdb=" O GLU 2 169 " (cutoff:3.500A) Processing helix chain '2' and resid 187 through 199 removed outlier: 3.620A pdb=" N ASP 2 199 " --> pdb=" O SER 2 195 " (cutoff:3.500A) Processing helix chain '2' and resid 208 through 213 Processing helix chain '2' and resid 217 through 224 Processing helix chain '2' and resid 227 through 247 removed outlier: 4.034A pdb=" N ALA 2 233 " --> pdb=" O ASN 2 229 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE 2 234 " --> pdb=" O GLU 2 230 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN 2 245 " --> pdb=" O GLU 2 241 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET 2 246 " --> pdb=" O VAL 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 248 through 252 removed outlier: 3.987A pdb=" N SER 2 251 " --> pdb=" O PRO 2 248 " (cutoff:3.500A) Processing helix chain '2' and resid 274 through 278 removed outlier: 3.624A pdb=" N LEU 2 278 " --> pdb=" O GLN 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 357 through 361 removed outlier: 3.660A pdb=" N VAL 2 361 " --> pdb=" O PRO 2 358 " (cutoff:3.500A) Processing helix chain '2' and resid 377 through 379 No H-bonds generated for 'chain '2' and resid 377 through 379' Processing helix chain '2' and resid 399 through 407 Processing helix chain '2' and resid 432 through 444 Processing helix chain '2' and resid 447 through 456 Processing helix chain '2' and resid 463 through 475 removed outlier: 3.674A pdb=" N PHE 2 475 " --> pdb=" O ALA 2 471 " (cutoff:3.500A) Processing helix chain '2' and resid 503 through 515 removed outlier: 3.923A pdb=" N PHE 2 507 " --> pdb=" O ALA 2 503 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU 2 508 " --> pdb=" O LYS 2 504 " (cutoff:3.500A) Processing helix chain '2' and resid 549 through 554 Processing helix chain '2' and resid 563 through 567 removed outlier: 3.593A pdb=" N MET 2 567 " --> pdb=" O PHE 2 564 " (cutoff:3.500A) Processing helix chain '2' and resid 568 through 582 Processing helix chain '2' and resid 607 through 611 removed outlier: 3.549A pdb=" N GLY 2 610 " --> pdb=" O PRO 2 607 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG 2 611 " --> pdb=" O ILE 2 608 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 607 through 611' Processing helix chain '2' and resid 617 through 622 Processing helix chain '2' and resid 625 through 630 Processing helix chain '2' and resid 643 through 662 Processing helix chain '2' and resid 690 through 704 removed outlier: 3.631A pdb=" N GLU 2 703 " --> pdb=" O ILE 2 699 " (cutoff:3.500A) Processing helix chain '2' and resid 710 through 712 No H-bonds generated for 'chain '2' and resid 710 through 712' Processing helix chain '2' and resid 713 through 732 removed outlier: 3.617A pdb=" N ASN 2 719 " --> pdb=" O GLU 2 715 " (cutoff:3.500A) Processing helix chain '2' and resid 737 through 755 removed outlier: 3.800A pdb=" N VAL 2 741 " --> pdb=" O THR 2 737 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS 2 755 " --> pdb=" O HIS 2 751 " (cutoff:3.500A) Processing helix chain '2' and resid 761 through 778 removed outlier: 3.800A pdb=" N ASN 2 778 " --> pdb=" O GLU 2 774 " (cutoff:3.500A) Processing helix chain '2' and resid 781 through 792 Processing helix chain '2' and resid 792 through 797 Processing helix chain '2' and resid 801 through 824 Processing helix chain '2' and resid 838 through 847 Processing helix chain '2' and resid 855 through 858 Processing helix chain '2' and resid 859 through 865 Processing helix chain '3' and resid 12 through 30 Processing helix chain '3' and resid 37 through 49 Processing helix chain '3' and resid 57 through 64 removed outlier: 3.540A pdb=" N GLU 3 62 " --> pdb=" O ASP 3 58 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE 3 63 " --> pdb=" O GLU 3 59 " (cutoff:3.500A) Processing helix chain '3' and resid 64 through 69 Processing helix chain '3' and resid 69 through 74 removed outlier: 3.639A pdb=" N THR 3 73 " --> pdb=" O GLU 3 69 " (cutoff:3.500A) Processing helix chain '3' and resid 74 through 92 removed outlier: 3.543A pdb=" N GLU 3 78 " --> pdb=" O GLN 3 74 " (cutoff:3.500A) Processing helix chain '3' and resid 111 through 113 No H-bonds generated for 'chain '3' and resid 111 through 113' Processing helix chain '3' and resid 122 through 126 removed outlier: 3.577A pdb=" N LEU 3 126 " --> pdb=" O SER 3 123 " (cutoff:3.500A) Processing helix chain '3' and resid 229 through 231 No H-bonds generated for 'chain '3' and resid 229 through 231' Processing helix chain '3' and resid 282 through 295 Processing helix chain '3' and resid 297 through 306 Processing helix chain '3' and resid 313 through 326 Processing helix chain '3' and resid 353 through 365 Processing helix chain '3' and resid 377 through 382 Processing helix chain '3' and resid 399 through 404 Processing helix chain '3' and resid 413 through 417 Processing helix chain '3' and resid 418 through 423 Processing helix chain '3' and resid 425 through 432 removed outlier: 3.801A pdb=" N GLU 3 430 " --> pdb=" O HIS 3 426 " (cutoff:3.500A) Processing helix chain '3' and resid 467 through 473 Processing helix chain '3' and resid 475 through 480 Processing helix chain '3' and resid 493 through 509 Processing helix chain '3' and resid 561 through 573 Processing helix chain '3' and resid 580 through 597 removed outlier: 3.665A pdb=" N ALA 3 592 " --> pdb=" O SER 3 588 " (cutoff:3.500A) Processing helix chain '3' and resid 612 through 629 removed outlier: 3.696A pdb=" N GLU 3 616 " --> pdb=" O ALA 3 612 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA 3 628 " --> pdb=" O ALA 3 624 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG 3 629 " --> pdb=" O ILE 3 625 " (cutoff:3.500A) Processing helix chain '3' and resid 635 through 650 removed outlier: 3.798A pdb=" N LYS 3 641 " --> pdb=" O GLU 3 637 " (cutoff:3.500A) Processing helix chain '4' and resid 113 through 128 removed outlier: 4.084A pdb=" N VAL 4 117 " --> pdb=" O CYS 4 113 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN 4 118 " --> pdb=" O VAL 4 114 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER 4 120 " --> pdb=" O ASP 4 116 " (cutoff:3.500A) Processing helix chain '4' and resid 129 through 135 removed outlier: 3.982A pdb=" N GLN 4 132 " --> pdb=" O LYS 4 129 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU 4 133 " --> pdb=" O ILE 4 130 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU 4 135 " --> pdb=" O GLN 4 132 " (cutoff:3.500A) Processing helix chain '4' and resid 155 through 167 removed outlier: 3.868A pdb=" N LEU 4 162 " --> pdb=" O MET 4 158 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU 4 163 " --> pdb=" O GLU 4 159 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N CYS 4 164 " --> pdb=" O ARG 4 160 " (cutoff:3.500A) Processing helix chain '4' and resid 176 through 183 Processing helix chain '4' and resid 183 through 193 removed outlier: 4.072A pdb=" N LYS 4 189 " --> pdb=" O ALA 4 185 " (cutoff:3.500A) Processing helix chain '4' and resid 193 through 214 removed outlier: 3.662A pdb=" N ILE 4 198 " --> pdb=" O PRO 4 194 " (cutoff:3.500A) Proline residue: 4 199 - end of helix removed outlier: 3.551A pdb=" N ASP 4 202 " --> pdb=" O ILE 4 198 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE 4 203 " --> pdb=" O PRO 4 199 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 237 removed outlier: 3.981A pdb=" N LEU 4 237 " --> pdb=" O MET 4 234 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 242 removed outlier: 3.550A pdb=" N VAL 4 242 " --> pdb=" O PRO 4 239 " (cutoff:3.500A) Processing helix chain '4' and resid 304 through 307 Processing helix chain '4' and resid 340 through 342 No H-bonds generated for 'chain '4' and resid 340 through 342' Processing helix chain '4' and resid 401 through 412 Processing helix chain '4' and resid 416 through 425 removed outlier: 3.680A pdb=" N SER 4 424 " --> pdb=" O ALA 4 420 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE 4 425 " --> pdb=" O LEU 4 421 " (cutoff:3.500A) Processing helix chain '4' and resid 432 through 445 Processing helix chain '4' and resid 474 through 486 removed outlier: 3.630A pdb=" N LEU 4 486 " --> pdb=" O VAL 4 482 " (cutoff:3.500A) Processing helix chain '4' and resid 495 through 497 No H-bonds generated for 'chain '4' and resid 495 through 497' Processing helix chain '4' and resid 498 through 503 removed outlier: 3.707A pdb=" N THR 4 503 " --> pdb=" O ALA 4 499 " (cutoff:3.500A) Processing helix chain '4' and resid 520 through 525 Processing helix chain '4' and resid 534 through 538 removed outlier: 3.744A pdb=" N MET 4 538 " --> pdb=" O PHE 4 535 " (cutoff:3.500A) Processing helix chain '4' and resid 539 through 544 Processing helix chain '4' and resid 545 through 553 removed outlier: 4.514A pdb=" N VAL 4 549 " --> pdb=" O VAL 4 545 " (cutoff:3.500A) Processing helix chain '4' and resid 588 through 593 Processing helix chain '4' and resid 596 through 601 Processing helix chain '4' and resid 614 through 627 Processing helix chain '4' and resid 628 through 630 No H-bonds generated for 'chain '4' and resid 628 through 630' Processing helix chain '4' and resid 643 through 658 removed outlier: 3.761A pdb=" N ASP 4 649 " --> pdb=" O ASN 4 645 " (cutoff:3.500A) Processing helix chain '4' and resid 663 through 681 Processing helix chain '4' and resid 691 through 708 removed outlier: 3.972A pdb=" N GLU 4 695 " --> pdb=" O PRO 4 691 " (cutoff:3.500A) Processing helix chain '4' and resid 714 through 730 removed outlier: 3.799A pdb=" N LEU 4 729 " --> pdb=" O TRP 4 725 " (cutoff:3.500A) Processing helix chain '5' and resid 25 through 46 Processing helix chain '5' and resid 53 through 65 Processing helix chain '5' and resid 74 through 81 Processing helix chain '5' and resid 81 through 91 removed outlier: 3.791A pdb=" N GLU 5 85 " --> pdb=" O ASP 5 81 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 112 Proline residue: 5 97 - end of helix Processing helix chain '5' and resid 141 through 145 removed outlier: 3.644A pdb=" N VAL 5 145 " --> pdb=" O SER 5 142 " (cutoff:3.500A) Processing helix chain '5' and resid 253 through 255 No H-bonds generated for 'chain '5' and resid 253 through 255' Processing helix chain '5' and resid 314 through 327 Processing helix chain '5' and resid 329 through 338 Processing helix chain '5' and resid 345 through 358 Processing helix chain '5' and resid 385 through 397 Processing helix chain '5' and resid 431 through 435 removed outlier: 3.614A pdb=" N LEU 5 435 " --> pdb=" O ALA 5 432 " (cutoff:3.500A) Processing helix chain '5' and resid 458 through 464 Processing helix chain '5' and resid 508 through 513 Processing helix chain '5' and resid 524 through 547 removed outlier: 3.863A pdb=" N THR 5 530 " --> pdb=" O LEU 5 526 " (cutoff:3.500A) Processing helix chain '5' and resid 575 through 588 removed outlier: 3.799A pdb=" N LYS 5 581 " --> pdb=" O GLU 5 577 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU 5 588 " --> pdb=" O THR 5 584 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 611 removed outlier: 3.901A pdb=" N LYS 5 601 " --> pdb=" O GLN 5 597 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU 5 602 " --> pdb=" O ALA 5 598 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL 5 603 " --> pdb=" O SER 5 599 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN 5 604 " --> pdb=" O GLU 5 600 " (cutoff:3.500A) Processing helix chain '5' and resid 633 through 651 removed outlier: 3.664A pdb=" N MET 5 650 " --> pdb=" O SER 5 646 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU 5 651 " --> pdb=" O ILE 5 647 " (cutoff:3.500A) Processing helix chain '5' and resid 657 through 678 removed outlier: 4.378A pdb=" N GLU 5 674 " --> pdb=" O VAL 5 670 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA 5 675 " --> pdb=" O SER 5 671 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA 5 676 " --> pdb=" O THR 5 672 " (cutoff:3.500A) Processing helix chain '6' and resid 14 through 31 Processing helix chain '6' and resid 38 through 44 Processing helix chain '6' and resid 45 through 49 removed outlier: 3.872A pdb=" N VAL 6 48 " --> pdb=" O LYS 6 45 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 66 Processing helix chain '6' and resid 66 through 76 removed outlier: 3.633A pdb=" N ALA 6 70 " --> pdb=" O SER 6 66 " (cutoff:3.500A) Processing helix chain '6' and resid 76 through 96 Proline residue: 6 82 - end of helix removed outlier: 3.659A pdb=" N ALA 6 95 " --> pdb=" O ALA 6 91 " (cutoff:3.500A) Processing helix chain '6' and resid 97 through 105 removed outlier: 4.069A pdb=" N GLN 6 102 " --> pdb=" O GLU 6 98 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLN 6 103 " --> pdb=" O SER 6 99 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE 6 105 " --> pdb=" O ARG 6 101 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 125 Processing helix chain '6' and resid 126 through 130 removed outlier: 3.895A pdb=" N VAL 6 130 " --> pdb=" O ALA 6 127 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 214 Processing helix chain '6' and resid 230 through 232 No H-bonds generated for 'chain '6' and resid 230 through 232' Processing helix chain '6' and resid 253 through 256 removed outlier: 3.585A pdb=" N LEU 6 256 " --> pdb=" O ILE 6 253 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 253 through 256' Processing helix chain '6' and resid 263 through 268 Processing helix chain '6' and resid 323 through 329 Processing helix chain '6' and resid 331 through 343 Processing helix chain '6' and resid 345 through 355 removed outlier: 3.728A pdb=" N SER 6 353 " --> pdb=" O ASN 6 349 " (cutoff:3.500A) Processing helix chain '6' and resid 361 through 374 removed outlier: 3.534A pdb=" N LEU 6 373 " --> pdb=" O LEU 6 369 " (cutoff:3.500A) Processing helix chain '6' and resid 402 through 414 Processing helix chain '6' and resid 423 through 425 No H-bonds generated for 'chain '6' and resid 423 through 425' Processing helix chain '6' and resid 426 through 431 removed outlier: 4.207A pdb=" N THR 6 431 " --> pdb=" O ALA 6 427 " (cutoff:3.500A) Processing helix chain '6' and resid 448 through 453 Processing helix chain '6' and resid 462 through 466 Processing helix chain '6' and resid 467 through 481 removed outlier: 3.731A pdb=" N GLN 6 480 " --> pdb=" O GLU 6 476 " (cutoff:3.500A) Processing helix chain '6' and resid 516 through 521 removed outlier: 3.839A pdb=" N ASN 6 520 " --> pdb=" O PRO 6 516 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL 6 521 " --> pdb=" O LEU 6 517 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 516 through 521' Processing helix chain '6' and resid 524 through 529 Processing helix chain '6' and resid 542 through 561 Processing helix chain '6' and resid 571 through 583 removed outlier: 3.674A pdb=" N ARG 6 583 " --> pdb=" O ILE 6 579 " (cutoff:3.500A) Processing helix chain '6' and resid 590 through 611 Processing helix chain '6' and resid 621 through 638 removed outlier: 3.686A pdb=" N GLU 6 625 " --> pdb=" O VAL 6 621 " (cutoff:3.500A) Processing helix chain '6' and resid 644 through 660 removed outlier: 3.704A pdb=" N VAL 6 648 " --> pdb=" O LEU 6 644 " (cutoff:3.500A) Processing helix chain '6' and resid 716 through 733 Processing helix chain '6' and resid 746 through 756 Processing helix chain '6' and resid 769 through 784 Processing helix chain '7' and resid 9 through 24 removed outlier: 3.722A pdb=" N GLU 7 13 " --> pdb=" O ASP 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 47 Processing helix chain '7' and resid 57 through 62 Processing helix chain '7' and resid 67 through 78 Processing helix chain '7' and resid 78 through 99 removed outlier: 4.816A pdb=" N VAL 7 84 " --> pdb=" O LYS 7 80 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU 7 85 " --> pdb=" O ARG 7 81 " (cutoff:3.500A) Processing helix chain '7' and resid 107 through 122 removed outlier: 3.697A pdb=" N HIS 7 118 " --> pdb=" O PHE 7 114 " (cutoff:3.500A) Processing helix chain '7' and resid 133 through 139 Processing helix chain '7' and resid 140 through 145 Processing helix chain '7' and resid 155 through 157 No H-bonds generated for 'chain '7' and resid 155 through 157' Processing helix chain '7' and resid 166 through 170 removed outlier: 3.629A pdb=" N ILE 7 170 " --> pdb=" O ALA 7 167 " (cutoff:3.500A) Processing helix chain '7' and resid 221 through 228 Processing helix chain '7' and resid 254 through 257 removed outlier: 3.502A pdb=" N VAL 7 257 " --> pdb=" O SER 7 254 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 254 through 257' Processing helix chain '7' and resid 273 through 275 No H-bonds generated for 'chain '7' and resid 273 through 275' Processing helix chain '7' and resid 329 through 339 removed outlier: 3.570A pdb=" N LEU 7 335 " --> pdb=" O GLU 7 331 " (cutoff:3.500A) Processing helix chain '7' and resid 341 through 348 Processing helix chain '7' and resid 356 through 367 Processing helix chain '7' and resid 374 through 378 removed outlier: 3.782A pdb=" N GLY 7 377 " --> pdb=" O SER 7 374 " (cutoff:3.500A) Processing helix chain '7' and resid 395 through 407 Processing helix chain '7' and resid 419 through 424 removed outlier: 3.746A pdb=" N THR 7 424 " --> pdb=" O GLY 7 420 " (cutoff:3.500A) Processing helix chain '7' and resid 441 through 446 Processing helix chain '7' and resid 455 through 459 removed outlier: 3.670A pdb=" N MET 7 459 " --> pdb=" O PHE 7 456 " (cutoff:3.500A) Processing helix chain '7' and resid 460 through 465 Processing helix chain '7' and resid 466 through 474 removed outlier: 4.607A pdb=" N VAL 7 470 " --> pdb=" O ALA 7 466 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU 7 472 " --> pdb=" O HIS 7 468 " (cutoff:3.500A) Processing helix chain '7' and resid 509 through 514 Processing helix chain '7' and resid 517 through 522 Processing helix chain '7' and resid 535 through 553 removed outlier: 3.951A pdb=" N LYS 7 540 " --> pdb=" O ARG 7 536 " (cutoff:3.500A) Processing helix chain '7' and resid 565 through 577 Processing helix chain '7' and resid 584 through 586 No H-bonds generated for 'chain '7' and resid 584 through 586' Processing helix chain '7' and resid 587 through 604 removed outlier: 4.071A pdb=" N ASP 7 601 " --> pdb=" O GLU 7 597 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA 7 602 " --> pdb=" O MET 7 598 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG 7 603 " --> pdb=" O ARG 7 599 " (cutoff:3.500A) Processing helix chain '7' and resid 613 through 631 removed outlier: 4.296A pdb=" N LEU 7 617 " --> pdb=" O PRO 7 613 " (cutoff:3.500A) Processing helix chain '7' and resid 636 through 654 removed outlier: 4.050A pdb=" N LEU 7 654 " --> pdb=" O ALA 7 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 24 removed outlier: 3.726A pdb=" N LEU A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 61 Processing helix chain 'A' and resid 68 through 96 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 114 through 133 Processing helix chain 'A' and resid 185 through 194 removed outlier: 5.033A pdb=" N MET A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.542A pdb=" N LYS B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 82 Processing helix chain 'B' and resid 91 through 103 Processing helix chain 'B' and resid 109 through 137 removed outlier: 3.579A pdb=" N ARG B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 156 Processing helix chain 'B' and resid 158 through 178 removed outlier: 3.841A pdb=" N GLU B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 170 " --> pdb=" O GLN B 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 23 Processing helix chain 'C' and resid 38 through 43 Processing helix chain 'C' and resid 62 through 66 Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.669A pdb=" N LEU C 100 " --> pdb=" O ASN C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 116 Processing helix chain 'C' and resid 119 through 136 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 156 through 178 removed outlier: 3.837A pdb=" N LYS C 161 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 41 removed outlier: 3.734A pdb=" N ARG D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 68 removed outlier: 3.767A pdb=" N VAL D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 105 removed outlier: 3.851A pdb=" N SER D 78 " --> pdb=" O GLN D 74 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 3.606A pdb=" N ALA D 109 " --> pdb=" O ASN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 148 removed outlier: 4.005A pdb=" N LEU D 143 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 152 Processing helix chain 'D' and resid 153 through 157 removed outlier: 3.799A pdb=" N LYS D 157 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 219 removed outlier: 5.269A pdb=" N GLN D 214 " --> pdb=" O GLU D 210 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 11 through 17 removed outlier: 3.641A pdb=" N ILE E 15 " --> pdb=" O PHE E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 46 removed outlier: 3.665A pdb=" N HIS E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.643A pdb=" N VAL E 61 " --> pdb=" O GLY E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 112 Processing helix chain 'E' and resid 125 through 130 removed outlier: 3.990A pdb=" N GLN E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 140 through 145 removed outlier: 3.892A pdb=" N GLU E 145 " --> pdb=" O SER E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 191 Processing helix chain 'E' and resid 200 through 212 removed outlier: 3.674A pdb=" N LEU E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU E 210 " --> pdb=" O GLU E 206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET E 211 " --> pdb=" O MET E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 232 removed outlier: 3.726A pdb=" N ALA E 229 " --> pdb=" O GLY E 225 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 247 Processing helix chain 'E' and resid 248 through 256 removed outlier: 4.796A pdb=" N HIS E 253 " --> pdb=" O PRO E 250 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG E 254 " --> pdb=" O PHE E 251 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET E 256 " --> pdb=" O HIS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 261 Processing helix chain 'E' and resid 282 through 286 Processing helix chain 'E' and resid 287 through 293 Processing helix chain 'E' and resid 295 through 303 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 323 through 329 Processing helix chain 'E' and resid 330 through 334 removed outlier: 3.610A pdb=" N LEU E 334 " --> pdb=" O PHE E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 351 Processing helix chain 'E' and resid 369 through 382 removed outlier: 3.795A pdb=" N MET E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 402 removed outlier: 3.734A pdb=" N SER E 402 " --> pdb=" O ILE E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 419 Processing helix chain 'E' and resid 419 through 439 removed outlier: 3.673A pdb=" N LEU E 425 " --> pdb=" O CYS E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 462 removed outlier: 3.680A pdb=" N VAL E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP E 462 " --> pdb=" O GLU E 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 457 through 462' Processing helix chain 'E' and resid 463 through 481 removed outlier: 3.784A pdb=" N ARG E 476 " --> pdb=" O GLY E 472 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET E 481 " --> pdb=" O ALA E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 501 removed outlier: 3.545A pdb=" N SER E 500 " --> pdb=" O THR E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 534 removed outlier: 3.627A pdb=" N LYS E 534 " --> pdb=" O GLU E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 574 Processing helix chain 'F' and resid 170 through 174 removed outlier: 3.916A pdb=" N ASN F 174 " --> pdb=" O PRO F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 202 Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.805A pdb=" N ILE F 220 " --> pdb=" O SER F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 246 removed outlier: 3.601A pdb=" N GLN F 246 " --> pdb=" O THR F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 279 removed outlier: 3.915A pdb=" N GLU F 268 " --> pdb=" O GLU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 345 Processing helix chain 'F' and resid 418 through 430 Processing helix chain 'F' and resid 463 through 474 removed outlier: 3.982A pdb=" N LEU F 467 " --> pdb=" O LYS F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 546 removed outlier: 4.341A pdb=" N ALA F 536 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS F 537 " --> pdb=" O PRO F 533 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN F 541 " --> pdb=" O LYS F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 567 removed outlier: 3.781A pdb=" N THR F 565 " --> pdb=" O ASP F 562 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 176 removed outlier: 3.632A pdb=" N ASN G 174 " --> pdb=" O PRO G 171 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR G 175 " --> pdb=" O TRP G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 202 removed outlier: 3.692A pdb=" N MET G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 224 removed outlier: 3.931A pdb=" N GLU G 222 " --> pdb=" O MET G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 279 removed outlier: 3.676A pdb=" N THR G 259 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA G 271 " --> pdb=" O GLN G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 344 Processing helix chain 'G' and resid 463 through 474 removed outlier: 3.701A pdb=" N LEU G 467 " --> pdb=" O LYS G 463 " (cutoff:3.500A) Processing helix chain 'G' and resid 532 through 547 removed outlier: 3.824A pdb=" N ALA G 536 " --> pdb=" O LEU G 532 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN G 547 " --> pdb=" O ILE G 543 " (cutoff:3.500A) Processing helix chain 'G' and resid 562 through 567 removed outlier: 4.022A pdb=" N THR G 565 " --> pdb=" O ASP G 562 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 19 removed outlier: 3.794A pdb=" N ARG H 11 " --> pdb=" O ASN H 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 10 removed outlier: 3.746A pdb=" N HIS K 10 " --> pdb=" O GLN K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 40 Processing helix chain 'K' and resid 44 through 54 Processing helix chain 'K' and resid 54 through 59 Processing helix chain 'K' and resid 59 through 65 Processing helix chain 'K' and resid 70 through 85 Processing helix chain 'K' and resid 87 through 92 Processing helix chain 'K' and resid 99 through 116 removed outlier: 3.795A pdb=" N LYS K 104 " --> pdb=" O ARG K 100 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN K 112 " --> pdb=" O GLU K 108 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU K 113 " --> pdb=" O LEU K 109 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA K 116 " --> pdb=" O ASN K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 121 removed outlier: 3.546A pdb=" N SER K 121 " --> pdb=" O THR K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 138 removed outlier: 4.341A pdb=" N PHE K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG K 132 " --> pdb=" O ALA K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 145 removed outlier: 4.238A pdb=" N ARG K 145 " --> pdb=" O TYR K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 165 Processing helix chain 'K' and resid 181 through 194 removed outlier: 3.675A pdb=" N ARG K 185 " --> pdb=" O SER K 181 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL K 186 " --> pdb=" O SER K 182 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY K 194 " --> pdb=" O PHE K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 205 removed outlier: 4.142A pdb=" N THR K 198 " --> pdb=" O GLY K 194 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN K 205 " --> pdb=" O HIS K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 210 No H-bonds generated for 'chain 'K' and resid 208 through 210' Processing helix chain 'K' and resid 211 through 223 Processing helix chain 'K' and resid 224 through 226 No H-bonds generated for 'chain 'K' and resid 224 through 226' Processing helix chain 'K' and resid 227 through 233 removed outlier: 3.818A pdb=" N LEU K 231 " --> pdb=" O THR K 227 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR K 233 " --> pdb=" O GLU K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 268 removed outlier: 3.942A pdb=" N PHE K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 301 Processing helix chain 'K' and resid 314 through 318 removed outlier: 4.215A pdb=" N ARG K 318 " --> pdb=" O ARG K 315 " (cutoff:3.500A) Processing helix chain 'K' and resid 330 through 348 Processing helix chain 'K' and resid 348 through 358 removed outlier: 4.374A pdb=" N THR K 358 " --> pdb=" O LYS K 354 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 387 removed outlier: 4.229A pdb=" N ILE K 370 " --> pdb=" O LYS K 366 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 394 removed outlier: 4.048A pdb=" N GLU K 393 " --> pdb=" O HIS K 390 " (cutoff:3.500A) Processing helix chain 'K' and resid 395 through 399 removed outlier: 3.762A pdb=" N ILE K 399 " --> pdb=" O SER K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 400 through 421 removed outlier: 3.976A pdb=" N PHE K 404 " --> pdb=" O GLY K 400 " (cutoff:3.500A) Processing helix chain 'K' and resid 423 through 454 removed outlier: 3.602A pdb=" N LYS K 432 " --> pdb=" O SER K 428 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR K 435 " --> pdb=" O LEU K 431 " (cutoff:3.500A) Processing helix chain 'K' and resid 456 through 473 removed outlier: 3.609A pdb=" N ALA K 466 " --> pdb=" O PHE K 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 473 through 478 removed outlier: 3.511A pdb=" N ARG K 477 " --> pdb=" O VAL K 473 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 485 Processing helix chain 'K' and resid 493 through 517 removed outlier: 3.568A pdb=" N LEU K 497 " --> pdb=" O SER K 493 " (cutoff:3.500A) Processing helix chain 'K' and resid 836 through 842 Processing helix chain 'K' and resid 843 through 845 No H-bonds generated for 'chain 'K' and resid 843 through 845' Processing helix chain 'K' and resid 846 through 857 removed outlier: 5.147A pdb=" N TRP K 852 " --> pdb=" O ASP K 848 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR K 853 " --> pdb=" O VAL K 849 " (cutoff:3.500A) Processing helix chain 'K' and resid 858 through 860 No H-bonds generated for 'chain 'K' and resid 858 through 860' Processing helix chain 'K' and resid 864 through 881 removed outlier: 3.706A pdb=" N ILE K 878 " --> pdb=" O MET K 874 " (cutoff:3.500A) Processing helix chain 'K' and resid 884 through 888 removed outlier: 3.662A pdb=" N LYS K 887 " --> pdb=" O LEU K 884 " (cutoff:3.500A) Processing helix chain 'K' and resid 890 through 905 removed outlier: 4.108A pdb=" N VAL K 896 " --> pdb=" O SER K 892 " (cutoff:3.500A) Processing helix chain 'K' and resid 908 through 915 removed outlier: 3.714A pdb=" N LYS K 913 " --> pdb=" O LYS K 909 " (cutoff:3.500A) Processing helix chain 'K' and resid 917 through 933 Processing helix chain 'K' and resid 936 through 943 Processing helix chain 'K' and resid 948 through 957 Processing helix chain 'L' and resid 56 through 62 Processing helix chain 'L' and resid 65 through 74 Processing helix chain 'L' and resid 83 through 103 removed outlier: 3.676A pdb=" N LYS L 94 " --> pdb=" O LYS L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 119 Processing helix chain 'L' and resid 121 through 132 Processing sheet with id=AA1, first strand: chain '2' and resid 203 through 207 Processing sheet with id=AA2, first strand: chain '2' and resid 280 through 291 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 280 through 291 current: chain '2' and resid 311 through 316 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 311 through 316 current: chain '2' and resid 369 through 375 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 369 through 375 current: chain '2' and resid 411 through 422 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '2' and resid 518 through 522 removed outlier: 6.214A pdb=" N VAL 2 519 " --> pdb=" O LEU 2 560 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASP 2 562 " --> pdb=" O VAL 2 519 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR 2 521 " --> pdb=" O ASP 2 562 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU 2 495 " --> pdb=" O CYS 2 636 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE 2 638 " --> pdb=" O LEU 2 495 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS 2 497 " --> pdb=" O ILE 2 638 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 583 through 588 Processing sheet with id=AA5, first strand: chain '2' and resid 833 through 837 Processing sheet with id=AA6, first strand: chain '3' and resid 52 through 56 removed outlier: 6.163A pdb=" N LEU 3 53 " --> pdb=" O GLY 3 106 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLU 3 108 " --> pdb=" O LEU 3 53 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N MET 3 55 " --> pdb=" O GLU 3 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '3' and resid 115 through 116 removed outlier: 3.686A pdb=" N GLU 3 133 " --> pdb=" O VAL 3 116 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '3' and resid 129 through 139 current: chain '3' and resid 159 through 163 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 159 through 163 current: chain '3' and resid 221 through 227 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 221 through 227 current: chain '3' and resid 260 through 272 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 260 through 272 current: chain '5' and resid 178 through 183 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 178 through 183 current: chain '5' and resid 245 through 251 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 245 through 251 current: chain '5' and resid 291 through 300 Processing sheet with id=AA8, first strand: chain '3' and resid 256 through 258 Processing sheet with id=AA9, first strand: chain '3' and resid 330 through 331 Processing sheet with id=AB1, first strand: chain '3' and resid 368 through 372 removed outlier: 6.503A pdb=" N ILE 3 369 " --> pdb=" O CYS 3 410 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ASP 3 412 " --> pdb=" O ILE 3 369 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR 3 371 " --> pdb=" O ASP 3 412 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL 3 344 " --> pdb=" O ALA 3 453 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA 3 455 " --> pdb=" O VAL 3 344 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU 3 346 " --> pdb=" O ALA 3 455 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 383 through 385 Processing sheet with id=AB3, first strand: chain '3' and resid 433 through 438 Processing sheet with id=AB4, first strand: chain '3' and resid 604 through 606 Processing sheet with id=AB5, first strand: chain '4' and resid 104 through 107 removed outlier: 3.772A pdb=" N GLN K 289 " --> pdb=" O ILE K 277 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '4' and resid 141 through 142 Processing sheet with id=AB7, first strand: chain '4' and resid 171 through 175 Processing sheet with id=AB8, first strand: chain '4' and resid 245 through 255 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 245 through 255 current: chain '4' and resid 275 through 279 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 275 through 279 current: chain '4' and resid 332 through 338 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 332 through 338 current: chain '4' and resid 371 through 385 Processing sheet with id=AB9, first strand: chain '4' and resid 450 through 451 Processing sheet with id=AC1, first strand: chain '4' and resid 489 through 493 removed outlier: 6.462A pdb=" N GLN 4 490 " --> pdb=" O CYS 4 531 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASP 4 533 " --> pdb=" O GLN 4 490 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR 4 492 " --> pdb=" O ASP 4 533 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE 4 465 " --> pdb=" O ALA 4 574 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ALA 4 576 " --> pdb=" O ILE 4 465 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU 4 467 " --> pdb=" O ALA 4 576 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 504 through 508 Processing sheet with id=AC3, first strand: chain '4' and resid 554 through 559 Processing sheet with id=AC4, first strand: chain '4' and resid 661 through 662 removed outlier: 6.840A pdb=" N LYS 4 661 " --> pdb=" O VAL 4 713 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain '5' and resid 69 through 73 Processing sheet with id=AC6, first strand: chain '5' and resid 362 through 363 Processing sheet with id=AC7, first strand: chain '5' and resid 400 through 403 removed outlier: 6.446A pdb=" N VAL 5 401 " --> pdb=" O CYS 5 442 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL 5 376 " --> pdb=" O ALA 5 485 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '5' and resid 465 through 470 removed outlier: 3.731A pdb=" N THR 5 475 " --> pdb=" O ILE 5 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 593 through 594 removed outlier: 6.695A pdb=" N ARG 5 593 " --> pdb=" O ALA 5 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain '6' and resid 54 through 58 removed outlier: 6.270A pdb=" N ILE 6 55 " --> pdb=" O SER 6 112 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE 6 114 " --> pdb=" O ILE 6 55 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE 6 57 " --> pdb=" O PHE 6 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain '6' and resid 163 through 168 removed outlier: 5.692A pdb=" N ALA 6 153 " --> pdb=" O ASP 6 166 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLN 6 168 " --> pdb=" O SER 6 151 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N SER 6 151 " --> pdb=" O GLN 6 168 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR 6 198 " --> pdb=" O SER 6 151 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA 6 153 " --> pdb=" O SER 6 196 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N SER 6 196 " --> pdb=" O ALA 6 153 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N PHE 6 155 " --> pdb=" O VAL 6 194 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N VAL 6 194 " --> pdb=" O PHE 6 155 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N CYS 6 157 " --> pdb=" O LEU 6 192 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N LEU 6 192 " --> pdb=" O CYS 6 157 " (cutoff:3.500A) removed outlier: 14.447A pdb=" N THR 6 222 " --> pdb=" O TYR 6 293 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N MET 6 295 " --> pdb=" O THR 6 222 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP 6 224 " --> pdb=" O MET 6 295 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ARG 6 228 " --> pdb=" O ALA 6 299 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N HIS 6 301 " --> pdb=" O ARG 6 228 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL 6 244 " --> pdb=" O CYS 6 300 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE 6 302 " --> pdb=" O ASP 6 242 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP 6 242 " --> pdb=" O ILE 6 302 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLN 6 304 " --> pdb=" O LYS 6 240 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LYS 6 240 " --> pdb=" O GLN 6 304 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG 6 206 " --> pdb=" O VAL 6 141 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR 6 143 " --> pdb=" O LYS 6 204 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LYS 6 204 " --> pdb=" O THR 6 143 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 378 through 379 Processing sheet with id=AD4, first strand: chain '6' and resid 418 through 421 removed outlier: 6.462A pdb=" N ILE 6 418 " --> pdb=" O CYS 6 459 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASP 6 461 " --> pdb=" O ILE 6 418 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR 6 420 " --> pdb=" O ASP 6 461 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY 6 456 " --> pdb=" O SER 6 499 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU 6 501 " --> pdb=" O GLY 6 456 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N CYS 6 458 " --> pdb=" O LEU 6 501 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA 6 503 " --> pdb=" O CYS 6 458 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE 6 460 " --> pdb=" O ALA 6 503 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL 6 393 " --> pdb=" O ILE 6 500 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY 6 397 " --> pdb=" O ALA 6 504 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '6' and resid 432 through 436 Processing sheet with id=AD6, first strand: chain '6' and resid 482 through 487 Processing sheet with id=AD7, first strand: chain '6' and resid 588 through 589 removed outlier: 6.973A pdb=" N LYS 6 588 " --> pdb=" O VAL 6 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain '6' and resid 788 through 792 removed outlier: 6.744A pdb=" N THR 6 798 " --> pdb=" O VAL 6 791 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '7' and resid 26 through 27 Processing sheet with id=AE1, first strand: chain '7' and resid 52 through 56 Processing sheet with id=AE2, first strand: chain '7' and resid 159 through 160 removed outlier: 4.458A pdb=" N LYS 7 177 " --> pdb=" O THR 7 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '7' and resid 173 through 183 current: chain '7' and resid 203 through 207 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 203 through 207 current: chain '7' and resid 265 through 271 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 265 through 271 current: chain '7' and resid 308 through 317 Processing sheet with id=AE3, first strand: chain '7' and resid 410 through 414 removed outlier: 6.408A pdb=" N GLN 7 411 " --> pdb=" O CYS 7 452 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ASP 7 454 " --> pdb=" O GLN 7 411 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR 7 413 " --> pdb=" O ASP 7 454 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU 7 387 " --> pdb=" O LEU 7 528 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N MET 7 530 " --> pdb=" O LEU 7 387 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET 7 389 " --> pdb=" O MET 7 530 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '7' and resid 425 through 429 Processing sheet with id=AE5, first strand: chain '7' and resid 475 through 480 Processing sheet with id=AE6, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.546A pdb=" N LEU A 180 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE E 50 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL E 22 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU E 53 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU E 24 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL E 55 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL E 26 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA E 97 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU E 120 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL E 99 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AE8, first strand: chain 'B' and resid 43 through 46 Processing sheet with id=AE9, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.603A pdb=" N LEU B 29 " --> pdb=" O GLY B 32 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.427A pdb=" N TYR D 172 " --> pdb=" O MET D 224 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 6 through 9 Processing sheet with id=AF3, first strand: chain 'C' and resid 50 through 51 removed outlier: 4.268A pdb=" N THR C 50 " --> pdb=" O GLY C 57 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 182 through 186 Processing sheet with id=AF5, first strand: chain 'E' and resid 103 through 104 Processing sheet with id=AF6, first strand: chain 'E' and resid 270 through 276 Processing sheet with id=AF7, first strand: chain 'E' and resid 442 through 443 removed outlier: 6.353A pdb=" N TYR E 448 " --> pdb=" O ILE E 491 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N MET E 493 " --> pdb=" O TYR E 448 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE E 450 " --> pdb=" O MET E 493 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 146 through 149 removed outlier: 4.545A pdb=" N THR F 592 " --> pdb=" O THR F 581 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR F 581 " --> pdb=" O THR F 592 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL F 556 " --> pdb=" O ILE F 584 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS F 161 " --> pdb=" O MET F 561 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER F 509 " --> pdb=" O VAL F 182 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 455 through 460 removed outlier: 6.748A pdb=" N LEU F 457 " --> pdb=" O THR F 331 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N THR F 331 " --> pdb=" O LEU F 457 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL F 459 " --> pdb=" O VAL F 329 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL F 329 " --> pdb=" O VAL F 459 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS F 325 " --> pdb=" O MET F 299 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN F 293 " --> pdb=" O THR F 331 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR F 490 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 146 through 149 removed outlier: 4.467A pdb=" N THR G 592 " --> pdb=" O THR G 581 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR G 581 " --> pdb=" O THR G 592 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL G 556 " --> pdb=" O ILE G 584 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER G 509 " --> pdb=" O VAL G 182 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 457 through 460 removed outlier: 3.745A pdb=" N LYS G 325 " --> pdb=" O MET G 299 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR G 289 " --> pdb=" O CYS G 292 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE G 227 " --> pdb=" O LEU G 503 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 13 through 16 Processing sheet with id=AG4, first strand: chain 'K' and resid 522 through 525 2425 hydrogen bonds defined for protein. 6927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 31.01 Time building geometry restraints manager: 15.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13843 1.34 - 1.46: 11377 1.46 - 1.58: 28920 1.58 - 1.70: 150 1.70 - 1.83: 533 Bond restraints: 54823 Sorted by residual: bond pdb=" O3A ANP 6 903 " pdb=" PB ANP 6 903 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" O3A ANP 41502 " pdb=" PB ANP 41502 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" O3A ANP 71500 " pdb=" PB ANP 71500 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP 31502 " pdb=" PB ANP 31502 " ideal model delta sigma weight residual 1.700 1.562 0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" N3B ANP 6 903 " pdb=" PG ANP 6 903 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 54818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 73568 3.33 - 6.67: 707 6.67 - 10.00: 39 10.00 - 13.33: 9 13.33 - 16.67: 2 Bond angle restraints: 74325 Sorted by residual: angle pdb=" N VAL 6 288 " pdb=" CA VAL 6 288 " pdb=" C VAL 6 288 " ideal model delta sigma weight residual 113.71 107.34 6.37 9.50e-01 1.11e+00 4.50e+01 angle pdb=" N SER 6 330 " pdb=" CA SER 6 330 " pdb=" C SER 6 330 " ideal model delta sigma weight residual 111.03 117.36 -6.33 1.11e+00 8.12e-01 3.25e+01 angle pdb=" PB ANP 6 903 " pdb=" N3B ANP 6 903 " pdb=" PG ANP 6 903 " ideal model delta sigma weight residual 126.95 110.28 16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" CA TYR A 41 " pdb=" CB TYR A 41 " pdb=" CG TYR A 41 " ideal model delta sigma weight residual 113.90 122.53 -8.63 1.80e+00 3.09e-01 2.30e+01 angle pdb=" PB ANP 41502 " pdb=" N3B ANP 41502 " pdb=" PG ANP 41502 " ideal model delta sigma weight residual 126.95 113.43 13.52 3.00e+00 1.11e-01 2.03e+01 ... (remaining 74320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.69: 32044 26.69 - 53.38: 1289 53.38 - 80.06: 183 80.06 - 106.75: 31 106.75 - 133.44: 3 Dihedral angle restraints: 33550 sinusoidal: 14317 harmonic: 19233 Sorted by residual: dihedral pdb=" CA ASP 5 524 " pdb=" C ASP 5 524 " pdb=" N VAL 5 525 " pdb=" CA VAL 5 525 " ideal model delta harmonic sigma weight residual -180.00 -148.58 -31.42 0 5.00e+00 4.00e-02 3.95e+01 dihedral pdb=" CA MET 6 329 " pdb=" C MET 6 329 " pdb=" N SER 6 330 " pdb=" CA SER 6 330 " ideal model delta harmonic sigma weight residual 180.00 -149.97 -30.03 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA ASP F 473 " pdb=" C ASP F 473 " pdb=" N SER F 474 " pdb=" CA SER F 474 " ideal model delta harmonic sigma weight residual 180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 33547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 7538 0.082 - 0.164: 829 0.164 - 0.246: 56 0.246 - 0.329: 6 0.329 - 0.411: 4 Chirality restraints: 8433 Sorted by residual: chirality pdb=" P DG J 18 " pdb=" OP1 DG J 18 " pdb=" OP2 DG J 18 " pdb=" O5' DG J 18 " both_signs ideal model delta sigma weight residual True 2.35 -2.76 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" P DA M 1 " pdb=" OP1 DA M 1 " pdb=" OP2 DA M 1 " pdb=" O5' DA M 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.74 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" P DT I 4 " pdb=" OP1 DT I 4 " pdb=" OP2 DT I 4 " pdb=" O5' DT I 4 " both_signs ideal model delta sigma weight residual True 2.35 2.73 -0.39 2.00e-01 2.50e+01 3.78e+00 ... (remaining 8430 not shown) Planarity restraints: 9343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE 2 150 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C ILE 2 150 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE 2 150 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG 2 151 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR 4 690 " 0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO 4 691 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO 4 691 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO 4 691 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 191 " 0.247 9.50e-02 1.11e+02 1.11e-01 7.55e+00 pdb=" NE ARG F 191 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG F 191 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 191 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 191 " 0.009 2.00e-02 2.50e+03 ... (remaining 9340 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 124 2.59 - 3.16: 40469 3.16 - 3.74: 77829 3.74 - 4.32: 107861 4.32 - 4.90: 181991 Nonbonded interactions: 408274 Sorted by model distance: nonbonded pdb="MG MG 31501 " pdb=" O2G ANP 31502 " model vdw 2.008 2.170 nonbonded pdb=" OG SER 3 355 " pdb="MG MG 31501 " model vdw 2.015 2.170 nonbonded pdb=" OG SER 7 397 " pdb="MG MG 71501 " model vdw 2.022 2.170 nonbonded pdb=" O2G ANP 71500 " pdb="MG MG 71501 " model vdw 2.022 2.170 nonbonded pdb="MG MG 31501 " pdb=" O2B ANP 31502 " model vdw 2.032 2.170 ... (remaining 408269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'F' and (resid 145 through 351 or resid 455 through 594)) selection = (chain 'G' and (resid 145 through 300 or resid 324 through 594)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.050 Extract box with map and model: 1.930 Check model and map are aligned: 0.370 Set scattering table: 0.480 Process input model: 139.560 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 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 : 0.006 0.150 54823 Z= 0.373 Angle : 0.909 16.668 74325 Z= 0.519 Chirality : 0.052 0.411 8433 Planarity : 0.007 0.111 9343 Dihedral : 14.707 133.440 21020 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.38 % Allowed : 3.01 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.10), residues: 6460 helix: 0.61 (0.09), residues: 2928 sheet: 0.43 (0.16), residues: 1002 loop : -0.20 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 425 HIS 0.013 0.002 HIS 4 393 PHE 0.025 0.003 PHE 2 862 TYR 0.026 0.002 TYR G 239 ARG 0.013 0.001 ARG 3 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 1026 time to evaluate : 5.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 275 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8392 (pp30) REVERT: 2 779 THR cc_start: 0.7253 (p) cc_final: 0.6953 (t) REVERT: 3 264 ILE cc_start: 0.9241 (pt) cc_final: 0.8730 (pt) REVERT: 4 121 PHE cc_start: 0.6530 (t80) cc_final: 0.6266 (t80) REVERT: 4 280 VAL cc_start: 0.8813 (t) cc_final: 0.7681 (p) REVERT: 5 72 ILE cc_start: 0.9390 (mt) cc_final: 0.9118 (mm) REVERT: 5 320 MET cc_start: 0.6636 (mtm) cc_final: 0.6303 (mtp) REVERT: 5 433 MET cc_start: 0.3790 (tpt) cc_final: 0.3194 (ptt) REVERT: 6 239 ASP cc_start: 0.7116 (m-30) cc_final: 0.6775 (m-30) REVERT: 6 243 ILE cc_start: 0.8983 (mp) cc_final: 0.8456 (mm) REVERT: 7 208 VAL cc_start: 0.8847 (t) cc_final: 0.8644 (m) REVERT: 7 240 SER cc_start: 0.7890 (m) cc_final: 0.7558 (p) REVERT: A 178 ASP cc_start: 0.7891 (m-30) cc_final: 0.7597 (m-30) REVERT: B 54 LYS cc_start: 0.9353 (tptt) cc_final: 0.8952 (tppt) REVERT: B 94 GLU cc_start: 0.8861 (mp0) cc_final: 0.8497 (mp0) REVERT: B 106 ASP cc_start: 0.7781 (m-30) cc_final: 0.6994 (m-30) REVERT: C 62 TYR cc_start: 0.7893 (m-80) cc_final: 0.7638 (m-10) REVERT: D 170 MET cc_start: 0.8759 (mmm) cc_final: 0.8376 (mmm) REVERT: F 242 ILE cc_start: 0.7825 (mt) cc_final: 0.7526 (tp) REVERT: G 295 LEU cc_start: 0.6913 (tp) cc_final: 0.6687 (tt) REVERT: K 85 CYS cc_start: 0.8563 (m) cc_final: 0.7953 (m) REVERT: K 104 LYS cc_start: 0.9139 (tmtt) cc_final: 0.7986 (tttp) REVERT: L 106 MET cc_start: 0.8138 (ttp) cc_final: 0.6821 (ttm) outliers start: 22 outliers final: 2 residues processed: 1045 average time/residue: 0.7127 time to fit residues: 1205.7512 Evaluate side-chains 501 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 498 time to evaluate : 6.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 275 GLN Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain G residue 251 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 551 optimal weight: 7.9990 chunk 494 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 333 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 511 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 311 optimal weight: 30.0000 chunk 380 optimal weight: 0.9990 chunk 592 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 ASN 2 355 GLN 3 128 ASN 3 284 GLN 3 503 HIS 3 570 HIS 4 143 HIS 4 393 HIS 4 394 GLN 4 657 ASN 5 75 ASN 5 604 ASN 6 10 GLN 6 211 GLN 6 303 GLN 6 728 HIS 6 802 HIS 7 236 GLN 7 474 GLN B 139 ASN C 101 GLN C 147 HIS F 196 GLN F 424 GLN F 469 ASN F 578 ASN G 528 ASN K 135 ASN K 469 HIS L 131 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 54823 Z= 0.261 Angle : 0.647 11.967 74325 Z= 0.346 Chirality : 0.043 0.238 8433 Planarity : 0.005 0.076 9343 Dihedral : 12.318 134.837 7986 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.60 % Allowed : 8.35 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.10), residues: 6460 helix: 1.43 (0.09), residues: 2939 sheet: 0.39 (0.15), residues: 1057 loop : -0.02 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 425 HIS 0.010 0.001 HIS 5 539 PHE 0.024 0.002 PHE 6 202 TYR 0.059 0.002 TYR A 41 ARG 0.016 0.001 ARG F 434 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 459 time to evaluate : 6.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 275 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8645 (pp30) REVERT: 2 680 MET cc_start: 0.5478 (mpp) cc_final: 0.5257 (mpp) REVERT: 3 200 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8026 (p0) REVERT: 4 331 HIS cc_start: 0.5705 (t70) cc_final: 0.5401 (t-170) REVERT: 4 435 VAL cc_start: 0.8751 (t) cc_final: 0.8510 (m) REVERT: 6 239 ASP cc_start: 0.7383 (m-30) cc_final: 0.7168 (m-30) REVERT: 7 428 MET cc_start: 0.7455 (tmm) cc_final: 0.7233 (tmm) REVERT: A 178 ASP cc_start: 0.8126 (m-30) cc_final: 0.7812 (m-30) REVERT: A 190 MET cc_start: 0.8190 (mmm) cc_final: 0.7960 (mmm) REVERT: C 62 TYR cc_start: 0.8182 (m-80) cc_final: 0.7961 (m-10) REVERT: D 159 MET cc_start: 0.7645 (tpp) cc_final: 0.7437 (ttt) REVERT: D 170 MET cc_start: 0.8682 (mmm) cc_final: 0.8479 (mmm) REVERT: F 548 MET cc_start: 0.6829 (mtt) cc_final: 0.6302 (mtt) REVERT: G 558 MET cc_start: 0.5878 (tmm) cc_final: 0.3749 (mtm) outliers start: 93 outliers final: 41 residues processed: 531 average time/residue: 0.6417 time to fit residues: 573.2818 Evaluate side-chains 418 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 375 time to evaluate : 6.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 250 TYR Chi-restraints excluded: chain 2 residue 275 GLN Chi-restraints excluded: chain 3 residue 73 THR Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 322 CYS Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 615 LEU Chi-restraints excluded: chain 4 residue 120 SER Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 713 VAL Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 604 ASN Chi-restraints excluded: chain 6 residue 28 LEU Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 224 ASP Chi-restraints excluded: chain 6 residue 507 VAL Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 514 VAL Chi-restraints excluded: chain 7 residue 580 THR Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 483 LYS Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 435 THR Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain K residue 306 ASP Chi-restraints excluded: chain K residue 360 VAL Chi-restraints excluded: chain K residue 407 ASN Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 131 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 329 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 493 optimal weight: 0.8980 chunk 403 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 594 optimal weight: 0.8980 chunk 641 optimal weight: 6.9990 chunk 529 optimal weight: 4.9990 chunk 589 optimal weight: 8.9990 chunk 202 optimal weight: 1.9990 chunk 476 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 318 GLN 4 527 ASN ** 6 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 557 HIS 6 783 HIS 7 158 HIS B 140 GLN B 166 GLN C 147 HIS G 469 ASN K 10 HIS K 429 HIS L 131 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 54823 Z= 0.223 Angle : 0.575 13.782 74325 Z= 0.305 Chirality : 0.042 0.238 8433 Planarity : 0.004 0.056 9343 Dihedral : 11.977 134.125 7982 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.65 % Allowed : 8.85 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.10), residues: 6460 helix: 1.72 (0.10), residues: 2948 sheet: 0.34 (0.15), residues: 1070 loop : 0.05 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 425 HIS 0.018 0.001 HIS L 131 PHE 0.020 0.001 PHE G 285 TYR 0.051 0.001 TYR A 41 ARG 0.008 0.000 ARG F 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 389 time to evaluate : 6.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 275 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8948 (pp30) REVERT: 3 364 MET cc_start: 0.7470 (mmm) cc_final: 0.7215 (mmp) REVERT: 4 234 MET cc_start: 0.7609 (ttm) cc_final: 0.7298 (ttm) REVERT: 4 677 MET cc_start: 0.7291 (mtp) cc_final: 0.6911 (mpp) REVERT: 5 86 MET cc_start: 0.8853 (tpp) cc_final: 0.8608 (tpp) REVERT: 6 721 LEU cc_start: 0.5121 (OUTLIER) cc_final: 0.4919 (tt) REVERT: A 22 MET cc_start: 0.8413 (mmm) cc_final: 0.8191 (mmm) REVERT: A 178 ASP cc_start: 0.8185 (m-30) cc_final: 0.7876 (m-30) REVERT: A 190 MET cc_start: 0.8111 (mmm) cc_final: 0.7654 (mmm) REVERT: C 140 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8183 (tm-30) REVERT: D 170 MET cc_start: 0.8681 (mmm) cc_final: 0.8390 (mmm) REVERT: F 548 MET cc_start: 0.6852 (mtt) cc_final: 0.6358 (mtt) REVERT: K 105 MET cc_start: 0.7683 (tmm) cc_final: 0.7212 (tmm) outliers start: 96 outliers final: 50 residues processed: 464 average time/residue: 0.6196 time to fit residues: 493.6363 Evaluate side-chains 395 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 343 time to evaluate : 6.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 192 MET Chi-restraints excluded: chain 2 residue 250 TYR Chi-restraints excluded: chain 2 residue 275 GLN Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 401 MET Chi-restraints excluded: chain 3 residue 444 LYS Chi-restraints excluded: chain 4 residue 120 SER Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 326 SER Chi-restraints excluded: chain 4 residue 549 VAL Chi-restraints excluded: chain 4 residue 713 VAL Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 602 LEU Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 507 VAL Chi-restraints excluded: chain 6 residue 721 LEU Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 478 ILE Chi-restraints excluded: chain 7 residue 521 LEU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 483 LYS Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 407 ASN Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 586 optimal weight: 5.9990 chunk 446 optimal weight: 4.9990 chunk 308 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 283 optimal weight: 20.0000 chunk 398 optimal weight: 0.9990 chunk 596 optimal weight: 6.9990 chunk 631 optimal weight: 7.9990 chunk 311 optimal weight: 30.0000 chunk 565 optimal weight: 6.9990 chunk 170 optimal weight: 0.0980 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 426 HIS 4 383 HIS 4 394 GLN ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 458 HIS ** 6 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 610 ASN 7 234 HIS 7 555 HIS A 17 GLN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN F 344 GLN K 124 HIS ** K 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 131 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 54823 Z= 0.346 Angle : 0.650 12.566 74325 Z= 0.343 Chirality : 0.044 0.299 8433 Planarity : 0.005 0.053 9343 Dihedral : 11.968 144.927 7982 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.95 % Allowed : 9.99 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.10), residues: 6460 helix: 1.57 (0.09), residues: 2953 sheet: 0.16 (0.15), residues: 1052 loop : -0.13 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 425 HIS 0.044 0.001 HIS C 147 PHE 0.026 0.002 PHE B 92 TYR 0.046 0.002 TYR A 41 ARG 0.014 0.001 ARG F 451 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 369 time to evaluate : 6.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 275 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8886 (pp30) REVERT: 2 680 MET cc_start: 0.5476 (mpp) cc_final: 0.5128 (mmp) REVERT: 2 703 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6705 (pp20) REVERT: 2 724 MET cc_start: 0.5365 (mmt) cc_final: 0.4790 (mpp) REVERT: 2 818 MET cc_start: 0.2795 (mtm) cc_final: 0.1187 (mmm) REVERT: 3 200 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8328 (p0) REVERT: 4 677 MET cc_start: 0.7622 (mtp) cc_final: 0.7153 (mpp) REVERT: 5 462 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7299 (mm-30) REVERT: 6 721 LEU cc_start: 0.5187 (OUTLIER) cc_final: 0.4935 (tt) REVERT: B 153 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: B 165 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8353 (ttt90) REVERT: D 170 MET cc_start: 0.8722 (mmm) cc_final: 0.8480 (mmm) REVERT: F 195 MET cc_start: 0.6837 (tmm) cc_final: 0.6604 (tmm) REVERT: F 548 MET cc_start: 0.6782 (mtt) cc_final: 0.6325 (mtt) REVERT: L 69 LEU cc_start: 0.8992 (mt) cc_final: 0.8697 (mt) outliers start: 113 outliers final: 67 residues processed: 468 average time/residue: 0.6094 time to fit residues: 492.4816 Evaluate side-chains 404 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 330 time to evaluate : 5.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 192 MET Chi-restraints excluded: chain 2 residue 275 GLN Chi-restraints excluded: chain 2 residue 703 GLU Chi-restraints excluded: chain 2 residue 738 VAL Chi-restraints excluded: chain 3 residue 73 THR Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 322 CYS Chi-restraints excluded: chain 3 residue 355 SER Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 444 LYS Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 4 residue 120 SER Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 326 SER Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 4 residue 502 LEU Chi-restraints excluded: chain 4 residue 549 VAL Chi-restraints excluded: chain 5 residue 174 GLN Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 462 GLU Chi-restraints excluded: chain 5 residue 481 CYS Chi-restraints excluded: chain 5 residue 602 LEU Chi-restraints excluded: chain 6 residue 62 LEU Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 430 LEU Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 490 VAL Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 659 ILE Chi-restraints excluded: chain 6 residue 721 LEU Chi-restraints excluded: chain 7 residue 45 ILE Chi-restraints excluded: chain 7 residue 190 VAL Chi-restraints excluded: chain 7 residue 372 ASP Chi-restraints excluded: chain 7 residue 478 ILE Chi-restraints excluded: chain 7 residue 521 LEU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 407 ASN Chi-restraints excluded: chain K residue 491 VAL Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 131 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 525 optimal weight: 7.9990 chunk 358 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 469 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 538 optimal weight: 6.9990 chunk 436 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 322 optimal weight: 9.9990 chunk 566 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 186 GLN 2 719 ASN 2 799 ASN 4 477 GLN ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 10 GLN ** 6 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN K 297 ASN K 922 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 54823 Z= 0.307 Angle : 0.602 12.717 74325 Z= 0.317 Chirality : 0.042 0.201 8433 Planarity : 0.004 0.043 9343 Dihedral : 11.935 146.952 7982 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.07 % Allowed : 11.16 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.10), residues: 6460 helix: 1.66 (0.09), residues: 2951 sheet: 0.10 (0.16), residues: 1051 loop : -0.22 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 425 HIS 0.046 0.001 HIS L 131 PHE 0.019 0.002 PHE B 92 TYR 0.046 0.002 TYR A 41 ARG 0.005 0.000 ARG L 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 347 time to evaluate : 5.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 250 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: 2 275 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.9004 (pp30) REVERT: 2 429 ASP cc_start: 0.6980 (p0) cc_final: 0.6658 (p0) REVERT: 2 680 MET cc_start: 0.5949 (mpp) cc_final: 0.5736 (mpp) REVERT: 2 703 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6897 (pp20) REVERT: 3 200 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8300 (p0) REVERT: 5 343 TYR cc_start: 0.4748 (p90) cc_final: 0.4066 (p90) REVERT: 5 462 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7328 (mm-30) REVERT: 5 523 HIS cc_start: 0.3542 (OUTLIER) cc_final: 0.2506 (t70) REVERT: 6 340 MET cc_start: 0.5316 (OUTLIER) cc_final: 0.4669 (ptp) REVERT: 6 466 MET cc_start: 0.7347 (ttp) cc_final: 0.6267 (ttp) REVERT: A 190 MET cc_start: 0.7883 (mmm) cc_final: 0.7492 (tmm) REVERT: B 153 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8475 (pm20) REVERT: B 165 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8319 (ttt90) REVERT: D 170 MET cc_start: 0.8699 (mmm) cc_final: 0.8381 (mmm) REVERT: F 539 MET cc_start: 0.7837 (tpp) cc_final: 0.7631 (tpp) REVERT: F 548 MET cc_start: 0.6661 (mtt) cc_final: 0.6306 (mtt) REVERT: L 69 LEU cc_start: 0.9133 (mt) cc_final: 0.8846 (mt) outliers start: 120 outliers final: 74 residues processed: 445 average time/residue: 0.6040 time to fit residues: 467.3778 Evaluate side-chains 412 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 329 time to evaluate : 6.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 192 MET Chi-restraints excluded: chain 2 residue 250 TYR Chi-restraints excluded: chain 2 residue 275 GLN Chi-restraints excluded: chain 2 residue 284 THR Chi-restraints excluded: chain 2 residue 341 VAL Chi-restraints excluded: chain 2 residue 552 VAL Chi-restraints excluded: chain 2 residue 703 GLU Chi-restraints excluded: chain 3 residue 73 THR Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 322 CYS Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 444 LYS Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 3 residue 512 THR Chi-restraints excluded: chain 4 residue 120 SER Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 326 SER Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 4 residue 392 LEU Chi-restraints excluded: chain 4 residue 502 LEU Chi-restraints excluded: chain 4 residue 545 VAL Chi-restraints excluded: chain 4 residue 549 VAL Chi-restraints excluded: chain 5 residue 112 THR Chi-restraints excluded: chain 5 residue 156 VAL Chi-restraints excluded: chain 5 residue 174 GLN Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 394 GLU Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 462 GLU Chi-restraints excluded: chain 5 residue 481 CYS Chi-restraints excluded: chain 5 residue 515 MET Chi-restraints excluded: chain 5 residue 523 HIS Chi-restraints excluded: chain 5 residue 525 VAL Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain 6 residue 340 MET Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 494 LEU Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 7 residue 372 ASP Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 478 ILE Chi-restraints excluded: chain 7 residue 521 LEU Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain G residue 592 THR Chi-restraints excluded: chain K residue 200 MET Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 407 ASN Chi-restraints excluded: chain K residue 484 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 212 optimal weight: 0.4980 chunk 568 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 370 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 631 optimal weight: 20.0000 chunk 524 optimal weight: 0.2980 chunk 292 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 331 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 393 HIS ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 267 ASN 6 471 GLN 7 356 HIS ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS F 344 GLN G 469 ASN L 131 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 54823 Z= 0.173 Angle : 0.546 14.945 74325 Z= 0.284 Chirality : 0.041 0.268 8433 Planarity : 0.004 0.042 9343 Dihedral : 11.747 142.905 7982 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.57 % Allowed : 12.19 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.10), residues: 6460 helix: 1.92 (0.10), residues: 2947 sheet: 0.24 (0.16), residues: 1058 loop : -0.12 (0.12), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 6 326 HIS 0.004 0.001 HIS 2 158 PHE 0.027 0.001 PHE 6 463 TYR 0.046 0.001 TYR A 41 ARG 0.006 0.000 ARG L 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 354 time to evaluate : 5.979 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: 2 250 TYR cc_start: 0.9276 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: 2 275 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8949 (pp30) REVERT: 2 429 ASP cc_start: 0.7013 (p0) cc_final: 0.6671 (p0) REVERT: 2 724 MET cc_start: 0.5001 (mmt) cc_final: 0.4197 (mpp) REVERT: 3 200 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8286 (p0) REVERT: 3 364 MET cc_start: 0.7761 (mmp) cc_final: 0.7541 (mmp) REVERT: 6 224 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: 6 329 MET cc_start: 0.7607 (ppp) cc_final: 0.7258 (ppp) REVERT: 6 721 LEU cc_start: 0.5254 (OUTLIER) cc_final: 0.4996 (tt) REVERT: B 153 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8508 (pm20) REVERT: B 165 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8292 (ttt90) REVERT: B 166 GLN cc_start: 0.9195 (tp40) cc_final: 0.8890 (mm-40) REVERT: C 140 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8409 (tm-30) REVERT: D 170 MET cc_start: 0.8716 (mmm) cc_final: 0.8328 (mmm) REVERT: F 548 MET cc_start: 0.6621 (mtt) cc_final: 0.6264 (mtt) REVERT: G 558 MET cc_start: 0.6731 (tmm) cc_final: 0.4455 (mtm) outliers start: 91 outliers final: 53 residues processed: 429 average time/residue: 0.6732 time to fit residues: 501.8761 Evaluate side-chains 392 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 332 time to evaluate : 6.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 250 TYR Chi-restraints excluded: chain 2 residue 275 GLN Chi-restraints excluded: chain 2 residue 531 LEU Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 355 SER Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 3 residue 512 THR Chi-restraints excluded: chain 4 residue 120 SER Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 4 residue 393 HIS Chi-restraints excluded: chain 4 residue 549 VAL Chi-restraints excluded: chain 5 residue 174 GLN Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 394 GLU Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 224 ASP Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 490 VAL Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 721 LEU Chi-restraints excluded: chain 7 residue 45 ILE Chi-restraints excluded: chain 7 residue 190 VAL Chi-restraints excluded: chain 7 residue 372 ASP Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 521 LEU Chi-restraints excluded: chain 7 residue 564 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 407 ASN Chi-restraints excluded: chain K residue 514 PHE Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 609 optimal weight: 0.0270 chunk 71 optimal weight: 10.0000 chunk 359 optimal weight: 1.9990 chunk 461 optimal weight: 10.0000 chunk 357 optimal weight: 1.9990 chunk 531 optimal weight: 7.9990 chunk 352 optimal weight: 10.0000 chunk 629 optimal weight: 1.9990 chunk 393 optimal weight: 0.8980 chunk 383 optimal weight: 10.0000 chunk 290 optimal weight: 4.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 54823 Z= 0.165 Angle : 0.548 17.315 74325 Z= 0.282 Chirality : 0.040 0.271 8433 Planarity : 0.003 0.042 9343 Dihedral : 11.637 140.562 7982 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.31 % Allowed : 12.37 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.11), residues: 6460 helix: 2.02 (0.10), residues: 2942 sheet: 0.31 (0.16), residues: 1065 loop : -0.09 (0.13), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 6 326 HIS 0.016 0.001 HIS 4 393 PHE 0.018 0.001 PHE 6 463 TYR 0.048 0.001 TYR A 41 ARG 0.006 0.000 ARG 4 254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 353 time to evaluate : 6.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 250 TYR cc_start: 0.9283 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: 2 429 ASP cc_start: 0.7016 (p0) cc_final: 0.6633 (p0) REVERT: 2 785 MET cc_start: 0.6461 (mtm) cc_final: 0.6160 (mtp) REVERT: 3 200 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8449 (p0) REVERT: 4 394 GLN cc_start: 0.2561 (OUTLIER) cc_final: 0.1980 (pm20) REVERT: 4 448 ARG cc_start: 0.6904 (ppt170) cc_final: 0.6598 (tmm160) REVERT: 5 462 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7825 (mm-30) REVERT: 5 523 HIS cc_start: 0.3398 (OUTLIER) cc_final: 0.2407 (t70) REVERT: 6 224 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7933 (m-30) REVERT: 6 329 MET cc_start: 0.7410 (ppp) cc_final: 0.7156 (ppp) REVERT: 6 371 MET cc_start: 0.4909 (ttt) cc_final: 0.4459 (ttm) REVERT: 6 466 MET cc_start: 0.8106 (tmm) cc_final: 0.7660 (tmm) REVERT: 6 721 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.5007 (tt) REVERT: A 190 MET cc_start: 0.7902 (mmm) cc_final: 0.7532 (tmm) REVERT: B 153 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8557 (pm20) REVERT: C 160 THR cc_start: 0.9049 (m) cc_final: 0.8771 (p) REVERT: F 538 MET cc_start: 0.7248 (ttp) cc_final: 0.7018 (ttp) REVERT: F 539 MET cc_start: 0.7758 (tpp) cc_final: 0.7522 (tpp) outliers start: 76 outliers final: 55 residues processed: 415 average time/residue: 0.6158 time to fit residues: 442.4890 Evaluate side-chains 398 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 335 time to evaluate : 6.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 250 TYR Chi-restraints excluded: chain 3 residue 73 THR Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 355 SER Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 401 MET Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 3 residue 512 THR Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 4 residue 393 HIS Chi-restraints excluded: chain 4 residue 394 GLN Chi-restraints excluded: chain 4 residue 549 VAL Chi-restraints excluded: chain 4 residue 677 MET Chi-restraints excluded: chain 5 residue 174 GLN Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 394 GLU Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 462 GLU Chi-restraints excluded: chain 5 residue 523 HIS Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 224 ASP Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 490 VAL Chi-restraints excluded: chain 6 residue 494 LEU Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 721 LEU Chi-restraints excluded: chain 7 residue 190 VAL Chi-restraints excluded: chain 7 residue 372 ASP Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 521 LEU Chi-restraints excluded: chain 7 residue 564 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 514 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 389 optimal weight: 7.9990 chunk 251 optimal weight: 4.9990 chunk 375 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 121 optimal weight: 0.4980 chunk 400 optimal weight: 10.0000 chunk 428 optimal weight: 8.9990 chunk 311 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 494 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 393 HIS ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 541 ASN 6 103 GLN ** 6 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 474 GLN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 54823 Z= 0.220 Angle : 0.573 11.964 74325 Z= 0.294 Chirality : 0.041 0.274 8433 Planarity : 0.004 0.045 9343 Dihedral : 11.606 140.728 7979 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.41 % Allowed : 12.38 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.11), residues: 6460 helix: 2.03 (0.10), residues: 2934 sheet: 0.26 (0.16), residues: 1053 loop : -0.15 (0.12), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 98 HIS 0.007 0.001 HIS 4 393 PHE 0.017 0.001 PHE C 104 TYR 0.049 0.001 TYR A 41 ARG 0.007 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 340 time to evaluate : 6.117 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: 2 250 TYR cc_start: 0.9323 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: 2 429 ASP cc_start: 0.7141 (p0) cc_final: 0.6692 (p0) REVERT: 2 703 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6906 (pp20) REVERT: 4 398 GLU cc_start: 0.5377 (OUTLIER) cc_final: 0.4888 (pm20) REVERT: 4 538 MET cc_start: 0.7163 (mmm) cc_final: 0.6816 (mmm) REVERT: 5 462 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7752 (mm-30) REVERT: 5 523 HIS cc_start: 0.3552 (OUTLIER) cc_final: 0.2586 (t70) REVERT: 6 371 MET cc_start: 0.5011 (ttt) cc_final: 0.4456 (ttm) REVERT: 6 466 MET cc_start: 0.8114 (tmm) cc_final: 0.7545 (tmm) REVERT: 6 721 LEU cc_start: 0.5286 (OUTLIER) cc_final: 0.4954 (tt) REVERT: A 32 TYR cc_start: 0.7535 (t80) cc_final: 0.7327 (t80) REVERT: B 153 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: F 538 MET cc_start: 0.7237 (ttp) cc_final: 0.6994 (ttp) REVERT: L 92 MET cc_start: 0.8251 (mmm) cc_final: 0.7866 (mmm) outliers start: 82 outliers final: 62 residues processed: 407 average time/residue: 0.6074 time to fit residues: 428.7505 Evaluate side-chains 396 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 327 time to evaluate : 5.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 250 TYR Chi-restraints excluded: chain 2 residue 341 VAL Chi-restraints excluded: chain 2 residue 703 GLU Chi-restraints excluded: chain 3 residue 73 THR Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 355 SER Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 3 residue 512 THR Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 4 residue 398 GLU Chi-restraints excluded: chain 4 residue 439 LEU Chi-restraints excluded: chain 4 residue 545 VAL Chi-restraints excluded: chain 4 residue 549 VAL Chi-restraints excluded: chain 4 residue 677 MET Chi-restraints excluded: chain 5 residue 174 GLN Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 394 GLU Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 462 GLU Chi-restraints excluded: chain 5 residue 523 HIS Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain 6 residue 441 PHE Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 490 VAL Chi-restraints excluded: chain 6 residue 494 LEU Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 721 LEU Chi-restraints excluded: chain 7 residue 45 ILE Chi-restraints excluded: chain 7 residue 190 VAL Chi-restraints excluded: chain 7 residue 313 HIS Chi-restraints excluded: chain 7 residue 372 ASP Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 521 LEU Chi-restraints excluded: chain 7 residue 564 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 514 PHE Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 572 optimal weight: 7.9990 chunk 602 optimal weight: 6.9990 chunk 550 optimal weight: 7.9990 chunk 586 optimal weight: 7.9990 chunk 353 optimal weight: 0.9980 chunk 255 optimal weight: 1.9990 chunk 460 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 529 optimal weight: 10.0000 chunk 554 optimal weight: 7.9990 chunk 584 optimal weight: 0.3980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 132 GLN 4 527 ASN ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 115 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 54823 Z= 0.289 Angle : 0.621 17.740 74325 Z= 0.318 Chirality : 0.042 0.254 8433 Planarity : 0.004 0.048 9343 Dihedral : 11.677 142.134 7979 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.50 % Allowed : 12.49 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.10), residues: 6460 helix: 1.89 (0.10), residues: 2931 sheet: 0.16 (0.16), residues: 1010 loop : -0.29 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 6 617 HIS 0.005 0.001 HIS 7 118 PHE 0.019 0.001 PHE B 92 TYR 0.049 0.001 TYR A 41 ARG 0.008 0.000 ARG 2 786 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 326 time to evaluate : 6.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 250 TYR cc_start: 0.9358 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: 2 429 ASP cc_start: 0.6876 (p0) cc_final: 0.6503 (p0) REVERT: 2 703 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6918 (pp20) REVERT: 3 200 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8462 (p0) REVERT: 3 306 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7610 (tt) REVERT: 4 398 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.5091 (pm20) REVERT: 4 538 MET cc_start: 0.7069 (mmm) cc_final: 0.6759 (mmm) REVERT: 5 523 HIS cc_start: 0.3633 (OUTLIER) cc_final: 0.2702 (t70) REVERT: 6 104 MET cc_start: 0.8499 (mmm) cc_final: 0.7734 (mmt) REVERT: 6 371 MET cc_start: 0.5167 (ttt) cc_final: 0.4600 (ttm) REVERT: 6 466 MET cc_start: 0.8107 (tmm) cc_final: 0.7747 (tmm) REVERT: 6 721 LEU cc_start: 0.5235 (OUTLIER) cc_final: 0.4924 (tt) REVERT: B 153 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8491 (pm20) REVERT: F 569 MET cc_start: 0.7321 (pmm) cc_final: 0.6400 (ptp) REVERT: L 92 MET cc_start: 0.8392 (mmm) cc_final: 0.8089 (mmm) outliers start: 87 outliers final: 66 residues processed: 399 average time/residue: 0.6076 time to fit residues: 421.0062 Evaluate side-chains 389 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 315 time to evaluate : 6.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 250 TYR Chi-restraints excluded: chain 2 residue 341 VAL Chi-restraints excluded: chain 2 residue 703 GLU Chi-restraints excluded: chain 3 residue 73 THR Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 169 MET Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 306 LEU Chi-restraints excluded: chain 3 residue 355 SER Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 444 LYS Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 3 residue 512 THR Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 4 residue 398 GLU Chi-restraints excluded: chain 4 residue 439 LEU Chi-restraints excluded: chain 4 residue 502 LEU Chi-restraints excluded: chain 4 residue 545 VAL Chi-restraints excluded: chain 4 residue 549 VAL Chi-restraints excluded: chain 5 residue 174 GLN Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 394 GLU Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 523 HIS Chi-restraints excluded: chain 5 residue 538 VAL Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 490 VAL Chi-restraints excluded: chain 6 residue 494 LEU Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 721 LEU Chi-restraints excluded: chain 7 residue 45 ILE Chi-restraints excluded: chain 7 residue 190 VAL Chi-restraints excluded: chain 7 residue 313 HIS Chi-restraints excluded: chain 7 residue 372 ASP Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 478 ILE Chi-restraints excluded: chain 7 residue 521 LEU Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 484 ILE Chi-restraints excluded: chain K residue 514 PHE Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 385 optimal weight: 2.9990 chunk 620 optimal weight: 0.9990 chunk 378 optimal weight: 9.9990 chunk 294 optimal weight: 20.0000 chunk 431 optimal weight: 1.9990 chunk 650 optimal weight: 3.9990 chunk 598 optimal weight: 0.6980 chunk 518 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 400 optimal weight: 9.9990 chunk 317 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 231 GLN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 ASN E 262 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 54823 Z= 0.200 Angle : 0.593 14.030 74325 Z= 0.302 Chirality : 0.041 0.282 8433 Planarity : 0.003 0.043 9343 Dihedral : 11.612 140.032 7979 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.27 % Allowed : 12.73 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.10), residues: 6460 helix: 1.95 (0.10), residues: 2941 sheet: 0.21 (0.16), residues: 1037 loop : -0.23 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP 6 326 HIS 0.005 0.001 HIS 2 158 PHE 0.018 0.001 PHE C 104 TYR 0.050 0.001 TYR A 41 ARG 0.007 0.000 ARG H 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12920 Ramachandran restraints generated. 6460 Oldfield, 0 Emsley, 6460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 333 time to evaluate : 6.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 250 TYR cc_start: 0.9327 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: 2 429 ASP cc_start: 0.6930 (p0) cc_final: 0.6585 (p0) REVERT: 3 200 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8428 (p0) REVERT: 4 538 MET cc_start: 0.7011 (mmm) cc_final: 0.6704 (mmm) REVERT: 5 523 HIS cc_start: 0.3699 (OUTLIER) cc_final: 0.2774 (t70) REVERT: 6 371 MET cc_start: 0.5096 (ttt) cc_final: 0.4630 (ttm) REVERT: 6 466 MET cc_start: 0.8119 (tmm) cc_final: 0.7872 (tmm) REVERT: 6 721 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4910 (tt) REVERT: B 153 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8511 (pm20) REVERT: C 160 THR cc_start: 0.9131 (m) cc_final: 0.8835 (p) REVERT: F 299 MET cc_start: 0.5981 (tmm) cc_final: 0.5663 (tmm) REVERT: F 569 MET cc_start: 0.7249 (pmm) cc_final: 0.6277 (ptp) outliers start: 74 outliers final: 59 residues processed: 397 average time/residue: 0.6079 time to fit residues: 422.2753 Evaluate side-chains 385 residues out of total 5806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 321 time to evaluate : 6.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 250 TYR Chi-restraints excluded: chain 2 residue 326 THR Chi-restraints excluded: chain 2 residue 341 VAL Chi-restraints excluded: chain 3 residue 73 THR Chi-restraints excluded: chain 3 residue 139 CYS Chi-restraints excluded: chain 3 residue 200 ASP Chi-restraints excluded: chain 3 residue 355 SER Chi-restraints excluded: chain 3 residue 369 ILE Chi-restraints excluded: chain 3 residue 408 VAL Chi-restraints excluded: chain 3 residue 444 LYS Chi-restraints excluded: chain 3 residue 459 TYR Chi-restraints excluded: chain 3 residue 512 THR Chi-restraints excluded: chain 4 residue 172 ILE Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 247 THR Chi-restraints excluded: chain 4 residue 315 VAL Chi-restraints excluded: chain 4 residue 342 VAL Chi-restraints excluded: chain 4 residue 439 LEU Chi-restraints excluded: chain 4 residue 545 VAL Chi-restraints excluded: chain 4 residue 549 VAL Chi-restraints excluded: chain 5 residue 174 GLN Chi-restraints excluded: chain 5 residue 311 THR Chi-restraints excluded: chain 5 residue 394 GLU Chi-restraints excluded: chain 5 residue 433 MET Chi-restraints excluded: chain 5 residue 523 HIS Chi-restraints excluded: chain 5 residue 538 VAL Chi-restraints excluded: chain 6 residue 105 PHE Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain 6 residue 458 CYS Chi-restraints excluded: chain 6 residue 490 VAL Chi-restraints excluded: chain 6 residue 494 LEU Chi-restraints excluded: chain 6 residue 500 ILE Chi-restraints excluded: chain 6 residue 721 LEU Chi-restraints excluded: chain 7 residue 45 ILE Chi-restraints excluded: chain 7 residue 190 VAL Chi-restraints excluded: chain 7 residue 313 HIS Chi-restraints excluded: chain 7 residue 372 ASP Chi-restraints excluded: chain 7 residue 386 VAL Chi-restraints excluded: chain 7 residue 521 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain E residue 572 THR Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 332 HIS Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 476 VAL Chi-restraints excluded: chain G residue 480 LYS Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 238 VAL Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 395 ILE Chi-restraints excluded: chain K residue 514 PHE Chi-restraints excluded: chain L residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 653 random chunks: chunk 411 optimal weight: 2.9990 chunk 551 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 477 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 518 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 532 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 464 ASN 4 547 HIS ** 5 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 567 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.090798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.063645 restraints weight = 218495.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063933 restraints weight = 139362.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.063230 restraints weight = 121249.515| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 54823 Z= 0.179 Angle : 0.588 15.963 74325 Z= 0.297 Chirality : 0.041 0.285 8433 Planarity : 0.003 0.048 9343 Dihedral : 11.526 138.026 7979 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.00 % Allowed : 13.09 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.11), residues: 6460 helix: 2.03 (0.10), residues: 2941 sheet: 0.23 (0.16), residues: 1045 loop : -0.17 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 425 HIS 0.008 0.001 HIS 5 539 PHE 0.017 0.001 PHE C 104 TYR 0.049 0.001 TYR A 41 ARG 0.007 0.000 ARG H 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10692.73 seconds wall clock time: 193 minutes 7.57 seconds (11587.57 seconds total)