Starting phenix.real_space_refine on Sun Dec 10 01:07:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9c_15924/12_2023/8b9c_15924_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9c_15924/12_2023/8b9c_15924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9c_15924/12_2023/8b9c_15924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9c_15924/12_2023/8b9c_15924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9c_15924/12_2023/8b9c_15924_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9c_15924/12_2023/8b9c_15924_trim_updated.pdb" } resolution = 4.6 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= 0.035 sd= 0.305 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 68 5.49 5 Mg 4 5.21 5 S 246 5.16 5 C 37281 2.51 5 N 10117 2.21 5 O 11247 1.98 5 H 59018 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 117985 Number of models: 1 Model: "" Number of chains: 26 Chain: "2" Number of atoms: 9140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 9140 Classifications: {'peptide': 568} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 545} Chain breaks: 5 Chain: "3" Number of atoms: 9653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 9653 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 29, 'TRANS': 583} Chain breaks: 4 Chain: "4" Number of atoms: 10055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 10055 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 25, 'TRANS': 602} Chain breaks: 3 Chain: "5" Number of atoms: 8560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8560 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 20, 'TRANS': 512} Chain breaks: 10 Chain: "6" Number of atoms: 9908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 9908 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 23, 'TRANS': 599} Chain breaks: 5 Chain: "7" Number of atoms: 10387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 10387 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 30, 'TRANS': 625} Chain breaks: 3 Chain: "A" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 4382 Classifications: {'peptide': 258} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 8944 Classifications: {'peptide': 561} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 5, 'PTRANS': 30, 'TRANS': 525} Chain breaks: 2 Chain: "C" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3202 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 191} Chain breaks: 1 Chain: "D" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 3191 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain breaks: 1 Chain: "E" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2775 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain breaks: 2 Chain: "F" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3709 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain breaks: 1 Chain: "G" Number of atoms: 9185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 9185 Classifications: {'peptide': 565} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 549} Chain breaks: 3 Chain: "P" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 805 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain breaks: 2 Chain: "Q" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 1128 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain breaks: 1 Chain: "R" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 656 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "S" Number of atoms: 6428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 6428 Classifications: {'peptide': 391} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 370} Chain: "X" Number of atoms: 10978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 10978 Classifications: {'peptide': 665} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 644} Chain breaks: 6 Chain: "Y" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1575 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "J" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3192 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 191} Chain: "2" 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: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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 21704 SG CYS 4 349 93.093 167.593 127.399 1.00101.09 S ATOM 21745 SG CYS 4 352 93.268 171.145 127.929 1.00 96.38 S ATOM 22034 SG CYS 4 371 91.181 169.610 124.925 1.00110.38 S ATOM 22115 SG CYS 4 376 94.991 170.043 124.847 1.00117.84 S ATOM 31132 SG CYS 5 186 100.819 121.257 95.704 1.00 83.56 S ATOM 31487 SG CYS 5 236 101.623 124.216 98.040 1.00 30.00 S ATOM 40128 SG CYS 6 311 112.115 150.795 126.128 1.00 80.21 S ATOM 40168 SG CYS 6 314 114.941 153.313 125.488 1.00 79.97 S ATOM 40473 SG CYS 6 333 111.587 154.399 124.862 1.00 77.95 S ATOM 40537 SG CYS 6 338 113.012 151.936 122.458 1.00 91.55 S ATOM 50395 SG CYS 7 262 71.600 158.658 107.386 1.00 92.80 S ATOM 50435 SG CYS 7 265 70.158 160.210 104.442 1.00 96.91 S ATOM 50729 SG CYS 7 284 71.747 156.374 104.595 1.00105.78 S ATOM 50795 SG CYS 7 289 73.513 159.347 103.633 1.00118.44 S Time building chain proxies: 37.18, per 1000 atoms: 0.32 Number of scatterers: 117985 At special positions: 0 Unit cell: (201.79, 233.532, 217.661, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 246 16.00 P 68 15.00 Mg 4 11.99 O 11247 8.00 N 10117 7.00 C 37281 6.00 H 59018 1.00 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 - 3.50 Amino acid : False - 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: 66.57 Conformation dependent library (CDL) restraints added in 8.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 41003 " pdb="ZN ZN 41003 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41003 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41003 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41003 " - pdb=" SG CYS 4 376 " pdb=" ZN 51502 " pdb="ZN ZN 51502 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 51502 " - pdb=" SG CYS 5 186 " pdb=" ZN 62000 " pdb="ZN ZN 62000 " - pdb=" SG CYS 6 333 " pdb="ZN ZN 62000 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 62000 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 62000 " - pdb=" SG CYS 6 311 " pdb=" ZN 7 903 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 7 903 " - pdb=" SG CYS 7 262 " Number of angles added : 18 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13764 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 283 helices and 62 sheets defined 54.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 40.81 Creating SS restraints... Processing helix chain '2' and resid 182 through 188 removed outlier: 3.781A pdb=" N SER 2 187 " --> pdb=" O LEU 2 183 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN 2 188 " --> pdb=" O GLU 2 184 " (cutoff:3.500A) Processing helix chain '2' and resid 193 through 200 removed outlier: 4.390A pdb=" N GLN 2 200 " --> pdb=" O GLU 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 201 through 218 removed outlier: 3.633A pdb=" N GLU 2 217 " --> pdb=" O SER 2 213 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 238 removed outlier: 3.691A pdb=" N GLY 2 235 " --> pdb=" O ILE 2 231 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU 2 236 " --> pdb=" O ARG 2 232 " (cutoff:3.500A) Processing helix chain '2' and resid 245 through 253 removed outlier: 3.706A pdb=" N SER 2 252 " --> pdb=" O HIS 2 248 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS 2 253 " --> pdb=" O LEU 2 249 " (cutoff:3.500A) Processing helix chain '2' and resid 254 through 263 Processing helix chain '2' and resid 265 through 283 removed outlier: 4.038A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU 2 277 " --> pdb=" O LEU 2 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 291 removed outlier: 4.384A pdb=" N ILE 2 289 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER 2 291 " --> pdb=" O ALA 2 287 " (cutoff:3.500A) Processing helix chain '2' and resid 393 through 398 Proline residue: 2 398 - end of helix Processing helix chain '2' and resid 435 through 443 Processing helix chain '2' and resid 477 through 491 removed outlier: 3.586A pdb=" N ASP 2 490 " --> pdb=" O LYS 2 486 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ARG 2 491 " --> pdb=" O ILE 2 487 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 502 removed outlier: 5.533A pdb=" N ALA 2 502 " --> pdb=" O ILE 2 498 " (cutoff:3.500A) Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 560 Processing helix chain '2' and resid 595 through 600 removed outlier: 3.922A pdb=" N ALA 2 599 " --> pdb=" O ALA 2 595 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP 2 600 " --> pdb=" O LEU 2 596 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 595 through 600' Processing helix chain '2' and resid 614 through 626 Processing helix chain '2' and resid 662 through 668 removed outlier: 4.007A pdb=" N ASN 2 666 " --> pdb=" O PRO 2 662 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL 2 667 " --> pdb=" O LEU 2 663 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER 2 668 " --> pdb=" O ALA 2 664 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 662 through 668' Processing helix chain '2' and resid 670 through 678 removed outlier: 3.774A pdb=" N LEU 2 674 " --> pdb=" O THR 2 670 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASP 2 678 " --> pdb=" O LEU 2 674 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 707 removed outlier: 3.645A pdb=" N HIS 2 707 " --> pdb=" O HIS 2 703 " (cutoff:3.500A) Processing helix chain '2' and resid 745 through 756 Processing helix chain '2' and resid 759 through 773 Processing helix chain '2' and resid 779 through 801 removed outlier: 4.446A pdb=" N MET 2 783 " --> pdb=" O HIS 2 779 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASP 2 784 " --> pdb=" O GLN 2 780 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LYS 2 785 " --> pdb=" O MET 2 781 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 825 removed outlier: 3.698A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 850 removed outlier: 3.544A pdb=" N ALA 2 848 " --> pdb=" O SER 2 844 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN 2 849 " --> pdb=" O PHE 2 845 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LYS 2 850 " --> pdb=" O VAL 2 846 " (cutoff:3.500A) Processing helix chain '2' and resid 851 through 862 Processing helix chain '3' and resid 18 through 36 removed outlier: 4.352A pdb=" N GLY 3 22 " --> pdb=" O ASP 3 18 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP 3 23 " --> pdb=" O ALA 3 19 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 55 removed outlier: 3.602A pdb=" N SER 3 41 " --> pdb=" O SER 3 37 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA 3 54 " --> pdb=" O SER 3 50 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN 3 55 " --> pdb=" O ASN 3 51 " (cutoff:3.500A) Processing helix chain '3' and resid 99 through 107 removed outlier: 3.634A pdb=" N LEU 3 103 " --> pdb=" O SER 3 99 " (cutoff:3.500A) Processing helix chain '3' and resid 108 through 117 Processing helix chain '3' and resid 118 through 137 Proline residue: 3 123 - end of helix removed outlier: 5.563A pdb=" N ASP 3 137 " --> pdb=" O ALA 3 133 " (cutoff:3.500A) Processing helix chain '3' and resid 143 through 149 removed outlier: 3.983A pdb=" N SER 3 148 " --> pdb=" O ALA 3 144 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER 3 149 " --> pdb=" O SER 3 145 " (cutoff:3.500A) Processing helix chain '3' and resid 216 through 221 removed outlier: 3.966A pdb=" N THR 3 220 " --> pdb=" O ASP 3 216 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU 3 221 " --> pdb=" O ALA 3 217 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 216 through 221' Processing helix chain '3' and resid 261 through 266 removed outlier: 3.890A pdb=" N ALA 3 265 " --> pdb=" O MET 3 261 " (cutoff:3.500A) Proline residue: 3 266 - end of helix No H-bonds generated for 'chain '3' and resid 261 through 266' Processing helix chain '3' and resid 343 through 356 removed outlier: 4.152A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS 3 356 " --> pdb=" O LYS 3 352 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 369 removed outlier: 5.561A pdb=" N ALA 3 368 " --> pdb=" O SER 3 364 " (cutoff:3.500A) Proline residue: 3 369 - end of helix Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 426 removed outlier: 3.582A pdb=" N PHE 3 421 " --> pdb=" O GLN 3 417 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL 3 422 " --> pdb=" O LEU 3 418 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU 3 423 " --> pdb=" O LEU 3 419 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN 3 424 " --> pdb=" O ARG 3 420 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR 3 425 " --> pdb=" O PHE 3 421 " (cutoff:3.500A) Processing helix chain '3' and resid 433 through 438 removed outlier: 3.744A pdb=" N SER 3 437 " --> pdb=" O THR 3 433 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER 3 438 " --> pdb=" O GLY 3 434 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 433 through 438' Processing helix chain '3' and resid 439 through 444 Processing helix chain '3' and resid 460 through 466 removed outlier: 4.515A pdb=" N ASP 3 466 " --> pdb=" O MET 3 462 " (cutoff:3.500A) Processing helix chain '3' and resid 479 through 492 removed outlier: 4.448A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE 3 486 " --> pdb=" O ASP 3 482 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS 3 487 " --> pdb=" O ARG 3 483 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 534 removed outlier: 3.918A pdb=" N ALA 3 534 " --> pdb=" O HIS 3 530 " (cutoff:3.500A) Processing helix chain '3' and resid 536 through 544 removed outlier: 4.130A pdb=" N ARG 3 542 " --> pdb=" O SER 3 538 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE 3 543 " --> pdb=" O LEU 3 539 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ASP 3 544 " --> pdb=" O LEU 3 540 " (cutoff:3.500A) Processing helix chain '3' and resid 554 through 571 removed outlier: 3.546A pdb=" N ARG 3 570 " --> pdb=" O LEU 3 566 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR 3 571 " --> pdb=" O ARG 3 567 " (cutoff:3.500A) Processing helix chain '3' and resid 652 through 666 removed outlier: 3.758A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) Processing helix chain '3' and resid 672 through 689 removed outlier: 3.623A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS 3 681 " --> pdb=" O ASN 3 677 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 717 removed outlier: 4.258A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 removed outlier: 3.506A pdb=" N ALA 3 726 " --> pdb=" O ASN 3 722 " (cutoff:3.500A) Processing helix chain '4' and resid 186 through 200 removed outlier: 3.681A pdb=" N CYS 4 190 " --> pdb=" O SER 4 186 " (cutoff:3.500A) Processing helix chain '4' and resid 202 through 211 removed outlier: 4.642A pdb=" N ARG 4 206 " --> pdb=" O LYS 4 202 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU 4 211 " --> pdb=" O LYS 4 207 " (cutoff:3.500A) Processing helix chain '4' and resid 218 through 223 removed outlier: 3.898A pdb=" N GLU 4 222 " --> pdb=" O ASN 4 218 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU 4 223 " --> pdb=" O THR 4 219 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 218 through 223' Processing helix chain '4' and resid 224 through 237 Processing helix chain '4' and resid 245 through 252 removed outlier: 3.988A pdb=" N LEU 4 249 " --> pdb=" O ALA 4 245 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LYS 4 252 " --> pdb=" O LEU 4 248 " (cutoff:3.500A) Processing helix chain '4' and resid 253 through 264 removed outlier: 5.375A pdb=" N LEU 4 257 " --> pdb=" O GLN 4 253 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 286 removed outlier: 3.604A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE 4 284 " --> pdb=" O MET 4 280 " (cutoff:3.500A) Processing helix chain '4' and resid 292 through 300 removed outlier: 5.555A pdb=" N PHE 4 300 " --> pdb=" O ILE 4 296 " (cutoff:3.500A) Processing helix chain '4' and resid 502 through 515 removed outlier: 3.916A pdb=" N ARG 4 515 " --> pdb=" O GLU 4 511 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 528 removed outlier: 4.658A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Proline residue: 4 528 - end of helix Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 573 through 585 removed outlier: 3.595A pdb=" N ILE 4 577 " --> pdb=" O SER 4 573 " (cutoff:3.500A) Processing helix chain '4' and resid 597 through 603 removed outlier: 3.528A pdb=" N THR 4 602 " --> pdb=" O ALA 4 598 " (cutoff:3.500A) Processing helix chain '4' and resid 619 through 625 removed outlier: 3.806A pdb=" N ASP 4 625 " --> pdb=" O LEU 4 621 " (cutoff:3.500A) Processing helix chain '4' and resid 638 through 649 removed outlier: 4.020A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU 4 645 " --> pdb=" O THR 4 641 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N HIS 4 646 " --> pdb=" O ARG 4 642 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 Processing helix chain '4' and resid 695 through 702 removed outlier: 4.300A pdb=" N ARG 4 701 " --> pdb=" O PRO 4 697 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE 4 702 " --> pdb=" O LEU 4 698 " (cutoff:3.500A) Processing helix chain '4' and resid 713 through 730 removed outlier: 3.562A pdb=" N GLU 4 719 " --> pdb=" O LYS 4 715 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR 4 728 " --> pdb=" O LEU 4 724 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU 4 729 " --> pdb=" O THR 4 725 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU 4 730 " --> pdb=" O ASN 4 726 " (cutoff:3.500A) Processing helix chain '4' and resid 743 through 758 Processing helix chain '4' and resid 763 through 779 Processing helix chain '4' and resid 794 through 813 removed outlier: 4.097A pdb=" N LEU 4 798 " --> pdb=" O THR 4 794 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU 4 799 " --> pdb=" O THR 4 795 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) Processing helix chain '4' and resid 818 through 834 removed outlier: 3.969A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS 4 834 " --> pdb=" O ARG 4 830 " (cutoff:3.500A) Processing helix chain '5' and resid 21 through 38 removed outlier: 4.209A pdb=" N THR 5 25 " --> pdb=" O ASP 5 21 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE 5 28 " --> pdb=" O ASN 5 24 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU 5 37 " --> pdb=" O ASN 5 33 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE 5 38 " --> pdb=" O PHE 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 57 removed outlier: 3.504A pdb=" N ILE 5 54 " --> pdb=" O LEU 5 50 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL 5 56 " --> pdb=" O ASN 5 52 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 72 Processing helix chain '5' and resid 73 through 83 Proline residue: 5 83 - end of helix Processing helix chain '5' and resid 84 through 103 Proline residue: 5 88 - end of helix removed outlier: 3.788A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE 5 101 " --> pdb=" O VAL 5 97 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER 5 102 " --> pdb=" O ALA 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 350 through 364 removed outlier: 3.724A pdb=" N GLU 5 356 " --> pdb=" O GLU 5 352 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN 5 363 " --> pdb=" O GLN 5 359 " (cutoff:3.500A) Proline residue: 5 364 - end of helix Processing helix chain '5' and resid 365 through 376 removed outlier: 3.596A pdb=" N ILE 5 374 " --> pdb=" O LEU 5 370 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ALA 5 375 " --> pdb=" O THR 5 371 " (cutoff:3.500A) Proline residue: 5 376 - end of helix Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 421 through 433 removed outlier: 4.053A pdb=" N LEU 5 425 " --> pdb=" O ALA 5 421 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU 5 426 " --> pdb=" O LYS 5 422 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS 5 427 " --> pdb=" O SER 5 423 " (cutoff:3.500A) Processing helix chain '5' and resid 467 through 473 removed outlier: 5.209A pdb=" N ALA 5 472 " --> pdb=" O ALA 5 468 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP 5 473 " --> pdb=" O MET 5 469 " (cutoff:3.500A) Processing helix chain '5' and resid 487 through 497 removed outlier: 3.715A pdb=" N VAL 5 491 " --> pdb=" O ASP 5 487 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS 5 494 " --> pdb=" O ARG 5 490 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU 5 495 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) Processing helix chain '5' and resid 545 through 550 removed outlier: 4.829A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE 5 550 " --> pdb=" O ILE 5 546 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 545 through 550' Processing helix chain '5' and resid 561 through 577 removed outlier: 3.570A pdb=" N ASP 5 565 " --> pdb=" O ASN 5 561 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 610 Processing helix chain '5' and resid 615 through 636 Processing helix chain '5' and resid 649 through 668 removed outlier: 3.740A pdb=" N ALA 5 655 " --> pdb=" O ARG 5 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG 5 658 " --> pdb=" O GLU 5 654 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU 5 666 " --> pdb=" O SER 5 662 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU 5 668 " --> pdb=" O ALA 5 664 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 685 removed outlier: 4.012A pdb=" N GLN 5 685 " --> pdb=" O ILE 5 681 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 121 removed outlier: 3.563A pdb=" N GLU 6 109 " --> pdb=" O ASP 6 105 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN 6 117 " --> pdb=" O GLU 6 113 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 147 Processing helix chain '6' and resid 154 through 162 removed outlier: 3.781A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 173 Processing helix chain '6' and resid 174 through 193 Proline residue: 6 179 - end of helix removed outlier: 3.539A pdb=" N ARG 6 187 " --> pdb=" O LYS 6 183 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL 6 188 " --> pdb=" O GLY 6 184 " (cutoff:3.500A) Processing helix chain '6' and resid 406 through 411 removed outlier: 3.750A pdb=" N LEU 6 410 " --> pdb=" O ASP 6 406 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY 6 411 " --> pdb=" O VAL 6 407 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 406 through 411' Processing helix chain '6' and resid 500 through 509 removed outlier: 5.291A pdb=" N SER 6 509 " --> pdb=" O LEU 6 505 " (cutoff:3.500A) Processing helix chain '6' and resid 510 through 522 removed outlier: 3.759A pdb=" N ASP 6 522 " --> pdb=" O GLU 6 518 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 533 removed outlier: 3.716A pdb=" N ILE 6 533 " --> pdb=" O LEU 6 529 " (cutoff:3.500A) Processing helix chain '6' and resid 540 through 553 Processing helix chain '6' and resid 580 through 592 removed outlier: 4.224A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 604 through 610 Processing helix chain '6' and resid 626 through 632 removed outlier: 3.520A pdb=" N ASP 6 632 " --> pdb=" O LEU 6 628 " (cutoff:3.500A) Processing helix chain '6' and resid 645 through 659 removed outlier: 4.125A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN 6 658 " --> pdb=" O GLU 6 654 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 700 removed outlier: 5.212A pdb=" N ASN 6 700 " --> pdb=" O ARG 6 696 " (cutoff:3.500A) Processing helix chain '6' and resid 702 through 709 removed outlier: 3.814A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE 6 709 " --> pdb=" O ILE 6 705 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 737 removed outlier: 3.974A pdb=" N GLU 6 726 " --> pdb=" O LYS 6 722 " (cutoff:3.500A) Processing helix chain '6' and resid 747 through 761 removed outlier: 4.003A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE 6 761 " --> pdb=" O TYR 6 757 " (cutoff:3.500A) Processing helix chain '6' and resid 766 through 785 removed outlier: 3.901A pdb=" N VAL 6 774 " --> pdb=" O ARG 6 770 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU 6 775 " --> pdb=" O SER 6 771 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 815 removed outlier: 4.327A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 835 removed outlier: 3.791A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN 6 833 " --> pdb=" O ASP 6 829 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER 6 834 " --> pdb=" O LEU 6 830 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE 6 835 " --> pdb=" O LEU 6 831 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 27 removed outlier: 3.737A pdb=" N LEU 7 17 " --> pdb=" O ASP 7 13 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL 7 26 " --> pdb=" O THR 7 22 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 73 removed outlier: 3.857A pdb=" N ALA 7 65 " --> pdb=" O PRO 7 61 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET 7 66 " --> pdb=" O LYS 7 62 " (cutoff:3.500A) Processing helix chain '7' and resid 81 through 96 removed outlier: 3.620A pdb=" N ILE 7 85 " --> pdb=" O ASP 7 81 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY 7 96 " --> pdb=" O LYS 7 92 " (cutoff:3.500A) Processing helix chain '7' and resid 101 through 110 Processing helix chain '7' and resid 111 through 125 removed outlier: 4.508A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU 7 116 " --> pdb=" O HIS 7 112 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 155 removed outlier: 3.531A pdb=" N VAL 7 141 " --> pdb=" O ASP 7 137 " (cutoff:3.500A) Processing helix chain '7' and resid 193 through 199 removed outlier: 4.745A pdb=" N THR 7 197 " --> pdb=" O PRO 7 193 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG 7 198 " --> pdb=" O PRO 7 194 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG 7 199 " --> pdb=" O ASN 7 195 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 193 through 199' Processing helix chain '7' and resid 219 through 224 removed outlier: 3.781A pdb=" N LYS 7 223 " --> pdb=" O ALA 7 219 " (cutoff:3.500A) Proline residue: 7 224 - end of helix No H-bonds generated for 'chain '7' and resid 219 through 224' Processing helix chain '7' and resid 286 through 293 removed outlier: 3.506A pdb=" N GLN 7 293 " --> pdb=" O CYS 7 289 " (cutoff:3.500A) Processing helix chain '7' and resid 362 through 368 removed outlier: 3.676A pdb=" N LEU 7 366 " --> pdb=" O GLY 7 362 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS 7 367 " --> pdb=" O PHE 7 363 " (cutoff:3.500A) Processing helix chain '7' and resid 394 through 408 removed outlier: 3.678A pdb=" N ARG 7 400 " --> pdb=" O ASP 7 396 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 418 removed outlier: 3.584A pdb=" N ILE 7 418 " --> pdb=" O LEU 7 414 " (cutoff:3.500A) Processing helix chain '7' and resid 425 through 438 Processing helix chain '7' and resid 465 through 477 removed outlier: 3.763A pdb=" N LYS 7 475 " --> pdb=" O LYS 7 471 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE 7 476 " --> pdb=" O ALA 7 472 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER 7 477 " --> pdb=" O ILE 7 473 " (cutoff:3.500A) Processing helix chain '7' and resid 489 through 495 Processing helix chain '7' and resid 511 through 517 removed outlier: 3.781A pdb=" N ASP 7 517 " --> pdb=" O LEU 7 513 " (cutoff:3.500A) Processing helix chain '7' and resid 530 through 543 removed outlier: 3.840A pdb=" N THR 7 535 " --> pdb=" O GLU 7 531 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA 7 536 " --> pdb=" O SER 7 532 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE 7 537 " --> pdb=" O ASP 7 533 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N HIS 7 538 " --> pdb=" O ARG 7 534 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU 7 539 " --> pdb=" O THR 7 535 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL 7 540 " --> pdb=" O ALA 7 536 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU 7 542 " --> pdb=" O HIS 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 579 through 585 Processing helix chain '7' and resid 587 through 594 removed outlier: 3.928A pdb=" N ARG 7 593 " --> pdb=" O ALA 7 589 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 623 removed outlier: 3.571A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 648 removed outlier: 4.488A pdb=" N THR 7 647 " --> pdb=" O ALA 7 643 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS 7 648 " --> pdb=" O TYR 7 644 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 675 removed outlier: 3.535A pdb=" N TYR 7 659 " --> pdb=" O ALA 7 655 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE 7 665 " --> pdb=" O VAL 7 661 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG 7 666 " --> pdb=" O GLN 7 662 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 704 removed outlier: 4.340A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU 7 690 " --> pdb=" O PRO 7 686 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG 7 703 " --> pdb=" O LEU 7 699 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU 7 704 " --> pdb=" O ALA 7 700 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 729 removed outlier: 4.207A pdb=" N SER 7 723 " --> pdb=" O LEU 7 719 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU 7 725 " --> pdb=" O ARG 7 721 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER 7 726 " --> pdb=" O VAL 7 722 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR 7 728 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN 7 729 " --> pdb=" O GLU 7 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 71 through 96 Processing helix chain 'A' and resid 98 through 113 Proline residue: A 108 - end of helix removed outlier: 4.435A pdb=" N GLN A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 139 removed outlier: 3.538A pdb=" N LEU A 136 " --> pdb=" O PHE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 164 removed outlier: 5.626A pdb=" N THR A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.754A pdb=" N ASP A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 Processing helix chain 'A' and resid 193 through 206 removed outlier: 4.968A pdb=" N ALA A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.245A pdb=" N VAL A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 255 through 284 removed outlier: 3.763A pdb=" N LEU A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 4.319A pdb=" N GLU A 283 " --> pdb=" O PRO A 279 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 299 Proline residue: A 289 - end of helix removed outlier: 3.939A pdb=" N GLY A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 11 Processing helix chain 'B' and resid 17 through 32 Processing helix chain 'B' and resid 34 through 48 removed outlier: 5.281A pdb=" N GLN B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 79 Processing helix chain 'B' and resid 241 through 247 removed outlier: 4.012A pdb=" N TYR B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE B 247 " --> pdb=" O LYS B 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 241 through 247' Processing helix chain 'B' and resid 253 through 277 removed outlier: 3.552A pdb=" N ILE B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 removed outlier: 4.034A pdb=" N PHE B 283 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 279 through 284' Processing helix chain 'B' and resid 377 through 389 Processing helix chain 'B' and resid 410 through 423 Processing helix chain 'B' and resid 440 through 446 Processing helix chain 'B' and resid 460 through 476 removed outlier: 4.211A pdb=" N THR B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) Proline residue: B 471 - end of helix removed outlier: 3.722A pdb=" N THR B 475 " --> pdb=" O PRO B 471 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE B 476 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 548 through 555 removed outlier: 5.524A pdb=" N TYR B 555 " --> pdb=" O THR B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 616 through 621 removed outlier: 4.385A pdb=" N THR B 620 " --> pdb=" O TYR B 616 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU B 621 " --> pdb=" O LEU B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 621' Processing helix chain 'B' and resid 693 through 698 removed outlier: 3.521A pdb=" N ARG B 697 " --> pdb=" O ASN B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'C' and resid 3 through 24 removed outlier: 3.817A pdb=" N LEU C 11 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU C 12 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 13 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 61 Processing helix chain 'C' and resid 66 through 105 removed outlier: 3.587A pdb=" N ASN C 82 " --> pdb=" O CYS C 78 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 144 removed outlier: 3.671A pdb=" N LYS C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 203 removed outlier: 3.622A pdb=" N VAL C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ARG C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU C 199 " --> pdb=" O ASP C 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.918A pdb=" N ASN D 22 " --> pdb=" O PHE D 18 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU D 23 " --> pdb=" O ILE D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 removed outlier: 3.514A pdb=" N MET D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 83 removed outlier: 4.279A pdb=" N GLN D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER D 83 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 109 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 118 through 130 removed outlier: 4.233A pdb=" N ASN D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 161 removed outlier: 3.685A pdb=" N LEU D 141 " --> pdb=" O PRO D 137 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY D 143 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN D 146 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 201 Proline residue: D 183 - end of helix removed outlier: 3.551A pdb=" N GLU D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 200 " --> pdb=" O HIS D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 14 removed outlier: 4.090A pdb=" N GLY E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 32 removed outlier: 4.391A pdb=" N GLU E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 57 removed outlier: 4.458A pdb=" N ILE E 53 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 91 removed outlier: 3.575A pdb=" N ASP E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 Processing helix chain 'E' and resid 103 through 116 removed outlier: 3.629A pdb=" N ILE E 109 " --> pdb=" O PHE E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 140 removed outlier: 3.887A pdb=" N GLN E 133 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU E 134 " --> pdb=" O GLN E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 169 removed outlier: 4.212A pdb=" N PHE E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS E 168 " --> pdb=" O THR E 164 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU E 169 " --> pdb=" O PHE E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 193 removed outlier: 3.993A pdb=" N GLU E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE E 176 " --> pdb=" O MET E 172 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER E 183 " --> pdb=" O LYS E 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 73 removed outlier: 3.739A pdb=" N PHE F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER F 61 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS F 72 " --> pdb=" O LYS F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 104 removed outlier: 3.705A pdb=" N MET F 84 " --> pdb=" O PRO F 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS F 85 " --> pdb=" O HIS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 155 removed outlier: 3.845A pdb=" N VAL F 139 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE F 140 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS F 153 " --> pdb=" O SER F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 165 removed outlier: 5.674A pdb=" N GLU F 165 " --> pdb=" O LEU F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 175 removed outlier: 3.564A pdb=" N LEU F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 203 removed outlier: 3.652A pdb=" N LEU F 199 " --> pdb=" O ASN F 195 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS F 200 " --> pdb=" O ASP F 196 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TYR F 201 " --> pdb=" O SER F 197 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET F 202 " --> pdb=" O ILE F 198 " (cutoff:3.500A) Proline residue: F 203 - end of helix Processing helix chain 'F' and resid 278 through 289 removed outlier: 3.713A pdb=" N ILE F 282 " --> pdb=" O ARG F 278 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU F 285 " --> pdb=" O VAL F 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.915A pdb=" N ALA G 11 " --> pdb=" O GLN G 7 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 53 Processing helix chain 'G' and resid 63 through 74 removed outlier: 3.909A pdb=" N ARG G 69 " --> pdb=" O SER G 65 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN G 73 " --> pdb=" O ARG G 69 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU G 74 " --> pdb=" O HIS G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 4.842A pdb=" N GLU G 97 " --> pdb=" O GLU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 104 removed outlier: 4.096A pdb=" N TYR G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 146 through 151 Processing helix chain 'G' and resid 152 through 166 removed outlier: 3.867A pdb=" N ASP G 166 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 242 removed outlier: 4.857A pdb=" N SER G 242 " --> pdb=" O GLU G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 263 Processing helix chain 'G' and resid 266 through 282 removed outlier: 3.513A pdb=" N LEU G 272 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER G 279 " --> pdb=" O LEU G 275 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU G 280 " --> pdb=" O GLY G 276 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE G 282 " --> pdb=" O THR G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 303 Proline residue: G 293 - end of helix removed outlier: 3.543A pdb=" N GLN G 296 " --> pdb=" O TYR G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 341 removed outlier: 3.634A pdb=" N SER G 341 " --> pdb=" O SER G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 349 removed outlier: 3.769A pdb=" N ALA G 346 " --> pdb=" O ASN G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 367 removed outlier: 4.186A pdb=" N ARG G 358 " --> pdb=" O ASN G 354 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY G 367 " --> pdb=" O PHE G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 376 removed outlier: 3.568A pdb=" N GLN G 374 " --> pdb=" O LEU G 370 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU G 375 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N THR G 376 " --> pdb=" O THR G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 396 removed outlier: 4.730A pdb=" N GLY G 389 " --> pdb=" O LYS G 385 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE G 390 " --> pdb=" O ARG G 386 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP G 393 " --> pdb=" O GLY G 389 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS G 394 " --> pdb=" O ILE G 390 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN G 395 " --> pdb=" O ILE G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 435 removed outlier: 3.722A pdb=" N GLU G 426 " --> pdb=" O SER G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 485 removed outlier: 3.786A pdb=" N ASN G 476 " --> pdb=" O ARG G 472 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE G 477 " --> pdb=" O TRP G 473 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TRP G 478 " --> pdb=" O VAL G 474 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA G 483 " --> pdb=" O LEU G 479 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU G 484 " --> pdb=" O SER G 480 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP G 485 " --> pdb=" O TRP G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 517 removed outlier: 3.763A pdb=" N LEU G 492 " --> pdb=" O LYS G 488 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP G 501 " --> pdb=" O GLN G 497 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA G 512 " --> pdb=" O ASN G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 541 removed outlier: 4.101A pdb=" N ARG G 540 " --> pdb=" O LEU G 536 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 536 through 541' Processing helix chain 'G' and resid 542 through 561 removed outlier: 4.175A pdb=" N GLU G 560 " --> pdb=" O CYS G 556 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASP G 561 " --> pdb=" O ALA G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 616 removed outlier: 3.657A pdb=" N ALA G 608 " --> pdb=" O ASN G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 636 through 648 removed outlier: 5.186A pdb=" N GLY G 648 " --> pdb=" O LEU G 644 " (cutoff:3.500A) Processing helix chain 'P' and resid 327 through 338 removed outlier: 4.527A pdb=" N ASP P 336 " --> pdb=" O LEU P 332 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP P 337 " --> pdb=" O ALA P 333 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER P 338 " --> pdb=" O ASP P 334 " (cutoff:3.500A) Processing helix chain 'P' and resid 468 through 483 removed outlier: 3.645A pdb=" N ASN P 474 " --> pdb=" O ASN P 470 " (cutoff:3.500A) Processing helix chain 'P' and resid 842 through 858 removed outlier: 3.975A pdb=" N SER P 846 " --> pdb=" O ASN P 842 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA P 847 " --> pdb=" O PRO P 843 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N PHE P 848 " --> pdb=" O LYS P 844 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE P 849 " --> pdb=" O SER P 845 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP P 855 " --> pdb=" O SER P 851 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE P 856 " --> pdb=" O MET P 852 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 21 Processing helix chain 'S' and resid 24 through 34 Processing helix chain 'S' and resid 39 through 44 Processing helix chain 'S' and resid 64 through 76 Processing helix chain 'S' and resid 89 through 94 removed outlier: 3.991A pdb=" N ARG S 93 " --> pdb=" O PRO S 89 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP S 94 " --> pdb=" O PRO S 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 89 through 94' Processing helix chain 'S' and resid 113 through 119 removed outlier: 4.606A pdb=" N TYR S 117 " --> pdb=" O ASP S 113 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP S 118 " --> pdb=" O MET S 114 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ALA S 119 " --> pdb=" O ASP S 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 113 through 119' Processing helix chain 'S' and resid 130 through 150 removed outlier: 4.100A pdb=" N LYS S 135 " --> pdb=" O SER S 131 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N PHE S 136 " --> pdb=" O LYS S 132 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE S 137 " --> pdb=" O CYS S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 173 through 179 removed outlier: 3.776A pdb=" N LEU S 179 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 180 through 193 removed outlier: 5.029A pdb=" N VAL S 193 " --> pdb=" O ASP S 189 " (cutoff:3.500A) Processing helix chain 'S' and resid 210 through 225 Proline residue: S 222 - end of helix removed outlier: 4.572A pdb=" N VAL S 225 " --> pdb=" O LYS S 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 250 removed outlier: 4.508A pdb=" N LEU S 246 " --> pdb=" O ILE S 242 " (cutoff:3.500A) Proline residue: S 247 - end of helix removed outlier: 5.524A pdb=" N TYR S 250 " --> pdb=" O LEU S 246 " (cutoff:3.500A) Processing helix chain 'S' and resid 251 through 266 Proline residue: S 266 - end of helix Processing helix chain 'S' and resid 269 through 286 removed outlier: 3.835A pdb=" N ASP S 278 " --> pdb=" O TRP S 274 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS S 286 " --> pdb=" O THR S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 289 through 309 Processing helix chain 'S' and resid 314 through 319 removed outlier: 4.141A pdb=" N THR S 318 " --> pdb=" O ASP S 314 " (cutoff:3.500A) Processing helix chain 'S' and resid 353 through 365 Processing helix chain 'S' and resid 366 through 371 removed outlier: 3.824A pdb=" N THR S 370 " --> pdb=" O ASP S 366 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ALA S 371 " --> pdb=" O VAL S 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 366 through 371' Processing helix chain 'S' and resid 372 through 402 Processing helix chain 'S' and resid 226 through 233 Processing helix chain 'X' and resid 13 through 32 removed outlier: 3.561A pdb=" N ILE X 31 " --> pdb=" O LEU X 27 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLY X 32 " --> pdb=" O ALA X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 70 removed outlier: 3.813A pdb=" N VAL X 65 " --> pdb=" O TRP X 61 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP X 67 " --> pdb=" O LYS X 63 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 82 Processing helix chain 'X' and resid 86 through 106 Proline residue: X 90 - end of helix Processing helix chain 'X' and resid 117 through 137 removed outlier: 3.518A pdb=" N TYR X 121 " --> pdb=" O ASN X 117 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU X 131 " --> pdb=" O ASN X 127 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR X 136 " --> pdb=" O LEU X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 146 through 170 removed outlier: 5.137A pdb=" N GLY X 154 " --> pdb=" O ILE X 150 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLU X 155 " --> pdb=" O THR X 151 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS X 158 " --> pdb=" O GLY X 154 " (cutoff:3.500A) Processing helix chain 'X' and resid 173 through 188 removed outlier: 4.526A pdb=" N ARG X 177 " --> pdb=" O GLY X 173 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA X 178 " --> pdb=" O LYS X 174 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA X 179 " --> pdb=" O VAL X 175 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE X 180 " --> pdb=" O LEU X 176 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL X 186 " --> pdb=" O LEU X 182 " (cutoff:3.500A) Processing helix chain 'X' and resid 190 through 195 removed outlier: 3.683A pdb=" N ARG X 194 " --> pdb=" O ASP X 190 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N THR X 195 " --> pdb=" O ARG X 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 190 through 195' Processing helix chain 'X' and resid 196 through 215 removed outlier: 3.855A pdb=" N VAL X 201 " --> pdb=" O ARG X 197 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU X 202 " --> pdb=" O ASP X 198 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU X 206 " --> pdb=" O LEU X 202 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE X 209 " --> pdb=" O VAL X 205 " (cutoff:3.500A) Processing helix chain 'X' and resid 244 through 249 removed outlier: 3.514A pdb=" N ILE X 248 " --> pdb=" O SER X 244 " (cutoff:3.500A) Processing helix chain 'X' and resid 250 through 261 Processing helix chain 'X' and resid 262 through 273 removed outlier: 3.632A pdb=" N SER X 272 " --> pdb=" O THR X 268 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU X 273 " --> pdb=" O LEU X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 278 through 295 removed outlier: 4.245A pdb=" N ILE X 282 " --> pdb=" O ASP X 278 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE X 284 " --> pdb=" O ASP X 280 " (cutoff:3.500A) Proline residue: X 285 - end of helix removed outlier: 3.890A pdb=" N MET X 290 " --> pdb=" O LEU X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 304 removed outlier: 4.097A pdb=" N LEU X 302 " --> pdb=" O ASN X 298 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE X 303 " --> pdb=" O GLN X 299 " (cutoff:3.500A) Proline residue: X 304 - end of helix No H-bonds generated for 'chain 'X' and resid 298 through 304' Processing helix chain 'X' and resid 329 through 354 removed outlier: 3.818A pdb=" N HIS X 352 " --> pdb=" O ASN X 348 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR X 353 " --> pdb=" O VAL X 349 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER X 354 " --> pdb=" O ILE X 350 " (cutoff:3.500A) Processing helix chain 'X' and resid 378 through 384 removed outlier: 4.070A pdb=" N LEU X 382 " --> pdb=" O GLY X 378 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL X 383 " --> pdb=" O SER X 379 " (cutoff:3.500A) Processing helix chain 'X' and resid 385 through 396 removed outlier: 3.634A pdb=" N SER X 395 " --> pdb=" O LYS X 391 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS X 396 " --> pdb=" O LEU X 392 " (cutoff:3.500A) Processing helix chain 'X' and resid 430 through 448 Processing helix chain 'X' and resid 449 through 464 removed outlier: 4.397A pdb=" N THR X 462 " --> pdb=" O ASN X 458 " (cutoff:3.500A) Processing helix chain 'X' and resid 468 through 493 removed outlier: 3.575A pdb=" N ALA X 480 " --> pdb=" O LEU X 476 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP X 481 " --> pdb=" O LEU X 477 " (cutoff:3.500A) Processing helix chain 'X' and resid 498 through 503 removed outlier: 3.842A pdb=" N SER X 502 " --> pdb=" O ILE X 498 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU X 503 " --> pdb=" O LYS X 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 498 through 503' Processing helix chain 'X' and resid 506 through 524 removed outlier: 3.507A pdb=" N PHE X 510 " --> pdb=" O LYS X 506 " (cutoff:3.500A) Processing helix chain 'X' and resid 525 through 549 removed outlier: 3.674A pdb=" N ALA X 548 " --> pdb=" O SER X 544 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA X 549 " --> pdb=" O ARG X 545 " (cutoff:3.500A) Processing helix chain 'X' and resid 555 through 566 removed outlier: 4.031A pdb=" N PHE X 559 " --> pdb=" O THR X 555 " (cutoff:3.500A) Processing helix chain 'X' and resid 567 through 584 Proline residue: X 577 - end of helix removed outlier: 3.838A pdb=" N GLY X 580 " --> pdb=" O LEU X 576 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER X 581 " --> pdb=" O PRO X 577 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYS X 582 " --> pdb=" O LYS X 578 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR X 583 " --> pdb=" O ILE X 579 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER X 584 " --> pdb=" O GLY X 580 " (cutoff:3.500A) Processing helix chain 'X' and resid 585 through 606 removed outlier: 4.354A pdb=" N SER X 606 " --> pdb=" O LEU X 602 " (cutoff:3.500A) Processing helix chain 'X' and resid 658 through 668 removed outlier: 3.519A pdb=" N TYR X 666 " --> pdb=" O VAL X 662 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N THR X 668 " --> pdb=" O ALA X 664 " (cutoff:3.500A) Processing helix chain 'X' and resid 669 through 686 removed outlier: 4.621A pdb=" N ARG X 681 " --> pdb=" O ASN X 677 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE X 682 " --> pdb=" O PHE X 678 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ARG X 683 " --> pdb=" O LEU X 679 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLU X 684 " --> pdb=" O GLU X 680 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU X 685 " --> pdb=" O ARG X 681 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLU X 686 " --> pdb=" O PHE X 682 " (cutoff:3.500A) Processing helix chain 'X' and resid 687 through 702 removed outlier: 3.657A pdb=" N LYS X 691 " --> pdb=" O ASP X 687 " (cutoff:3.500A) Processing helix chain 'X' and resid 707 through 712 removed outlier: 4.061A pdb=" N PHE X 711 " --> pdb=" O GLN X 707 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ARG X 712 " --> pdb=" O ALA X 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 707 through 712' Processing helix chain 'X' and resid 713 through 724 removed outlier: 3.546A pdb=" N LEU X 718 " --> pdb=" O ASP X 714 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG X 720 " --> pdb=" O ILE X 716 " (cutoff:3.500A) Processing helix chain 'X' and resid 732 through 757 removed outlier: 4.500A pdb=" N LYS X 736 " --> pdb=" O SER X 732 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR X 737 " --> pdb=" O ARG X 733 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR X 744 " --> pdb=" O GLN X 740 " (cutoff:3.500A) Proline residue: X 757 - end of helix Processing helix chain 'X' and resid 758 through 766 removed outlier: 4.594A pdb=" N LEU X 764 " --> pdb=" O PHE X 760 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE X 765 " --> pdb=" O VAL X 761 " (cutoff:3.500A) Proline residue: X 766 - end of helix Processing helix chain 'X' and resid 773 through 779 Processing helix chain 'Y' and resid 55 through 61 Processing helix chain 'Y' and resid 64 through 76 removed outlier: 4.201A pdb=" N VAL Y 68 " --> pdb=" O GLY Y 64 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU Y 69 " --> pdb=" O LEU Y 65 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N HIS Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS Y 74 " --> pdb=" O LYS Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 103 removed outlier: 3.979A pdb=" N ILE Y 92 " --> pdb=" O LEU Y 88 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE Y 94 " --> pdb=" O ASN Y 90 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TYR Y 95 " --> pdb=" O ILE Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 107 through 122 removed outlier: 4.075A pdb=" N THR Y 117 " --> pdb=" O LYS Y 113 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL Y 118 " --> pdb=" O ILE Y 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 123 through 138 Processing helix chain 'J' and resid 1272 through 1278 Processing helix chain 'J' and resid 1322 through 1344 removed outlier: 3.576A pdb=" N GLN J1329 " --> pdb=" O GLN J1325 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY J1344 " --> pdb=" O LEU J1340 " (cutoff:3.500A) Processing helix chain 'J' and resid 1381 through 1397 removed outlier: 3.869A pdb=" N PHE J1396 " --> pdb=" O PHE J1392 " (cutoff:3.500A) Processing helix chain 'J' and resid 1398 through 1404 Processing helix chain 'J' and resid 1423 through 1435 Processing helix chain 'J' and resid 1436 through 1450 removed outlier: 4.057A pdb=" N TYR J1448 " --> pdb=" O VAL J1444 " (cutoff:3.500A) Processing helix chain 'J' and resid 1458 through 1468 removed outlier: 4.898A pdb=" N ASP J1464 " --> pdb=" O THR J1460 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE J1465 " --> pdb=" O SER J1461 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET J1466 " --> pdb=" O ILE J1462 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU J1467 " --> pdb=" O PHE J1463 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '2' and resid 240 through 244 Processing sheet with id= 2, first strand: chain '2' and resid 317 through 322 Processing sheet with id= 3, first strand: chain '2' and resid 385 through 392 removed outlier: 6.182A pdb=" N ARG 2 404 " --> pdb=" O GLU 2 392 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '2' and resid 539 through 544 Processing sheet with id= 5, first strand: chain '2' and resid 562 through 566 Processing sheet with id= 6, first strand: chain '2' and resid 627 through 632 removed outlier: 8.124A pdb=" N GLN 2 627 " --> pdb=" O ALA 2 642 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '3' and resid 94 through 98 Processing sheet with id= 8, first strand: chain '3' and resid 179 through 184 removed outlier: 5.392A pdb=" N ARG 3 291 " --> pdb=" O LEU 3 329 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '3' and resid 207 through 213 removed outlier: 4.054A pdb=" N ARG 3 208 " --> pdb=" O ALA 3 203 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL 3 200 " --> pdb=" O GLU 3 244 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '3' and resid 253 through 259 removed outlier: 5.628A pdb=" N ASP 3 279 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '3' and resid 428 through 432 removed outlier: 5.715A pdb=" N LEU 3 428 " --> pdb=" O ARG 3 467 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLY 3 468 " --> pdb=" O ARG 3 509 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE 3 403 " --> pdb=" O CYS 3 510 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL 3 512 " --> pdb=" O ILE 3 403 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '3' and resid 445 through 448 Processing sheet with id= 13, first strand: chain '4' and resid 239 through 244 removed outlier: 3.546A pdb=" N LEU 4 243 " --> pdb=" O ARG 4 304 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '4' and resid 325 through 330 Processing sheet with id= 15, first strand: chain '4' and resid 333 through 336 removed outlier: 3.843A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL 4 396 " --> pdb=" O THR 4 336 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '4' and resid 354 through 359 removed outlier: 4.545A pdb=" N HIS 4 354 " --> pdb=" O CYS 4 349 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE 4 346 " --> pdb=" O ILE 4 385 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '4' and resid 460 through 463 Processing sheet with id= 18, first strand: chain '4' and resid 587 through 592 removed outlier: 6.032A pdb=" N ARG 4 587 " --> pdb=" O GLY 4 626 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY 4 627 " --> pdb=" O ARG 4 668 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE 4 562 " --> pdb=" O SER 4 669 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE 4 671 " --> pdb=" O ILE 4 562 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '4' and resid 393 through 401 removed outlier: 6.515A pdb=" N ASP 4 393 " --> pdb=" O ASP 4 421 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N HIS 4 413 " --> pdb=" O GLU 4 401 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '4' and resid 652 through 657 removed outlier: 4.733A pdb=" N GLN 4 652 " --> pdb=" O ALA 4 667 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '5' and resid 59 through 63 Processing sheet with id= 22, first strand: chain '5' and resid 159 through 164 Processing sheet with id= 23, first strand: chain '5' and resid 172 through 176 removed outlier: 6.417A pdb=" N ASP 5 252 " --> pdb=" O ARG 5 280 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG 5 272 " --> pdb=" O GLU 5 260 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ASP 5 279 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '5' and resid 187 through 193 removed outlier: 3.906A pdb=" N HIS 5 188 " --> pdb=" O CYS 5 183 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '5' and resid 411 through 415 Processing sheet with id= 26, first strand: chain '5' and resid 435 through 440 Processing sheet with id= 27, first strand: chain '5' and resid 500 through 505 removed outlier: 5.057A pdb=" N GLN 5 500 " --> pdb=" O SER 5 515 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '6' and resid 149 through 153 Processing sheet with id= 29, first strand: chain '6' and resid 287 through 292 Processing sheet with id= 30, first strand: chain '6' and resid 308 through 311 removed outlier: 4.797A pdb=" N ALA 6 316 " --> pdb=" O CYS 6 311 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '6' and resid 355 through 362 removed outlier: 5.785A pdb=" N ASP 6 355 " --> pdb=" O GLY 6 383 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG 6 382 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '6' and resid 554 through 558 removed outlier: 9.859A pdb=" N THR 6 676 " --> pdb=" O GLY 6 567 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE 6 569 " --> pdb=" O THR 6 676 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE 6 678 " --> pdb=" O ILE 6 569 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY 6 575 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY 6 634 " --> pdb=" O ARG 6 675 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ARG 6 594 " --> pdb=" O ASN 6 633 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL 6 596 " --> pdb=" O ILE 6 635 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '6' and resid 570 through 575 Processing sheet with id= 34, first strand: chain '6' and resid 660 through 664 Processing sheet with id= 35, first strand: chain '7' and resid 76 through 80 Processing sheet with id= 36, first strand: chain '7' and resid 238 through 242 Processing sheet with id= 37, first strand: chain '7' and resid 246 through 249 removed outlier: 3.913A pdb=" N ARG 7 247 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLU 7 312 " --> pdb=" O SER 7 249 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ALA 7 309 " --> pdb=" O GLY 7 337 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY 7 337 " --> pdb=" O ALA 7 309 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '7' and resid 267 through 273 removed outlier: 3.702A pdb=" N TYR 7 267 " --> pdb=" O CYS 7 262 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL 7 269 " --> pdb=" O TYR 7 260 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU 7 256 " --> pdb=" O VAL 7 273 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain '7' and resid 479 through 484 removed outlier: 5.936A pdb=" N ARG 7 479 " --> pdb=" O ASN 7 518 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY 7 519 " --> pdb=" O ARG 7 560 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE 7 454 " --> pdb=" O THR 7 561 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE 7 563 " --> pdb=" O ILE 7 454 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '7' and resid 496 through 499 Processing sheet with id= 41, first strand: chain '7' and resid 544 through 549 removed outlier: 4.404A pdb=" N GLN 7 544 " --> pdb=" O ALA 7 559 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'A' and resid 223 through 227 removed outlier: 7.515A pdb=" N LYS A 223 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'B' and resid 204 through 207 removed outlier: 5.443A pdb=" N GLY B 663 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER B 664 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N CYS B 399 " --> pdb=" O SER B 664 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'B' and resid 236 through 239 removed outlier: 5.144A pdb=" N SER B 523 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'B' and resid 294 through 299 Processing sheet with id= 46, first strand: chain 'B' and resid 316 through 320 removed outlier: 5.335A pdb=" N LEU B 316 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG B 328 " --> pdb=" O THR B 320 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'B' and resid 340 through 343 Processing sheet with id= 48, first strand: chain 'B' and resid 579 through 582 removed outlier: 6.761A pdb=" N ARG B 579 " --> pdb=" O ILE B 607 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'B' and resid 680 through 684 removed outlier: 3.637A pdb=" N THR B 681 " --> pdb=" O LEU B 691 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 187 through 191 removed outlier: 4.605A pdb=" N SER C 187 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'F' and resid 255 through 261 removed outlier: 3.523A pdb=" N GLU F 265 " --> pdb=" O ILE F 260 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'F' and resid 274 through 277 removed outlier: 5.253A pdb=" N PHE F 229 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'G' and resid 1 through 4 removed outlier: 6.553A pdb=" N ILE G 139 " --> pdb=" O ARG G 118 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE G 120 " --> pdb=" O ILE G 139 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'G' and resid 105 through 109 removed outlier: 3.873A pdb=" N GLU G 113 " --> pdb=" O ASP G 108 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'G' and resid 317 through 323 Processing sheet with id= 56, first strand: chain 'G' and resid 525 through 530 removed outlier: 3.557A pdb=" N ILE G 572 " --> pdb=" O LEU G 530 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR G 578 " --> pdb=" O ASP G 573 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'S' and resid 48 through 51 removed outlier: 4.008A pdb=" N ALA S 55 " --> pdb=" O PHE S 51 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'S' and resid 107 through 112 removed outlier: 5.955A pdb=" N GLY S 166 " --> pdb=" O SER S 162 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASP S 156 " --> pdb=" O SER S 172 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TRP S 159 " --> pdb=" O ILE S 342 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL S 340 " --> pdb=" O PHE S 161 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'X' and resid 363 through 367 Processing sheet with id= 60, first strand: chain 'J' and resid 1283 through 1288 removed outlier: 4.610A pdb=" N LEU J1283 " --> pdb=" O PHE J1296 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS J1292 " --> pdb=" O CYS J1287 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'J' and resid 1304 through 1308 removed outlier: 7.268A pdb=" N TYR J1304 " --> pdb=" O LYS J1315 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU J1312 " --> pdb=" O PHE J1321 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN J1319 " --> pdb=" O CYS J1314 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'J' and resid 1355 through 1358 removed outlier: 4.822A pdb=" N ILE J1355 " --> pdb=" O CYS J1348 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL J1375 " --> pdb=" O ASP J1349 " (cutoff:3.500A) 2738 hydrogen bonds defined for protein. 8133 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 42.35 Time building geometry restraints manager: 70.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 58919 1.03 - 1.23: 2064 1.23 - 1.44: 23241 1.44 - 1.64: 34520 1.64 - 1.84: 401 Bond restraints: 119145 Sorted by residual: bond pdb=" O3A ANP 7 901 " pdb=" PB ANP 7 901 " ideal model delta sigma weight residual 1.700 1.541 0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" O3A ANP 41001 " pdb=" PB ANP 41001 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O3A ANP 31500 " pdb=" PB ANP 31500 " 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 21500 " pdb=" PB ANP 21500 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" N3B ANP 7 901 " pdb=" PG ANP 7 901 " ideal model delta sigma weight residual 1.795 1.671 0.124 2.00e-02 2.50e+03 3.84e+01 ... (remaining 119140 not shown) Histogram of bond angle deviations from ideal: 72.75 - 85.00: 3 85.00 - 97.26: 0 97.26 - 109.51: 82592 109.51 - 121.77: 111798 121.77 - 134.02: 21302 Bond angle restraints: 215695 Sorted by residual: angle pdb=" C VAL C 167 " pdb=" CA VAL C 167 " pdb=" HA VAL C 167 " ideal model delta sigma weight residual 109.00 72.75 36.25 3.00e+00 1.11e-01 1.46e+02 angle pdb=" N VAL C 167 " pdb=" CA VAL C 167 " pdb=" HA VAL C 167 " ideal model delta sigma weight residual 110.00 74.85 35.15 3.00e+00 1.11e-01 1.37e+02 angle pdb=" CB VAL C 167 " pdb=" CA VAL C 167 " pdb=" HA VAL C 167 " ideal model delta sigma weight residual 109.00 77.12 31.88 3.00e+00 1.11e-01 1.13e+02 angle pdb=" C ASP 7 627 " pdb=" N LEU 7 628 " pdb=" CA LEU 7 628 " ideal model delta sigma weight residual 121.54 132.96 -11.42 1.91e+00 2.74e-01 3.58e+01 angle pdb=" PB ANP 21500 " pdb=" N3B ANP 21500 " pdb=" PG ANP 21500 " ideal model delta sigma weight residual 126.95 109.29 17.66 3.00e+00 1.11e-01 3.46e+01 ... (remaining 215690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 52640 29.56 - 59.12: 1618 59.12 - 88.68: 267 88.68 - 118.23: 1 118.23 - 147.79: 2 Dihedral angle restraints: 54528 sinusoidal: 30091 harmonic: 24437 Sorted by residual: dihedral pdb=" CA ARG X 401 " pdb=" C ARG X 401 " pdb=" N ILE X 402 " pdb=" CA ILE X 402 " ideal model delta harmonic sigma weight residual -180.00 -148.39 -31.61 0 5.00e+00 4.00e-02 4.00e+01 dihedral pdb=" CA LEU 2 411 " pdb=" C LEU 2 411 " pdb=" N ALA 2 412 " pdb=" CA ALA 2 412 " ideal model delta harmonic sigma weight residual -180.00 -149.36 -30.64 0 5.00e+00 4.00e-02 3.75e+01 dihedral pdb=" CA ILE X 427 " pdb=" C ILE X 427 " pdb=" N PHE X 428 " pdb=" CA PHE X 428 " ideal model delta harmonic sigma weight residual -180.00 -149.78 -30.22 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 54525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 7672 0.058 - 0.117: 1373 0.117 - 0.175: 247 0.175 - 0.234: 5 0.234 - 0.292: 5 Chirality restraints: 9302 Sorted by residual: chirality pdb=" C3' ANP 31500 " pdb=" C2' ANP 31500 " pdb=" C4' ANP 31500 " pdb=" O3' ANP 31500 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C3' ANP 7 901 " pdb=" C2' ANP 7 901 " pdb=" C4' ANP 7 901 " pdb=" O3' ANP 7 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C3' ANP 21500 " pdb=" C2' ANP 21500 " pdb=" C4' ANP 21500 " pdb=" O3' ANP 21500 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 9299 not shown) Planarity restraints: 17068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP 7 627 " -0.037 2.00e-02 2.50e+03 7.44e-02 5.54e+01 pdb=" C ASP 7 627 " 0.129 2.00e-02 2.50e+03 pdb=" O ASP 7 627 " -0.051 2.00e-02 2.50e+03 pdb=" N LEU 7 628 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN 7 210 " 0.037 2.00e-02 2.50e+03 7.36e-02 5.41e+01 pdb=" C ASN 7 210 " -0.127 2.00e-02 2.50e+03 pdb=" O ASN 7 210 " 0.048 2.00e-02 2.50e+03 pdb=" N CYS 7 211 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS 6 737 " 0.037 2.00e-02 2.50e+03 7.16e-02 5.13e+01 pdb=" C LYS 6 737 " -0.124 2.00e-02 2.50e+03 pdb=" O LYS 6 737 " 0.046 2.00e-02 2.50e+03 pdb=" N ARG 6 738 " 0.041 2.00e-02 2.50e+03 ... (remaining 17065 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 7654 2.22 - 2.82: 246033 2.82 - 3.41: 304986 3.41 - 4.01: 398623 4.01 - 4.60: 622987 Nonbonded interactions: 1580283 Sorted by model distance: nonbonded pdb=" H VAL C 167 " pdb=" HA VAL C 167 " model vdw 1.629 1.816 nonbonded pdb=" H LEU X 768 " pdb=" OE1 GLN X 777 " model vdw 1.696 1.850 nonbonded pdb=" O PHE 3 345 " pdb="HD21 ASN 3 349 " model vdw 1.709 1.850 nonbonded pdb=" HG SER 3 438 " pdb=" OP1 DT Q 62 " model vdw 1.716 1.850 nonbonded pdb=" H GLN 3 417 " pdb=" O1A ANP 31500 " model vdw 1.717 1.850 ... (remaining 1580278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.270 Extract box with map and model: 7.570 Check model and map are aligned: 1.300 Set scattering table: 0.850 Process input model: 323.340 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.240 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:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 340.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 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 0.159 60127 Z= 0.352 Angle : 0.797 17.658 81489 Z= 0.425 Chirality : 0.047 0.292 9302 Planarity : 0.005 0.088 10217 Dihedral : 13.705 147.793 23020 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.10 % Favored : 97.88 % Rotamer: Outliers : 0.51 % Allowed : 2.41 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.52 (0.10), residues: 7043 helix: 0.96 (0.09), residues: 3274 sheet: -0.20 (0.16), residues: 907 loop : -0.02 (0.12), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP X 398 HIS 0.009 0.001 HIS 7 615 PHE 0.027 0.002 PHE X 293 TYR 0.034 0.002 TYR 4 558 ARG 0.006 0.001 ARG S 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1272 time to evaluate : 7.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 33 outliers final: 12 residues processed: 1294 average time/residue: 1.4095 time to fit residues: 3080.6099 Evaluate side-chains 758 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 746 time to evaluate : 7.096 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 1.6448 time to fit residues: 40.0978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 603 optimal weight: 50.0000 chunk 541 optimal weight: 4.9990 chunk 300 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 365 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 560 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 340 optimal weight: 1.9990 chunk 417 optimal weight: 9.9990 chunk 649 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 ASN A 213 HIS ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS F 186 HIS G 130 ASN ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 296 GLN ** G 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 ASN G 624 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 60127 Z= 0.365 Angle : 0.708 7.950 81489 Z= 0.394 Chirality : 0.041 0.251 9302 Planarity : 0.005 0.074 10217 Dihedral : 11.000 161.518 8531 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.75 % Favored : 97.23 % Rotamer: Outliers : 0.09 % Allowed : 1.68 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.25 (0.10), residues: 7043 helix: 0.89 (0.09), residues: 3372 sheet: -0.61 (0.15), residues: 943 loop : -0.31 (0.12), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP X 759 HIS 0.017 0.002 HIS 2 282 PHE 0.033 0.002 PHE X 291 TYR 0.047 0.002 TYR X 292 ARG 0.009 0.001 ARG 7 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 761 time to evaluate : 7.117 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 766 average time/residue: 1.3149 time to fit residues: 1702.9235 Evaluate side-chains 579 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 578 time to evaluate : 7.165 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.9398 time to fit residues: 10.5917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 360 optimal weight: 30.0000 chunk 201 optimal weight: 4.9990 chunk 540 optimal weight: 0.9980 chunk 442 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 chunk 650 optimal weight: 4.9990 chunk 702 optimal weight: 30.0000 chunk 579 optimal weight: 6.9990 chunk 645 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 521 optimal weight: 4.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 260 GLN ** 4 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 411 ASN 6 669 HIS 6 735 HIS 7 622 HIS ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 60127 Z= 0.210 Angle : 0.550 9.465 81489 Z= 0.305 Chirality : 0.039 0.228 9302 Planarity : 0.004 0.071 10217 Dihedral : 10.413 150.822 8531 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.03 % Allowed : 1.36 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.68 (0.10), residues: 7043 helix: 1.35 (0.09), residues: 3382 sheet: -0.46 (0.16), residues: 918 loop : -0.25 (0.12), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 119 HIS 0.011 0.001 HIS A 293 PHE 0.019 0.001 PHE X 293 TYR 0.017 0.001 TYR 6 828 ARG 0.020 0.000 ARG 3 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 703 time to evaluate : 7.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 2 outliers final: 0 residues processed: 704 average time/residue: 1.2506 time to fit residues: 1504.7631 Evaluate side-chains 550 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 7.164 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 642 optimal weight: 0.9990 chunk 489 optimal weight: 4.9990 chunk 337 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 310 optimal weight: 0.8980 chunk 436 optimal weight: 9.9990 chunk 652 optimal weight: 3.9990 chunk 691 optimal weight: 6.9990 chunk 341 optimal weight: 4.9990 chunk 618 optimal weight: 50.0000 chunk 186 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 248 HIS ** 2 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 551 GLN ** 4 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 518 ASN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN B 66 GLN D 139 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 HIS ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 60127 Z= 0.262 Angle : 0.563 7.188 81489 Z= 0.316 Chirality : 0.039 0.235 9302 Planarity : 0.004 0.060 10217 Dihedral : 10.276 156.375 8531 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.77 % 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: 0.47 (0.10), residues: 7043 helix: 1.24 (0.09), residues: 3368 sheet: -0.62 (0.16), residues: 919 loop : -0.40 (0.12), residues: 2756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 119 HIS 0.008 0.001 HIS D 167 PHE 0.018 0.001 PHE X 293 TYR 0.039 0.002 TYR 4 519 ARG 0.007 0.000 ARG G 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 635 time to evaluate : 7.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 635 average time/residue: 1.2743 time to fit residues: 1376.9160 Evaluate side-chains 503 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 6.375 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 575 optimal weight: 8.9990 chunk 392 optimal weight: 50.0000 chunk 10 optimal weight: 2.9990 chunk 514 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 589 optimal weight: 50.0000 chunk 477 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 352 optimal weight: 2.9990 chunk 620 optimal weight: 30.0000 chunk 174 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 433 ASN 2 508 HIS ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 499 GLN ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN C 122 ASN E 103 HIS G 22 HIS ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 60127 Z= 0.309 Angle : 0.607 12.614 81489 Z= 0.340 Chirality : 0.039 0.248 9302 Planarity : 0.004 0.060 10217 Dihedral : 10.293 154.690 8531 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.03 % Allowed : 1.40 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.77 % 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: 0.08 (0.10), residues: 7043 helix: 0.94 (0.09), residues: 3383 sheet: -0.74 (0.16), residues: 925 loop : -0.67 (0.12), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 190 HIS 0.010 0.001 HIS 4 465 PHE 0.031 0.002 PHE J1463 TYR 0.044 0.002 TYR 4 457 ARG 0.006 0.000 ARG G 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 582 time to evaluate : 7.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 584 average time/residue: 1.2683 time to fit residues: 1260.6422 Evaluate side-chains 484 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 482 time to evaluate : 7.144 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.9283 time to fit residues: 12.3291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 232 optimal weight: 10.0000 chunk 622 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 405 optimal weight: 40.0000 chunk 170 optimal weight: 5.9990 chunk 691 optimal weight: 6.9990 chunk 574 optimal weight: 5.9990 chunk 320 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 363 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 582 HIS ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 258 GLN ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 ASN X 416 ASN X 420 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 60127 Z= 0.307 Angle : 0.597 9.219 81489 Z= 0.337 Chirality : 0.039 0.238 9302 Planarity : 0.004 0.101 10217 Dihedral : 10.283 162.272 8531 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.83 % Favored : 95.16 % Rotamer: Outliers : 0.02 % Allowed : 1.30 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.77 % 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: -0.08 (0.10), residues: 7043 helix: 0.85 (0.09), residues: 3391 sheet: -0.86 (0.17), residues: 918 loop : -0.80 (0.12), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 190 HIS 0.012 0.001 HIS A 293 PHE 0.023 0.002 PHE X 460 TYR 0.022 0.002 TYR 5 298 ARG 0.009 0.001 ARG 4 668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 555 time to evaluate : 7.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 1 outliers final: 0 residues processed: 556 average time/residue: 1.2997 time to fit residues: 1227.2795 Evaluate side-chains 463 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 7.146 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 666 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 394 optimal weight: 10.0000 chunk 505 optimal weight: 2.9990 chunk 391 optimal weight: 8.9990 chunk 582 optimal weight: 30.0000 chunk 386 optimal weight: 0.9990 chunk 689 optimal weight: 5.9990 chunk 431 optimal weight: 50.0000 chunk 420 optimal weight: 50.0000 chunk 318 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 425 ASN 7 544 GLN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 374 GLN S 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 60127 Z= 0.227 Angle : 0.529 7.101 81489 Z= 0.297 Chirality : 0.038 0.242 9302 Planarity : 0.004 0.139 10217 Dihedral : 10.180 163.238 8531 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.77 % 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: 0.22 (0.10), residues: 7043 helix: 1.15 (0.09), residues: 3386 sheet: -0.81 (0.17), residues: 912 loop : -0.69 (0.12), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 398 HIS 0.008 0.001 HIS 4 354 PHE 0.020 0.001 PHE X 293 TYR 0.017 0.001 TYR 4 519 ARG 0.006 0.000 ARG 6 708 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 7.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 1.2791 time to fit residues: 1184.9555 Evaluate side-chains 462 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 462 time to evaluate : 7.172 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 426 optimal weight: 20.0000 chunk 275 optimal weight: 8.9990 chunk 411 optimal weight: 40.0000 chunk 207 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 438 optimal weight: 50.0000 chunk 469 optimal weight: 0.8980 chunk 340 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 541 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 856 GLN ** 5 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 500 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 60127 Z= 0.184 Angle : 0.503 8.240 81489 Z= 0.280 Chirality : 0.038 0.257 9302 Planarity : 0.004 0.057 10217 Dihedral : 10.062 166.069 8531 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.77 % 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: 0.57 (0.10), residues: 7043 helix: 1.46 (0.09), residues: 3393 sheet: -0.66 (0.17), residues: 911 loop : -0.55 (0.12), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 119 HIS 0.010 0.001 HIS A 293 PHE 0.023 0.001 PHE X 293 TYR 0.019 0.001 TYR 4 519 ARG 0.006 0.000 ARG 3 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 540 time to evaluate : 6.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 1.2821 time to fit residues: 1185.8378 Evaluate side-chains 453 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 7.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 626 optimal weight: 0.0980 chunk 660 optimal weight: 3.9990 chunk 602 optimal weight: 50.0000 chunk 642 optimal weight: 4.9990 chunk 386 optimal weight: 3.9990 chunk 279 optimal weight: 0.9990 chunk 504 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 580 optimal weight: 6.9990 chunk 607 optimal weight: 4.9990 chunk 639 optimal weight: 10.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 15 ASN 7 95 GLN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.6376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 60127 Z= 0.241 Angle : 0.539 8.303 81489 Z= 0.301 Chirality : 0.038 0.246 9302 Planarity : 0.004 0.073 10217 Dihedral : 10.057 169.388 8531 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.77 % 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: 0.40 (0.10), residues: 7043 helix: 1.32 (0.09), residues: 3406 sheet: -0.78 (0.17), residues: 907 loop : -0.63 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 190 HIS 0.008 0.001 HIS 4 354 PHE 0.027 0.001 PHE 4 545 TYR 0.016 0.001 TYR 5 298 ARG 0.013 0.000 ARG X 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 525 time to evaluate : 7.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 0 outliers final: 0 residues processed: 525 average time/residue: 1.3030 time to fit residues: 1171.3514 Evaluate side-chains 442 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 7.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 421 optimal weight: 50.0000 chunk 679 optimal weight: 5.9990 chunk 414 optimal weight: 30.0000 chunk 322 optimal weight: 0.0570 chunk 472 optimal weight: 1.9990 chunk 712 optimal weight: 20.0000 chunk 655 optimal weight: 0.9980 chunk 567 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 438 optimal weight: 50.0000 chunk 347 optimal weight: 0.4980 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 247 ASN 4 288 ASN ** 5 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 735 HIS ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 60127 Z= 0.136 Angle : 0.475 6.814 81489 Z= 0.261 Chirality : 0.038 0.238 9302 Planarity : 0.003 0.057 10217 Dihedral : 9.931 170.237 8531 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.77 % 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: 0.94 (0.10), residues: 7043 helix: 1.76 (0.09), residues: 3409 sheet: -0.60 (0.17), residues: 924 loop : -0.33 (0.12), residues: 2710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 119 HIS 0.010 0.001 HIS A 293 PHE 0.016 0.001 PHE X 291 TYR 0.013 0.001 TYR 2 227 ARG 0.011 0.000 ARG X 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14086 Ramachandran restraints generated. 7043 Oldfield, 0 Emsley, 7043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 7.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 1.3258 time to fit residues: 1204.8927 Evaluate side-chains 446 residues out of total 6482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 7.158 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 450 optimal weight: 5.9990 chunk 604 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 523 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 568 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 583 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 735 HIS ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN D 8 GLN ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.082388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.049326 restraints weight = 847269.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.051852 restraints weight = 325115.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.053395 restraints weight = 179306.981| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.6601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 60127 Z= 0.213 Angle : 0.512 7.148 81489 Z= 0.285 Chirality : 0.038 0.246 9302 Planarity : 0.004 0.057 10217 Dihedral : 9.943 170.682 8531 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.77 % 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: 0.75 (0.10), residues: 7043 helix: 1.61 (0.09), residues: 3410 sheet: -0.69 (0.17), residues: 904 loop : -0.44 (0.12), residues: 2729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 119 HIS 0.007 0.001 HIS 5 560 PHE 0.020 0.001 PHE X 444 TYR 0.016 0.001 TYR 4 580 ARG 0.007 0.000 ARG X 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23046.81 seconds wall clock time: 399 minutes 43.13 seconds (23983.13 seconds total)