Starting phenix.real_space_refine on Sun Feb 18 20:46:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmk_13537/02_2024/7pmk_13537_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmk_13537/02_2024/7pmk_13537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmk_13537/02_2024/7pmk_13537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmk_13537/02_2024/7pmk_13537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmk_13537/02_2024/7pmk_13537_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmk_13537/02_2024/7pmk_13537_updated.pdb" } resolution = 3.2 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= 0.048 sd= 1.677 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 78 5.49 5 Mg 3 5.21 5 S 330 5.16 5 C 47390 2.51 5 N 12782 2.21 5 O 14107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 74697 Number of models: 1 Model: "" Number of chains: 29 Chain: "2" Number of atoms: 5175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5175 Classifications: {'peptide': 655} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 26, 'TRANS': 628} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "3" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4759 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 578} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "4" Number of atoms: 4749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4749 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 573} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 5332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5332 Classifications: {'peptide': 673} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 647} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 5013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5013 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 613} Chain breaks: 5 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "7" Number of atoms: 4914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 4914 Classifications: {'peptide': 629} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 30, 'TRANS': 598} Chain breaks: 8 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1611 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 193} Chain breaks: 1 Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1609 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1381 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2004 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 230} Chain breaks: 2 Chain: "E" Number of atoms: 4569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4569 Classifications: {'peptide': 564} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 548} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 400} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3380 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3411 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 401} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 782 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain breaks: 1 Chain: "J" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 629 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 1 Chain: "K" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1120 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain breaks: 2 Chain: "L" Number of atoms: 3921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3921 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 457} Chain breaks: 2 Chain: "Q" Number of atoms: 6203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 6203 Classifications: {'peptide': 766} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 737} Chain breaks: 12 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4427 Classifications: {'peptide': 552} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 520} Chain breaks: 3 Chain: "X" Number of atoms: 5410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5410 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 20, 'TRANS': 644} Chain breaks: 7 Chain: "Y" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 791 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "2" 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: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" 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: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1347 SG CYS 2 341 105.269 140.740 86.000 1.00143.32 S ATOM 1370 SG CYS 2 344 108.619 141.502 83.903 1.00149.77 S ATOM 1528 SG CYS 2 364 107.839 143.208 87.039 1.00142.22 S ATOM 1549 SG CYS 2 367 106.246 144.278 84.087 1.00146.93 S ATOM 11385 SG CYS 4 349 87.728 173.869 95.937 1.00114.31 S ATOM 11406 SG CYS 4 352 87.978 177.370 96.832 1.00121.63 S ATOM 11553 SG CYS 4 371 85.340 176.075 94.348 1.00119.95 S ATOM 11595 SG CYS 4 376 89.100 176.580 93.341 1.00126.45 S ATOM 15820 SG CYS 5 183 89.867 128.363 72.751 1.00 91.04 S ATOM 15845 SG CYS 5 186 91.298 128.039 69.468 1.00 80.50 S ATOM 15992 SG CYS 5 211 93.677 128.878 72.204 1.00100.68 S ATOM 16020 SG CYS 5 236 91.158 131.480 71.015 1.00103.86 S ATOM 21384 SG CYS 6 311 105.131 157.575 94.704 1.00115.71 S ATOM 21406 SG CYS 6 314 107.940 160.004 94.276 1.00110.76 S ATOM 21563 SG CYS 6 333 104.311 161.389 94.440 1.00116.54 S ATOM 21597 SG CYS 6 338 105.514 159.614 91.471 1.00121.25 S ATOM 26557 SG CYS 7 262 64.375 165.169 80.081 1.00117.01 S ATOM 26580 SG CYS 7 265 62.603 166.376 77.097 1.00124.96 S ATOM 26730 SG CYS 7 284 64.669 162.919 77.337 1.00125.97 S ATOM 26767 SG CYS 7 289 66.353 166.215 76.828 1.00142.98 S ATOM 63043 SG CYS Q2108 99.340 52.181 184.801 1.00 74.93 S ATOM 63070 SG CYS Q2111 97.727 54.097 187.623 1.00 72.48 S ATOM 63219 SG CYS Q2130 100.458 55.669 185.155 1.00 70.26 S ATOM 63243 SG CYS Q2133 101.306 52.959 187.833 1.00 71.37 S ATOM 63506 SG CYS Q2164 82.167 73.349 146.247 1.00 65.02 S ATOM 63529 SG CYS Q2167 79.336 75.082 148.112 1.00 78.18 S ATOM 63630 SG CYS Q2179 78.807 72.210 145.322 1.00 68.73 S ATOM 63643 SG CYS Q2181 80.090 75.806 144.598 1.00 78.12 S Time building chain proxies: 30.43, per 1000 atoms: 0.41 Number of scatterers: 74697 At special positions: 0 Unit cell: (228.96, 231.08, 220.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 330 16.00 P 78 15.00 Mg 3 11.99 O 14107 8.00 N 12782 7.00 C 47390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 22.12 Conformation dependent library (CDL) restraints added in 9.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21502 " pdb="ZN ZN 21502 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 21502 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 21502 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 21502 " - pdb=" SG CYS 2 341 " pdb=" ZN 41001 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41001 " - 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 ZN 51502 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 51502 " - pdb=" SG CYS 5 183 " pdb=" ZN 61101 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 333 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 311 " pdb=" ZN 7 901 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 7 901 " - pdb=" SG CYS 7 289 " pdb=" ZN Q2301 " pdb="ZN ZN Q2301 " - pdb=" SG CYS Q2108 " pdb="ZN ZN Q2301 " - pdb=" SG CYS Q2133 " pdb="ZN ZN Q2301 " - pdb=" SG CYS Q2111 " pdb="ZN ZN Q2301 " - pdb=" SG CYS Q2130 " pdb=" ZN Q2302 " pdb="ZN ZN Q2302 " - pdb=" SG CYS Q2164 " pdb="ZN ZN Q2302 " - pdb=" SG CYS Q2181 " pdb="ZN ZN Q2302 " - pdb=" SG CYS Q2167 " pdb="ZN ZN Q2302 " - pdb=" SG CYS Q2179 " Number of angles added : 42 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17450 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 362 helices and 87 sheets defined 42.6% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.19 Creating SS restraints... Processing helix chain '2' and resid 183 through 187 Processing helix chain '2' and resid 194 through 198 Processing helix chain '2' and resid 201 through 217 Processing helix chain '2' and resid 226 through 236 Processing helix chain '2' and resid 246 through 250 Processing helix chain '2' and resid 254 through 262 Processing helix chain '2' and resid 264 through 282 removed outlier: 3.548A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 288 No H-bonds generated for 'chain '2' and resid 286 through 288' Processing helix chain '2' and resid 306 through 308 No H-bonds generated for 'chain '2' and resid 306 through 308' Processing helix chain '2' and resid 311 through 313 No H-bonds generated for 'chain '2' and resid 311 through 313' Processing helix chain '2' and resid 412 through 414 No H-bonds generated for 'chain '2' and resid 412 through 414' Processing helix chain '2' and resid 436 through 442 Processing helix chain '2' and resid 478 through 489 removed outlier: 3.779A pdb=" N ARG 2 489 " --> pdb=" O ARG 2 485 " (cutoff:3.500A) Processing helix chain '2' and resid 493 through 500 Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 549 through 559 Processing helix chain '2' and resid 568 through 570 No H-bonds generated for 'chain '2' and resid 568 through 570' Processing helix chain '2' and resid 573 through 576 No H-bonds generated for 'chain '2' and resid 573 through 576' Processing helix chain '2' and resid 595 through 598 No H-bonds generated for 'chain '2' and resid 595 through 598' Processing helix chain '2' and resid 609 through 611 No H-bonds generated for 'chain '2' and resid 609 through 611' Processing helix chain '2' and resid 614 through 625 removed outlier: 3.905A pdb=" N SER 2 619 " --> pdb=" O GLN 2 615 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE 2 620 " --> pdb=" O ASP 2 616 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N HIS 2 621 " --> pdb=" O ARG 2 617 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU 2 622 " --> pdb=" O THR 2 618 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ALA 2 623 " --> pdb=" O SER 2 619 " (cutoff:3.500A) Processing helix chain '2' and resid 653 through 655 No H-bonds generated for 'chain '2' and resid 653 through 655' Processing helix chain '2' and resid 663 through 666 No H-bonds generated for 'chain '2' and resid 663 through 666' Processing helix chain '2' and resid 671 through 676 removed outlier: 3.685A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) Processing helix chain '2' and resid 689 through 705 Processing helix chain '2' and resid 740 through 754 removed outlier: 3.957A pdb=" N GLU 2 754 " --> pdb=" O LYS 2 750 " (cutoff:3.500A) Processing helix chain '2' and resid 760 through 773 removed outlier: 3.636A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 783 through 798 Processing helix chain '2' and resid 807 through 823 removed outlier: 3.678A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) Processing helix chain '2' and resid 831 through 848 removed outlier: 3.543A pdb=" N ALA 2 848 " --> pdb=" O SER 2 844 " (cutoff:3.500A) Processing helix chain '2' and resid 851 through 865 removed outlier: 4.618A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE 2 863 " --> pdb=" O ARG 2 859 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR 2 864 " --> pdb=" O SER 2 860 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR 2 865 " --> pdb=" O PHE 2 861 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 34 removed outlier: 4.443A pdb=" N GLY 3 22 " --> pdb=" O ASP 3 18 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP 3 23 " --> pdb=" O ALA 3 19 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 54 Processing helix chain '3' and resid 100 through 106 Processing helix chain '3' and resid 108 through 116 Processing helix chain '3' and resid 118 through 135 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 162 through 164 No H-bonds generated for 'chain '3' and resid 162 through 164' Processing helix chain '3' and resid 173 through 175 No H-bonds generated for 'chain '3' and resid 173 through 175' Processing helix chain '3' and resid 280 through 282 No H-bonds generated for 'chain '3' and resid 280 through 282' Processing helix chain '3' and resid 344 through 355 Processing helix chain '3' and resid 359 through 366 Processing helix chain '3' and resid 375 through 385 Processing helix chain '3' and resid 394 through 396 No H-bonds generated for 'chain '3' and resid 394 through 396' Processing helix chain '3' and resid 415 through 425 Processing helix chain '3' and resid 439 through 442 No H-bonds generated for 'chain '3' and resid 439 through 442' Processing helix chain '3' and resid 461 through 464 No H-bonds generated for 'chain '3' and resid 461 through 464' Processing helix chain '3' and resid 475 through 477 No H-bonds generated for 'chain '3' and resid 475 through 477' Processing helix chain '3' and resid 480 through 485 removed outlier: 4.103A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) Processing helix chain '3' and resid 487 through 492 Processing helix chain '3' and resid 529 through 532 No H-bonds generated for 'chain '3' and resid 529 through 532' Processing helix chain '3' and resid 537 through 542 removed outlier: 4.870A pdb=" N ARG 3 542 " --> pdb=" O SER 3 538 " (cutoff:3.500A) Processing helix chain '3' and resid 555 through 569 Processing helix chain '3' and resid 653 through 666 Processing helix chain '3' and resid 673 through 687 removed outlier: 3.886A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 699 through 715 removed outlier: 3.559A pdb=" N GLU 3 703 " --> pdb=" O ARG 3 700 " (cutoff:3.500A) Processing helix chain '3' and resid 723 through 738 Processing helix chain '4' and resid 187 through 198 removed outlier: 3.798A pdb=" N PHE 4 197 " --> pdb=" O ASN 4 193 " (cutoff:3.500A) Processing helix chain '4' and resid 203 through 209 Processing helix chain '4' and resid 213 through 215 No H-bonds generated for 'chain '4' and resid 213 through 215' Processing helix chain '4' and resid 218 through 221 No H-bonds generated for 'chain '4' and resid 218 through 221' Processing helix chain '4' and resid 225 through 235 Processing helix chain '4' and resid 245 through 249 Processing helix chain '4' and resid 252 through 263 removed outlier: 3.818A pdb=" N GLU 4 255 " --> pdb=" O LYS 4 252 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP 4 256 " --> pdb=" O GLN 4 253 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN 4 263 " --> pdb=" O GLN 4 260 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 286 removed outlier: 3.623A pdb=" N ILE 4 284 " --> pdb=" O MET 4 280 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL 4 285 " --> pdb=" O VAL 4 281 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 298 Processing helix chain '4' and resid 314 through 316 No H-bonds generated for 'chain '4' and resid 314 through 316' Processing helix chain '4' and resid 319 through 321 No H-bonds generated for 'chain '4' and resid 319 through 321' Processing helix chain '4' and resid 386 through 388 No H-bonds generated for 'chain '4' and resid 386 through 388' Processing helix chain '4' and resid 421 through 423 No H-bonds generated for 'chain '4' and resid 421 through 423' Processing helix chain '4' and resid 506 through 514 Processing helix chain '4' and resid 518 through 526 Processing helix chain '4' and resid 534 through 545 Processing helix chain '4' and resid 574 through 584 Processing helix chain '4' and resid 620 through 623 No H-bonds generated for 'chain '4' and resid 620 through 623' Processing helix chain '4' and resid 634 through 636 No H-bonds generated for 'chain '4' and resid 634 through 636' Processing helix chain '4' and resid 639 through 650 removed outlier: 4.251A pdb=" N HIS 4 646 " --> pdb=" O ARG 4 642 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 688 through 691 No H-bonds generated for 'chain '4' and resid 688 through 691' Processing helix chain '4' and resid 696 through 701 removed outlier: 3.813A pdb=" N ARG 4 701 " --> pdb=" O PRO 4 697 " (cutoff:3.500A) Processing helix chain '4' and resid 714 through 728 removed outlier: 4.667A pdb=" N GLU 4 719 " --> pdb=" O LYS 4 715 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR 4 728 " --> pdb=" O LEU 4 724 " (cutoff:3.500A) Processing helix chain '4' and resid 746 through 757 Processing helix chain '4' and resid 764 through 779 removed outlier: 3.796A pdb=" N THR 4 768 " --> pdb=" O GLU 4 764 " (cutoff:3.500A) Processing helix chain '4' and resid 795 through 813 removed outlier: 4.695A pdb=" N LYS 4 812 " --> pdb=" O HIS 4 808 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU 4 813 " --> pdb=" O ALA 4 809 " (cutoff:3.500A) Processing helix chain '4' and resid 819 through 833 Processing helix chain '5' and resid 21 through 37 Processing helix chain '5' and resid 45 through 55 Processing helix chain '5' and resid 65 through 71 Processing helix chain '5' and resid 73 through 81 Processing helix chain '5' and resid 83 through 102 Proline residue: 5 88 - end of helix Processing helix chain '5' and resid 153 through 155 No H-bonds generated for 'chain '5' and resid 153 through 155' Processing helix chain '5' and resid 262 through 264 No H-bonds generated for 'chain '5' and resid 262 through 264' Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '5' and resid 351 through 361 Processing helix chain '5' and resid 366 through 373 Processing helix chain '5' and resid 382 through 393 Processing helix chain '5' and resid 422 through 432 Processing helix chain '5' and resid 441 through 443 No H-bonds generated for 'chain '5' and resid 441 through 443' Processing helix chain '5' and resid 446 through 449 No H-bonds generated for 'chain '5' and resid 446 through 449' Processing helix chain '5' and resid 468 through 471 No H-bonds generated for 'chain '5' and resid 468 through 471' Processing helix chain '5' and resid 482 through 484 No H-bonds generated for 'chain '5' and resid 482 through 484' Processing helix chain '5' and resid 487 through 498 removed outlier: 3.636A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE 5 493 " --> pdb=" O ASP 5 489 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS 5 494 " --> pdb=" O ARG 5 490 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLU 5 495 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA 5 496 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) Processing helix chain '5' and resid 536 through 539 No H-bonds generated for 'chain '5' and resid 536 through 539' Processing helix chain '5' and resid 544 through 549 removed outlier: 3.687A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) Processing helix chain '5' and resid 562 through 576 Processing helix chain '5' and resid 579 through 589 removed outlier: 3.559A pdb=" N ASN 5 585 " --> pdb=" O ASN 5 581 " (cutoff:3.500A) Processing helix chain '5' and resid 596 through 609 Processing helix chain '5' and resid 616 through 639 Processing helix chain '5' and resid 650 through 666 Processing helix chain '5' and resid 674 through 692 removed outlier: 4.075A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) Processing helix chain '5' and resid 711 through 721 removed outlier: 3.652A pdb=" N GLN 5 716 " --> pdb=" O ARG 5 712 " (cutoff:3.500A) Processing helix chain '5' and resid 730 through 739 Processing helix chain '5' and resid 746 through 757 removed outlier: 3.575A pdb=" N ASP 5 749 " --> pdb=" O LEU 5 746 " (cutoff:3.500A) Processing helix chain '6' and resid 106 through 121 Processing helix chain '6' and resid 135 through 145 Processing helix chain '6' and resid 155 through 172 removed outlier: 5.177A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASN 6 163 " --> pdb=" O SER 6 159 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY 6 164 " --> pdb=" O MET 6 160 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA 6 165 " --> pdb=" O ARG 6 161 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU 6 166 " --> pdb=" O GLU 6 162 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA 6 167 " --> pdb=" O ASN 6 163 " (cutoff:3.500A) Processing helix chain '6' and resid 174 through 197 Proline residue: 6 179 - end of helix Proline residue: 6 194 - end of helix removed outlier: 4.342A pdb=" N LEU 6 197 " --> pdb=" O ALA 6 193 " (cutoff:3.500A) Processing helix chain '6' and resid 276 through 278 No H-bonds generated for 'chain '6' and resid 276 through 278' Processing helix chain '6' and resid 281 through 283 No H-bonds generated for 'chain '6' and resid 281 through 283' Processing helix chain '6' and resid 383 through 385 No H-bonds generated for 'chain '6' and resid 383 through 385' Processing helix chain '6' and resid 501 through 507 removed outlier: 4.379A pdb=" N SER 6 507 " --> pdb=" O VAL 6 503 " (cutoff:3.500A) Processing helix chain '6' and resid 510 through 520 Processing helix chain '6' and resid 525 through 532 Processing helix chain '6' and resid 541 through 551 Processing helix chain '6' and resid 582 through 591 Processing helix chain '6' and resid 605 through 608 No H-bonds generated for 'chain '6' and resid 605 through 608' Processing helix chain '6' and resid 627 through 630 No H-bonds generated for 'chain '6' and resid 627 through 630' Processing helix chain '6' and resid 641 through 643 No H-bonds generated for 'chain '6' and resid 641 through 643' Processing helix chain '6' and resid 646 through 657 removed outlier: 3.919A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE 6 652 " --> pdb=" O ASP 6 648 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N HIS 6 653 " --> pdb=" O GLN 6 649 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU 6 654 " --> pdb=" O VAL 6 650 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU 6 657 " --> pdb=" O HIS 6 653 " (cutoff:3.500A) Processing helix chain '6' and resid 703 through 706 No H-bonds generated for 'chain '6' and resid 703 through 706' Processing helix chain '6' and resid 721 through 734 removed outlier: 3.860A pdb=" N GLU 6 726 " --> pdb=" O LYS 6 722 " (cutoff:3.500A) Processing helix chain '6' and resid 748 through 760 removed outlier: 3.665A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) Processing helix chain '6' and resid 767 through 784 removed outlier: 3.618A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 813 Processing helix chain '6' and resid 821 through 837 removed outlier: 4.381A pdb=" N SER 6 834 " --> pdb=" O LEU 6 830 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG 6 837 " --> pdb=" O GLN 6 833 " (cutoff:3.500A) Processing helix chain '7' and resid 14 through 27 Processing helix chain '7' and resid 31 through 33 No H-bonds generated for 'chain '7' and resid 31 through 33' Processing helix chain '7' and resid 62 through 71 Processing helix chain '7' and resid 82 through 94 Processing helix chain '7' and resid 102 through 108 Processing helix chain '7' and resid 110 through 124 removed outlier: 3.831A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 134 through 136 No H-bonds generated for 'chain '7' and resid 134 through 136' Processing helix chain '7' and resid 138 through 154 Processing helix chain '7' and resid 194 through 197 No H-bonds generated for 'chain '7' and resid 194 through 197' Processing helix chain '7' and resid 227 through 229 No H-bonds generated for 'chain '7' and resid 227 through 229' Processing helix chain '7' and resid 232 through 234 No H-bonds generated for 'chain '7' and resid 232 through 234' Processing helix chain '7' and resid 287 through 290 No H-bonds generated for 'chain '7' and resid 287 through 290' Processing helix chain '7' and resid 337 through 339 No H-bonds generated for 'chain '7' and resid 337 through 339' Processing helix chain '7' and resid 397 through 407 removed outlier: 5.073A pdb=" N MET 7 402 " --> pdb=" O GLU 7 398 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) Processing helix chain '7' and resid 410 through 417 Processing helix chain '7' and resid 426 through 437 removed outlier: 3.822A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU 7 435 " --> pdb=" O ALA 7 431 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU 7 436 " --> pdb=" O LEU 7 432 " (cutoff:3.500A) Processing helix chain '7' and resid 462 through 464 No H-bonds generated for 'chain '7' and resid 462 through 464' Processing helix chain '7' and resid 467 through 476 Processing helix chain '7' and resid 512 through 515 No H-bonds generated for 'chain '7' and resid 512 through 515' Processing helix chain '7' and resid 526 through 528 No H-bonds generated for 'chain '7' and resid 526 through 528' Processing helix chain '7' and resid 531 through 543 Processing helix chain '7' and resid 580 through 583 No H-bonds generated for 'chain '7' and resid 580 through 583' Processing helix chain '7' and resid 588 through 593 removed outlier: 3.779A pdb=" N ARG 7 593 " --> pdb=" O ALA 7 589 " (cutoff:3.500A) Processing helix chain '7' and resid 608 through 622 Processing helix chain '7' and resid 635 through 647 removed outlier: 3.630A pdb=" N GLU 7 640 " --> pdb=" O SER 7 636 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR 7 641 " --> pdb=" O LYS 7 637 " (cutoff:3.500A) Processing helix chain '7' and resid 654 through 672 removed outlier: 3.723A pdb=" N ASP 7 670 " --> pdb=" O ARG 7 666 " (cutoff:3.500A) Processing helix chain '7' and resid 686 through 702 Processing helix chain '7' and resid 710 through 727 Processing helix chain 'A' and resid 4 through 21 Processing helix chain 'A' and resid 34 through 57 Processing helix chain 'A' and resid 67 through 103 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 125 through 142 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.549A pdb=" N ASN B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 73 through 81 Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 138 through 162 removed outlier: 3.733A pdb=" N LYS B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 199 Proline residue: B 183 - end of helix removed outlier: 4.672A pdb=" N GLU B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 Processing helix chain 'C' and resid 27 through 31 Processing helix chain 'C' and resid 48 through 54 removed outlier: 4.556A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 97 through 100 No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.836A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 168 removed outlier: 3.660A pdb=" N PHE C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 192 Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 56 through 72 removed outlier: 3.549A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 106 Processing helix chain 'D' and resid 124 through 153 Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 171 through 174 No H-bonds generated for 'chain 'D' and resid 171 through 174' Processing helix chain 'D' and resid 177 through 197 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 280 through 287 removed outlier: 5.458A pdb=" N ASP D 284 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 19 Processing helix chain 'E' and resid 36 through 51 Processing helix chain 'E' and resid 64 through 73 removed outlier: 3.634A pdb=" N GLN E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 95 No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 100 through 103 No H-bonds generated for 'chain 'E' and resid 100 through 103' Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 224 through 240 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 267 through 280 removed outlier: 4.093A pdb=" N LEU E 280 " --> pdb=" O GLY E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 302 Proline residue: E 293 - end of helix Processing helix chain 'E' and resid 334 through 339 Processing helix chain 'E' and resid 342 through 348 Processing helix chain 'E' and resid 353 through 365 Processing helix chain 'E' and resid 370 through 373 No H-bonds generated for 'chain 'E' and resid 370 through 373' Processing helix chain 'E' and resid 382 through 395 removed outlier: 5.109A pdb=" N GLY E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 404 No H-bonds generated for 'chain 'E' and resid 402 through 404' Processing helix chain 'E' and resid 421 through 434 Processing helix chain 'E' and resid 462 through 484 removed outlier: 4.285A pdb=" N TRP E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 516 removed outlier: 3.707A pdb=" N VAL E 489 " --> pdb=" O ASP E 486 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLU E 490 " --> pdb=" O ARG E 487 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU E 515 " --> pdb=" O ALA E 512 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS E 516 " --> pdb=" O ILE E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 557 Processing helix chain 'E' and resid 605 through 615 Processing helix chain 'E' and resid 634 through 646 removed outlier: 4.383A pdb=" N SER E 638 " --> pdb=" O GLU E 635 " (cutoff:3.500A) Proline residue: E 639 - end of helix Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 724 through 731 Processing helix chain 'F' and resid 783 through 790 Processing helix chain 'F' and resid 819 through 843 Processing helix chain 'F' and resid 851 through 875 removed outlier: 3.595A pdb=" N SER F 872 " --> pdb=" O ARG F 868 " (cutoff:3.500A) Processing helix chain 'F' and resid 879 through 888 removed outlier: 3.950A pdb=" N GLU F 888 " --> pdb=" O SER F 884 " (cutoff:3.500A) Processing helix chain 'F' and resid 892 through 904 removed outlier: 4.300A pdb=" N ALA F 897 " --> pdb=" O ARG F 893 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 898 " --> pdb=" O ALA F 894 " (cutoff:3.500A) Processing helix chain 'F' and resid 908 through 922 Processing helix chain 'G' and resid 671 through 677 removed outlier: 4.068A pdb=" N TYR G 676 " --> pdb=" O ALA G 672 " (cutoff:3.500A) Processing helix chain 'G' and resid 713 through 715 No H-bonds generated for 'chain 'G' and resid 713 through 715' Processing helix chain 'G' and resid 724 through 731 Processing helix chain 'G' and resid 783 through 789 Processing helix chain 'G' and resid 819 through 843 Processing helix chain 'G' and resid 851 through 875 removed outlier: 3.575A pdb=" N ALA G 856 " --> pdb=" O ASN G 852 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG G 868 " --> pdb=" O LYS G 864 " (cutoff:3.500A) Processing helix chain 'G' and resid 879 through 887 Processing helix chain 'G' and resid 892 through 904 Processing helix chain 'G' and resid 908 through 922 Processing helix chain 'H' and resid 507 through 509 No H-bonds generated for 'chain 'H' and resid 507 through 509' Processing helix chain 'H' and resid 520 through 522 No H-bonds generated for 'chain 'H' and resid 520 through 522' Processing helix chain 'H' and resid 671 through 679 Processing helix chain 'H' and resid 713 through 715 No H-bonds generated for 'chain 'H' and resid 713 through 715' Processing helix chain 'H' and resid 724 through 731 Processing helix chain 'H' and resid 783 through 789 removed outlier: 3.930A pdb=" N GLU H 788 " --> pdb=" O SER H 784 " (cutoff:3.500A) Processing helix chain 'H' and resid 819 through 843 Processing helix chain 'H' and resid 851 through 876 removed outlier: 3.516A pdb=" N ASP H 876 " --> pdb=" O SER H 872 " (cutoff:3.500A) Processing helix chain 'H' and resid 879 through 888 Processing helix chain 'H' and resid 892 through 904 Processing helix chain 'H' and resid 908 through 922 Processing helix chain 'K' and resid 20 through 25 Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 84 through 96 Processing helix chain 'K' and resid 118 through 123 removed outlier: 3.782A pdb=" N GLU K 122 " --> pdb=" O SER K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 136 Processing helix chain 'K' and resid 144 through 158 Processing helix chain 'K' and resid 163 through 169 Processing helix chain 'K' and resid 178 through 187 Processing helix chain 'K' and resid 189 through 191 No H-bonds generated for 'chain 'K' and resid 189 through 191' Processing helix chain 'L' and resid 214 through 221 removed outlier: 4.063A pdb=" N GLN L 220 " --> pdb=" O ILE L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 233 removed outlier: 4.148A pdb=" N LEU L 232 " --> pdb=" O VAL L 228 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL L 233 " --> pdb=" O THR L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 242 Processing helix chain 'L' and resid 245 through 247 No H-bonds generated for 'chain 'L' and resid 245 through 247' Processing helix chain 'L' and resid 258 through 271 Processing helix chain 'L' and resid 291 through 304 removed outlier: 4.121A pdb=" N LEU L 295 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG L 296 " --> pdb=" O SER L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 323 through 333 Processing helix chain 'L' and resid 336 through 339 Processing helix chain 'L' and resid 356 through 363 removed outlier: 3.617A pdb=" N LEU L 361 " --> pdb=" O GLU L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 443 through 448 Processing helix chain 'L' and resid 469 through 472 No H-bonds generated for 'chain 'L' and resid 469 through 472' Processing helix chain 'L' and resid 476 through 479 Processing helix chain 'L' and resid 496 through 505 removed outlier: 3.567A pdb=" N PHE L 505 " --> pdb=" O GLN L 501 " (cutoff:3.500A) Processing helix chain 'L' and resid 546 through 550 Processing helix chain 'L' and resid 565 through 573 Processing helix chain 'L' and resid 603 through 605 No H-bonds generated for 'chain 'L' and resid 603 through 605' Processing helix chain 'L' and resid 609 through 615 Processing helix chain 'L' and resid 632 through 640 removed outlier: 3.729A pdb=" N LYS L 636 " --> pdb=" O ASP L 632 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER L 637 " --> pdb=" O SER L 633 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE L 638 " --> pdb=" O THR L 634 " (cutoff:3.500A) Processing helix chain 'L' and resid 642 through 644 No H-bonds generated for 'chain 'L' and resid 642 through 644' Processing helix chain 'L' and resid 661 through 674 removed outlier: 3.516A pdb=" N MET L 673 " --> pdb=" O LYS L 669 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP L 674 " --> pdb=" O LYS L 670 " (cutoff:3.500A) Processing helix chain 'L' and resid 697 through 706 Processing helix chain 'Q' and resid 1404 through 1411 Processing helix chain 'Q' and resid 1433 through 1440 removed outlier: 3.774A pdb=" N MET Q1439 " --> pdb=" O GLN Q1435 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1465 through 1467 No H-bonds generated for 'chain 'Q' and resid 1465 through 1467' Processing helix chain 'Q' and resid 1524 through 1538 Processing helix chain 'Q' and resid 1540 through 1545 Processing helix chain 'Q' and resid 1569 through 1583 removed outlier: 3.503A pdb=" N GLN Q1575 " --> pdb=" O ARG Q1572 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU Q1576 " --> pdb=" O LEU Q1573 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1599 through 1605 Processing helix chain 'Q' and resid 1631 through 1656 removed outlier: 4.400A pdb=" N GLY Q1643 " --> pdb=" O LEU Q1640 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN Q1654 " --> pdb=" O LYS Q1651 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1668 through 1682 removed outlier: 3.696A pdb=" N LYS Q1679 " --> pdb=" O LEU Q1675 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1700 through 1703 Processing helix chain 'Q' and resid 1707 through 1714 Processing helix chain 'Q' and resid 1739 through 1746 Processing helix chain 'Q' and resid 1785 through 1803 Processing helix chain 'Q' and resid 1807 through 1819 removed outlier: 4.709A pdb=" N ALA Q1817 " --> pdb=" O VAL Q1813 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N SER Q1818 " --> pdb=" O ASN Q1814 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1830 through 1853 Processing helix chain 'Q' and resid 1875 through 1890 removed outlier: 5.480A pdb=" N ALA Q1880 " --> pdb=" O GLU Q1876 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR Q1881 " --> pdb=" O ASN Q1877 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN Q1883 " --> pdb=" O TYR Q1879 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1893 through 1895 No H-bonds generated for 'chain 'Q' and resid 1893 through 1895' Processing helix chain 'Q' and resid 1940 through 1944 removed outlier: 4.016A pdb=" N PHE Q1944 " --> pdb=" O GLN Q1940 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1940 through 1944' Processing helix chain 'Q' and resid 1947 through 1973 Proline residue: Q1951 - end of helix Processing helix chain 'Q' and resid 2003 through 2006 Processing helix chain 'Q' and resid 2008 through 2025 Processing helix chain 'Q' and resid 2032 through 2035 No H-bonds generated for 'chain 'Q' and resid 2032 through 2035' Processing helix chain 'Q' and resid 2050 through 2064 Processing helix chain 'Q' and resid 2066 through 2083 removed outlier: 4.175A pdb=" N ILE Q2069 " --> pdb=" O LYS Q2066 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU Q2070 " --> pdb=" O SER Q2067 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE Q2072 " --> pdb=" O ILE Q2069 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS Q2081 " --> pdb=" O GLU Q2078 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2124 through 2128 Processing helix chain 'Q' and resid 2139 through 2158 Processing helix chain 'Q' and resid 2191 through 2208 Processing helix chain 'Q' and resid 2211 through 2221 removed outlier: 3.848A pdb=" N THR Q2221 " --> pdb=" O ILE Q2217 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 29 Proline residue: R 19 - end of helix removed outlier: 4.384A pdb=" N ARG R 27 " --> pdb=" O ARG R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 49 Processing helix chain 'R' and resid 58 through 73 Processing helix chain 'R' and resid 81 through 92 Processing helix chain 'R' and resid 166 through 168 No H-bonds generated for 'chain 'R' and resid 166 through 168' Processing helix chain 'R' and resid 211 through 231 removed outlier: 4.580A pdb=" N PHE R 218 " --> pdb=" O LYS R 214 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU R 219 " --> pdb=" O VAL R 215 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG R 221 " --> pdb=" O MET R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 274 Processing helix chain 'R' and resid 352 through 359 Processing helix chain 'R' and resid 381 through 393 Processing helix chain 'R' and resid 411 through 426 removed outlier: 3.850A pdb=" N ASP R 426 " --> pdb=" O GLN R 422 " (cutoff:3.500A) Processing helix chain 'R' and resid 454 through 471 removed outlier: 3.929A pdb=" N ARG R 471 " --> pdb=" O THR R 467 " (cutoff:3.500A) Processing helix chain 'R' and resid 473 through 478 Processing helix chain 'R' and resid 490 through 496 removed outlier: 4.456A pdb=" N VAL R 495 " --> pdb=" O TRP R 491 " (cutoff:3.500A) Processing helix chain 'R' and resid 514 through 519 Processing helix chain 'R' and resid 546 through 553 Processing helix chain 'R' and resid 594 through 609 removed outlier: 3.684A pdb=" N THR R 599 " --> pdb=" O LYS R 595 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU R 602 " --> pdb=" O GLU R 598 " (cutoff:3.500A) Processing helix chain 'R' and resid 624 through 630 removed outlier: 3.646A pdb=" N ASP R 627 " --> pdb=" O TRP R 624 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N HIS R 628 " --> pdb=" O ASP R 625 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 31 Processing helix chain 'X' and resid 51 through 65 Processing helix chain 'X' and resid 73 through 80 removed outlier: 3.924A pdb=" N ALA X 79 " --> pdb=" O ALA X 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 86 No H-bonds generated for 'chain 'X' and resid 83 through 86' Processing helix chain 'X' and resid 88 through 103 Processing helix chain 'X' and resid 118 through 135 removed outlier: 4.543A pdb=" N LYS X 123 " --> pdb=" O ALA X 119 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE X 124 " --> pdb=" O TYR X 120 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 187 removed outlier: 4.958A pdb=" N GLY X 154 " --> pdb=" O ILE X 150 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU X 155 " --> pdb=" O THR X 151 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS X 158 " --> pdb=" O GLY X 154 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS X 159 " --> pdb=" O GLU X 155 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN X 160 " --> pdb=" O LEU X 156 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU X 171 " --> pdb=" O ILE X 167 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER X 172 " --> pdb=" O LEU X 168 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY X 173 " --> pdb=" O SER X 169 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL X 175 " --> pdb=" O GLU X 171 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU X 176 " --> pdb=" O SER X 172 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG X 177 " --> pdb=" O GLY X 173 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL X 186 " --> pdb=" O LEU X 182 " (cutoff:3.500A) Processing helix chain 'X' and resid 196 through 214 Processing helix chain 'X' and resid 245 through 248 No H-bonds generated for 'chain 'X' and resid 245 through 248' Processing helix chain 'X' and resid 250 through 259 Processing helix chain 'X' and resid 262 through 271 Processing helix chain 'X' and resid 283 through 296 removed outlier: 5.633A pdb=" N ASP X 296 " --> pdb=" O TYR X 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 302 Processing helix chain 'X' and resid 330 through 351 removed outlier: 3.689A pdb=" N MET X 345 " --> pdb=" O LYS X 341 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS X 351 " --> pdb=" O LYS X 347 " (cutoff:3.500A) Processing helix chain 'X' and resid 381 through 383 No H-bonds generated for 'chain 'X' and resid 381 through 383' Processing helix chain 'X' and resid 385 through 394 Processing helix chain 'X' and resid 431 through 447 Processing helix chain 'X' and resid 449 through 460 Processing helix chain 'X' and resid 464 through 466 No H-bonds generated for 'chain 'X' and resid 464 through 466' Processing helix chain 'X' and resid 469 through 492 removed outlier: 3.522A pdb=" N PHE X 482 " --> pdb=" O PHE X 478 " (cutoff:3.500A) Processing helix chain 'X' and resid 498 through 505 removed outlier: 5.863A pdb=" N GLU X 503 " --> pdb=" O GLN X 500 " (cutoff:3.500A) Processing helix chain 'X' and resid 507 through 522 Processing helix chain 'X' and resid 526 through 549 Processing helix chain 'X' and resid 557 through 564 Processing helix chain 'X' and resid 568 through 582 Proline residue: X 577 - end of helix removed outlier: 4.620A pdb=" N SER X 581 " --> pdb=" O PRO X 577 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS X 582 " --> pdb=" O LYS X 578 " (cutoff:3.500A) Processing helix chain 'X' and resid 585 through 605 Processing helix chain 'X' and resid 659 through 666 removed outlier: 3.974A pdb=" N ASN X 665 " --> pdb=" O LYS X 661 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR X 666 " --> pdb=" O VAL X 662 " (cutoff:3.500A) Processing helix chain 'X' and resid 669 through 681 removed outlier: 4.373A pdb=" N ARG X 681 " --> pdb=" O ASN X 677 " (cutoff:3.500A) Processing helix chain 'X' and resid 687 through 702 Processing helix chain 'X' and resid 707 through 710 Processing helix chain 'X' and resid 713 through 723 Processing helix chain 'X' and resid 733 through 755 removed outlier: 3.644A pdb=" N TYR X 744 " --> pdb=" O GLN X 740 " (cutoff:3.500A) Processing helix chain 'X' and resid 757 through 764 removed outlier: 4.077A pdb=" N LEU X 763 " --> pdb=" O PHE X 760 " (cutoff:3.500A) Processing helix chain 'X' and resid 771 through 779 removed outlier: 4.885A pdb=" N TYR X 776 " --> pdb=" O GLU X 772 " (cutoff:3.500A) Processing helix chain 'Y' and resid 56 through 60 Processing helix chain 'Y' and resid 65 through 75 removed outlier: 5.487A pdb=" N HIS Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS Y 74 " --> pdb=" O LYS Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 84 through 102 removed outlier: 4.379A pdb=" N PHE Y 94 " --> pdb=" O ASN Y 90 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR Y 95 " --> pdb=" O ILE Y 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 121 Processing helix chain 'Y' and resid 123 through 137 removed outlier: 3.554A pdb=" N PHE Y 133 " --> pdb=" O ARG Y 129 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 241 through 245 removed outlier: 6.367A pdb=" N HIS 2 294 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL 2 244 " --> pdb=" O HIS 2 294 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ARG 2 296 " --> pdb=" O VAL 2 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '2' and resid 423 through 429 removed outlier: 6.575A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N THR 2 449 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU 2 407 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU 2 411 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N SER 2 455 " --> pdb=" O LEU 2 411 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE 2 456 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU 2 425 " --> pdb=" O ILE 2 456 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 339 through 341 Processing sheet with id= D, first strand: chain '2' and resid 679 through 683 removed outlier: 6.743A pdb=" N GLY 2 602 " --> pdb=" O SER 2 645 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE 2 647 " --> pdb=" O GLY 2 602 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ALA 2 649 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE 2 606 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '2' and resid 578 through 582 Processing sheet with id= F, first strand: chain '2' and resid 628 through 633 Processing sheet with id= G, first strand: chain '2' and resid 331 through 337 removed outlier: 7.047A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 95 through 99 removed outlier: 6.751A pdb=" N LYS 3 154 " --> pdb=" O ILE 3 96 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE 3 98 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER 3 156 " --> pdb=" O ILE 3 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain '3' and resid 165 through 167 removed outlier: 8.193A pdb=" N LEU 3 166 " --> pdb=" O LEU 3 179 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER 3 181 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL 3 297 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLY 3 323 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS 3 299 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ILE 3 321 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU 3 301 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THR 3 319 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 185 through 187 Processing sheet with id= K, first strand: chain '3' and resid 209 through 213 Processing sheet with id= L, first strand: chain '3' and resid 545 through 549 removed outlier: 7.014A pdb=" N GLY 3 468 " --> pdb=" O SER 3 511 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE 3 513 " --> pdb=" O GLY 3 468 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL 3 470 " --> pdb=" O ILE 3 513 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ALA 3 515 " --> pdb=" O VAL 3 470 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE 3 472 " --> pdb=" O ALA 3 515 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '3' and resid 444 through 449 removed outlier: 3.786A pdb=" N GLU 3 454 " --> pdb=" O ASP 3 449 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '3' and resid 494 through 499 Processing sheet with id= O, first strand: chain '3' and resid 193 through 198 removed outlier: 6.655A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '4' and resid 240 through 244 removed outlier: 6.838A pdb=" N LYS 4 302 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU 4 243 " --> pdb=" O LYS 4 302 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG 4 304 " --> pdb=" O LEU 4 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '4' and resid 414 through 420 removed outlier: 3.986A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE 4 442 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N THR 4 459 " --> pdb=" O ILE 4 442 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '4' and resid 355 through 359 Processing sheet with id= S, first strand: chain '4' and resid 704 through 708 removed outlier: 6.429A pdb=" N VAL 4 589 " --> pdb=" O CYS 4 630 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ASP 4 632 " --> pdb=" O VAL 4 589 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR 4 591 " --> pdb=" O ASP 4 632 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '4' and resid 604 through 606 Processing sheet with id= U, first strand: chain '4' and resid 653 through 658 Processing sheet with id= V, first strand: chain '4' and resid 339 through 344 removed outlier: 6.695A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '5' and resid 60 through 64 removed outlier: 6.558A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL 5 63 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE 5 138 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain '5' and resid 273 through 279 removed outlier: 3.646A pdb=" N SER 5 168 " --> pdb=" O LYS 5 257 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN 5 259 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE 5 166 " --> pdb=" O GLN 5 259 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE 5 297 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE 5 330 " --> pdb=" O ILE 5 297 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER 5 299 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE 5 328 " --> pdb=" O SER 5 299 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR 5 301 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '5' and resid 189 through 193 removed outlier: 4.307A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '5' and resid 552 through 556 removed outlier: 6.562A pdb=" N GLY 5 475 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU 5 520 " --> pdb=" O GLY 5 475 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '5' and resid 451 through 456 Processing sheet with id= AB, first strand: chain '5' and resid 501 through 506 Processing sheet with id= AC, first strand: chain '5' and resid 727 through 729 Processing sheet with id= AD, first strand: chain '5' and resid 173 through 178 removed outlier: 6.609A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '6' and resid 150 through 154 removed outlier: 6.374A pdb=" N GLN 6 264 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE 6 153 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N SER 6 266 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain '6' and resid 394 through 400 removed outlier: 6.860A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR 6 297 " --> pdb=" O LYS 6 358 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LYS 6 358 " --> pdb=" O THR 6 297 " (cutoff:3.500A) removed outlier: 13.791A pdb=" N THR 6 376 " --> pdb=" O TYR 6 450 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE 6 452 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP 6 378 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG 6 382 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N HIS 6 458 " --> pdb=" O ARG 6 382 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR 6 398 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL 6 459 " --> pdb=" O LYS 6 396 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS 6 396 " --> pdb=" O VAL 6 459 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain '6' and resid 309 through 311 Processing sheet with id= AH, first strand: chain '6' and resid 571 through 575 removed outlier: 6.596A pdb=" N LEU 6 711 " --> pdb=" O CYS 6 572 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL 6 574 " --> pdb=" O LEU 6 711 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE 6 713 " --> pdb=" O VAL 6 574 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain '6' and resid 595 through 599 removed outlier: 6.923A pdb=" N ILE 6 635 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR 6 598 " --> pdb=" O ILE 6 635 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS 6 637 " --> pdb=" O THR 6 598 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain '6' and resid 610 through 613 Processing sheet with id= AK, first strand: chain '6' and resid 660 through 665 Processing sheet with id= AL, first strand: chain '6' and resid 301 through 306 removed outlier: 6.742A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '7' and resid 77 through 81 removed outlier: 6.416A pdb=" N PHE 7 201 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE 7 80 " --> pdb=" O PHE 7 201 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR 7 203 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain '7' and resid 348 through 354 removed outlier: 6.936A pdb=" N LYS 7 314 " --> pdb=" O THR 7 246 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL 7 248 " --> pdb=" O GLU 7 312 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLU 7 312 " --> pdb=" O VAL 7 248 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N THR 7 374 " --> pdb=" O SER 7 330 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASN 7 332 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASN 7 336 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N PHE 7 380 " --> pdb=" O ASN 7 336 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR 7 352 " --> pdb=" O GLN 7 379 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL 7 381 " --> pdb=" O ASP 7 350 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP 7 350 " --> pdb=" O VAL 7 381 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 269 through 272 removed outlier: 4.470A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain '7' and resid 596 through 599 removed outlier: 6.537A pdb=" N GLY 7 519 " --> pdb=" O SER 7 562 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU 7 564 " --> pdb=" O GLY 7 519 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '7' and resid 545 through 550 Processing sheet with id= AR, first strand: chain '7' and resid 252 through 257 removed outlier: 6.840A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'A' and resid 162 through 166 Processing sheet with id= AT, first strand: chain 'A' and resid 172 through 176 removed outlier: 3.815A pdb=" N GLY A 172 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'B' and resid 68 through 72 Processing sheet with id= AV, first strand: chain 'C' and resid 43 through 47 Processing sheet with id= AW, first strand: chain 'D' and resid 227 through 231 Processing sheet with id= AX, first strand: chain 'D' and resid 255 through 260 Processing sheet with id= AY, first strand: chain 'E' and resid 56 through 61 removed outlier: 6.605A pdb=" N LEU E 27 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL E 59 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE E 29 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE E 61 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL E 31 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER E 80 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE E 30 " --> pdb=" O SER E 80 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU E 82 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N SER E 32 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL E 84 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP E 119 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU E 83 " --> pdb=" O ASP E 119 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR E 121 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'E' and resid 316 through 322 Processing sheet with id= BA, first strand: chain 'E' and resid 525 through 530 removed outlier: 8.307A pdb=" N CYS E 528 " --> pdb=" O PRO E 566 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL E 568 " --> pdb=" O CYS E 528 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU E 530 " --> pdb=" O VAL E 568 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA E 570 " --> pdb=" O LEU E 530 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'F' and resid 526 through 530 removed outlier: 3.647A pdb=" N THR F 495 " --> pdb=" O VAL F 502 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR F 504 " --> pdb=" O TYR F 493 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TYR F 493 " --> pdb=" O THR F 504 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS F 506 " --> pdb=" O ARG F 491 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ARG F 491 " --> pdb=" O LYS F 506 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'F' and resid 536 through 539 Processing sheet with id= BD, first strand: chain 'F' and resid 578 through 584 removed outlier: 7.020A pdb=" N GLY F 591 " --> pdb=" O THR F 579 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL F 581 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE F 589 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA F 583 " --> pdb=" O ARG F 587 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ARG F 587 " --> pdb=" O ALA F 583 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR F 596 " --> pdb=" O THR F 592 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'F' and resid 615 through 621 removed outlier: 6.770A pdb=" N VAL F 628 " --> pdb=" O VAL F 616 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU F 618 " --> pdb=" O PHE F 626 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N PHE F 626 " --> pdb=" O LEU F 618 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA F 620 " --> pdb=" O ARG F 624 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG F 624 " --> pdb=" O ALA F 620 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU F 642 " --> pdb=" O TYR F 650 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N TYR F 650 " --> pdb=" O GLU F 642 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'F' and resid 686 through 689 removed outlier: 3.630A pdb=" N SER F 686 " --> pdb=" O PHE F 698 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'F' and resid 773 through 775 removed outlier: 6.251A pdb=" N ILE F 755 " --> pdb=" O PRO F 744 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL F 757 " --> pdb=" O VAL F 742 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL F 742 " --> pdb=" O VAL F 757 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'G' and resid 526 through 530 removed outlier: 3.510A pdb=" N GLN G 510 " --> pdb=" O ASN G 507 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR G 495 " --> pdb=" O VAL G 502 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR G 504 " --> pdb=" O TYR G 493 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TYR G 493 " --> pdb=" O THR G 504 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LYS G 506 " --> pdb=" O ARG G 491 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG G 491 " --> pdb=" O LYS G 506 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'G' and resid 536 through 539 Processing sheet with id= BJ, first strand: chain 'G' and resid 578 through 583 removed outlier: 6.852A pdb=" N GLY G 591 " --> pdb=" O THR G 579 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL G 581 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE G 589 " --> pdb=" O VAL G 581 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA G 583 " --> pdb=" O ARG G 587 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG G 587 " --> pdb=" O ALA G 583 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR G 596 " --> pdb=" O THR G 592 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASN G 601 " --> pdb=" O PRO G 606 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'G' and resid 615 through 621 removed outlier: 6.593A pdb=" N VAL G 628 " --> pdb=" O VAL G 616 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU G 618 " --> pdb=" O PHE G 626 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE G 626 " --> pdb=" O LEU G 618 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA G 620 " --> pdb=" O ARG G 624 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG G 624 " --> pdb=" O ALA G 620 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU G 642 " --> pdb=" O TYR G 650 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR G 650 " --> pdb=" O GLU G 642 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'G' and resid 686 through 689 Processing sheet with id= BM, first strand: chain 'G' and resid 772 through 775 removed outlier: 5.895A pdb=" N ILE G 755 " --> pdb=" O PRO G 744 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL G 757 " --> pdb=" O VAL G 742 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL G 742 " --> pdb=" O VAL G 757 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'H' and resid 526 through 530 removed outlier: 3.771A pdb=" N THR H 495 " --> pdb=" O VAL H 502 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR H 504 " --> pdb=" O TYR H 493 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N TYR H 493 " --> pdb=" O THR H 504 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'H' and resid 536 through 539 Processing sheet with id= BP, first strand: chain 'H' and resid 578 through 584 removed outlier: 6.927A pdb=" N GLY H 591 " --> pdb=" O THR H 579 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL H 581 " --> pdb=" O ILE H 589 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE H 589 " --> pdb=" O VAL H 581 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA H 583 " --> pdb=" O ARG H 587 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG H 587 " --> pdb=" O ALA H 583 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR H 596 " --> pdb=" O THR H 592 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'H' and resid 615 through 621 removed outlier: 6.866A pdb=" N VAL H 628 " --> pdb=" O VAL H 616 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU H 618 " --> pdb=" O PHE H 626 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N PHE H 626 " --> pdb=" O LEU H 618 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA H 620 " --> pdb=" O ARG H 624 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG H 624 " --> pdb=" O ALA H 620 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU H 642 " --> pdb=" O TYR H 650 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TYR H 650 " --> pdb=" O GLU H 642 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'H' and resid 686 through 689 removed outlier: 3.508A pdb=" N SER H 686 " --> pdb=" O PHE H 698 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU H 722 " --> pdb=" O LEU H 704 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU H 706 " --> pdb=" O PRO H 720 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SER H 708 " --> pdb=" O TRP H 718 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TRP H 718 " --> pdb=" O SER H 708 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'H' and resid 772 through 775 removed outlier: 5.728A pdb=" N ILE H 755 " --> pdb=" O PRO H 744 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL H 757 " --> pdb=" O VAL H 742 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N VAL H 742 " --> pdb=" O VAL H 757 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'K' and resid 15 through 18 Processing sheet with id= BU, first strand: chain 'L' and resid 250 through 253 removed outlier: 6.196A pdb=" N GLN L 283 " --> pdb=" O PHE L 251 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU L 253 " --> pdb=" O GLN L 283 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS L 285 " --> pdb=" O LEU L 253 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLU L 343 " --> pdb=" O LEU L 314 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU L 316 " --> pdb=" O GLU L 343 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER L 345 " --> pdb=" O LEU L 316 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS L 369 " --> pdb=" O LEU L 344 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU L 346 " --> pdb=" O LYS L 369 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU L 371 " --> pdb=" O LEU L 346 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE L 348 " --> pdb=" O GLU L 371 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE L 373 " --> pdb=" O ILE L 348 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR L 350 " --> pdb=" O ILE L 373 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL L 375 " --> pdb=" O TYR L 350 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LYS L 427 " --> pdb=" O ILE L 370 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU L 372 " --> pdb=" O LYS L 427 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR L 429 " --> pdb=" O LEU L 372 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE L 374 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE L 431 " --> pdb=" O PHE L 374 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASN L 376 " --> pdb=" O ILE L 431 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS L 456 " --> pdb=" O ILE L 428 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU L 430 " --> pdb=" O LYS L 456 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR L 458 " --> pdb=" O LEU L 430 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N CYS L 432 " --> pdb=" O THR L 458 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR L 460 " --> pdb=" O CYS L 432 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU L 485 " --> pdb=" O LEU L 457 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE L 459 " --> pdb=" O GLU L 485 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TRP L 487 " --> pdb=" O ILE L 459 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS L 514 " --> pdb=" O LEU L 486 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ILE L 488 " --> pdb=" O LYS L 514 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR L 516 " --> pdb=" O ILE L 488 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LYS L 555 " --> pdb=" O LEU L 515 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE L 517 " --> pdb=" O LYS L 555 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP L 557 " --> pdb=" O PHE L 517 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER L 584 " --> pdb=" O LEU L 556 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU L 621 " --> pdb=" O LEU L 585 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG L 650 " --> pdb=" O ILE L 622 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TYR L 686 " --> pdb=" O LEU L 651 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN L 711 " --> pdb=" O LEU L 687 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'Q' and resid 1345 through 1352 removed outlier: 5.766A pdb=" N THR Q1341 " --> pdb=" O VAL Q1324 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL Q1324 " --> pdb=" O THR Q1341 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'Q' and resid 1376 through 1379 removed outlier: 4.511A pdb=" N LEU Q1397 " --> pdb=" O SER Q1379 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS Q1360 " --> pdb=" O GLY Q1425 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY Q1425 " --> pdb=" O LYS Q1360 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'Q' and resid 1483 through 1486 Processing sheet with id= BY, first strand: chain 'Q' and resid 1508 through 1510 removed outlier: 6.189A pdb=" N GLU Q1559 " --> pdb=" O ILE Q1509 " (cutoff:3.500A) No H-bonds generated for sheet with id= BY Processing sheet with id= BZ, first strand: chain 'Q' and resid 1725 through 1727 removed outlier: 3.974A pdb=" N TYR Q1905 " --> pdb=" O CYS Q1922 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU Q1920 " --> pdb=" O ASP Q1907 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU Q1909 " --> pdb=" O SER Q1918 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER Q1918 " --> pdb=" O LEU Q1909 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TRP Q1911 " --> pdb=" O ASN Q1916 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ASN Q1916 " --> pdb=" O TRP Q1911 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'Q' and resid 1901 through 1906 removed outlier: 6.719A pdb=" N ASP Q1733 " --> pdb=" O LYS Q1903 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR Q1905 " --> pdb=" O VAL Q1731 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL Q1731 " --> pdb=" O TYR Q1905 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LYS Q1869 " --> pdb=" O ILE Q1858 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE Q1858 " --> pdb=" O LYS Q1869 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'Q' and resid 2106 through 2108 Processing sheet with id= CC, first strand: chain 'Q' and resid 2162 through 2164 Processing sheet with id= CD, first strand: chain 'R' and resid 171 through 173 removed outlier: 6.491A pdb=" N THR R 638 " --> pdb=" O VAL R 540 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N PHE R 542 " --> pdb=" O THR R 638 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL R 640 " --> pdb=" O PHE R 542 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS R 657 " --> pdb=" O MET R 639 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU R 641 " --> pdb=" O LYS R 657 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE R 659 " --> pdb=" O LEU R 641 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'R' and resid 180 through 184 removed outlier: 4.241A pdb=" N ARG R 180 " --> pdb=" O VAL R 193 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'R' and resid 325 through 332 removed outlier: 3.668A pdb=" N GLN R 280 " --> pdb=" O TYR R 332 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TRP R 296 " --> pdb=" O ILE R 307 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU R 329 " --> pdb=" O THR R 342 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N MET R 344 " --> pdb=" O LEU R 327 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU R 327 " --> pdb=" O MET R 344 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'R' and resid 681 through 688 removed outlier: 3.851A pdb=" N LYS R 681 " --> pdb=" O VAL R 676 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU R 431 " --> pdb=" O VAL R 400 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU R 402 " --> pdb=" O LEU R 431 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE R 433 " --> pdb=" O LEU R 402 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR R 480 " --> pdb=" O LEU R 432 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TRP R 434 " --> pdb=" O THR R 480 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE R 482 " --> pdb=" O TRP R 434 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'X' and resid 32 through 35 Processing sheet with id= CI, first strand: chain 'X' and resid 364 through 367 2968 hydrogen bonds defined for protein. 8313 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: 34.49 Time building geometry restraints manager: 24.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23205 1.34 - 1.46: 16021 1.46 - 1.58: 36329 1.58 - 1.71: 142 1.71 - 1.83: 536 Bond restraints: 76233 Sorted by residual: bond pdb=" O3A ANP 31500 " pdb=" PB ANP 31500 " ideal model delta sigma weight residual 1.700 1.544 0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" O3A ANP 21500 " pdb=" PB ANP 21500 " ideal model delta sigma weight residual 1.700 1.546 0.154 2.00e-02 2.50e+03 5.93e+01 bond pdb=" O3A ANP 51500 " pdb=" PB ANP 51500 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" N3B ANP 31500 " pdb=" PG ANP 31500 " ideal model delta sigma weight residual 1.795 1.683 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" N3B ANP 21500 " pdb=" PG ANP 21500 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.91e+01 ... (remaining 76228 not shown) Histogram of bond angle deviations from ideal: 98.00 - 105.29: 1842 105.29 - 112.59: 37743 112.59 - 119.89: 29494 119.89 - 127.19: 33382 127.19 - 134.49: 897 Bond angle restraints: 103358 Sorted by residual: angle pdb=" CA TRP 5 343 " pdb=" CB TRP 5 343 " pdb=" CG TRP 5 343 " ideal model delta sigma weight residual 113.60 123.28 -9.68 1.90e+00 2.77e-01 2.60e+01 angle pdb=" N ASP R 544 " pdb=" CA ASP R 544 " pdb=" C ASP R 544 " ideal model delta sigma weight residual 114.75 120.20 -5.45 1.26e+00 6.30e-01 1.87e+01 angle pdb=" CA GLN Q1593 " pdb=" CB GLN Q1593 " pdb=" CG GLN Q1593 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CA TYR G 922 " pdb=" CB TYR G 922 " pdb=" CG TYR G 922 " ideal model delta sigma weight residual 113.90 121.48 -7.58 1.80e+00 3.09e-01 1.78e+01 angle pdb=" N GLY R 662 " pdb=" CA GLY R 662 " pdb=" C GLY R 662 " ideal model delta sigma weight residual 112.83 117.97 -5.14 1.22e+00 6.72e-01 1.77e+01 ... (remaining 103353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 42307 17.89 - 35.78: 2952 35.78 - 53.67: 722 53.67 - 71.56: 231 71.56 - 89.45: 82 Dihedral angle restraints: 46294 sinusoidal: 19482 harmonic: 26812 Sorted by residual: dihedral pdb=" CA ASP R 489 " pdb=" C ASP R 489 " pdb=" N LEU R 490 " pdb=" CA LEU R 490 " ideal model delta harmonic sigma weight residual -180.00 -133.87 -46.13 0 5.00e+00 4.00e-02 8.51e+01 dihedral pdb=" CA HIS L 601 " pdb=" C HIS L 601 " pdb=" N THR L 602 " pdb=" CA THR L 602 " ideal model delta harmonic sigma weight residual 180.00 149.74 30.26 0 5.00e+00 4.00e-02 3.66e+01 dihedral pdb=" CA LEU 4 533 " pdb=" C LEU 4 533 " pdb=" N GLU 4 534 " pdb=" CA GLU 4 534 " ideal model delta harmonic sigma weight residual 180.00 -150.15 -29.85 0 5.00e+00 4.00e-02 3.56e+01 ... (remaining 46291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 10903 0.094 - 0.189: 868 0.189 - 0.283: 9 0.283 - 0.378: 3 0.378 - 0.472: 2 Chirality restraints: 11785 Sorted by residual: chirality pdb=" P DT I 101 " pdb=" OP1 DT I 101 " pdb=" OP2 DT I 101 " pdb=" O5' DT I 101 " both_signs ideal model delta sigma weight residual True 2.35 2.82 -0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CA HIS 2 561 " pdb=" N HIS 2 561 " pdb=" C HIS 2 561 " pdb=" CB HIS 2 561 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" P DC J 101 " pdb=" OP1 DC J 101 " pdb=" OP2 DC J 101 " pdb=" O5' DC J 101 " both_signs ideal model delta sigma weight residual True 2.35 -2.71 -0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 11782 not shown) Planarity restraints: 12920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE X 565 " -0.032 2.00e-02 2.50e+03 2.38e-02 9.88e+00 pdb=" CG PHE X 565 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE X 565 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE X 565 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE X 565 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE X 565 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE X 565 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR 6 609 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C THR 6 609 " -0.053 2.00e-02 2.50e+03 pdb=" O THR 6 609 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA 6 610 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 528 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO R 529 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO R 529 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 529 " -0.040 5.00e-02 4.00e+02 ... (remaining 12917 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 103 2.54 - 3.13: 59266 3.13 - 3.72: 118264 3.72 - 4.31: 169553 4.31 - 4.90: 274876 Nonbonded interactions: 622062 Sorted by model distance: nonbonded pdb=" O2G ANP 51500 " pdb="MG MG 51501 " model vdw 1.956 2.170 nonbonded pdb=" O2A ANP 51500 " pdb="MG MG 51501 " model vdw 1.956 2.170 nonbonded pdb=" OG SER 5 423 " pdb="MG MG 51501 " model vdw 1.962 2.170 nonbonded pdb=" O2G ANP 31500 " pdb="MG MG 31501 " model vdw 1.974 2.170 nonbonded pdb=" O2G ANP 21500 " pdb="MG MG 21501 " model vdw 1.986 2.170 ... (remaining 622057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'F' and (resid 474 through 663 or resid 670 through 789 or (resid 790 and \ (name N or name CA or name C or name O or name CB )) or resid 814 through 892 o \ r (resid 893 through 894 and (name N or name CA or name C or name O or name CB ) \ ) or resid 895 through 901 or (resid 902 and (name N or name CA or name C or nam \ e O or name CB )) or resid 903 through 911 or (resid 912 and (name N or name CA \ or name C or name O or name CB )) or resid 913 through 923)) selection = (chain 'G' and (resid 474 through 789 or (resid 790 and (name N or name CA or na \ me C or name O or name CB )) or resid 814 through 901 or (resid 902 and (name N \ or name CA or name C or name O or name CB )) or resid 903 through 909 or (resid \ 910 and (name N or name CA or name C or name O or name CB )) or resid 911 throug \ h 923)) selection = (chain 'H' and (resid 474 through 663 or resid 670 through 892 or (resid 893 thr \ ough 894 and (name N or name CA or name C or name O or name CB )) or resid 895 t \ hrough 909 or (resid 910 and (name N or name CA or name C or name O or name CB ) \ ) or resid 911 or (resid 912 and (name N or name CA or name C or name O or name \ CB )) or resid 913 through 923)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.070 Extract box with map and model: 13.380 Check model and map are aligned: 0.850 Set scattering table: 0.530 Process input model: 171.210 Find NCS groups from input model: 3.720 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.007 0.156 76233 Z= 0.422 Angle : 0.940 11.189 103358 Z= 0.520 Chirality : 0.052 0.472 11785 Planarity : 0.007 0.101 12920 Dihedral : 14.396 89.450 28844 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.55 % Favored : 97.44 % Rotamer: Outliers : 0.32 % Allowed : 3.93 % Favored : 95.76 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.09), residues: 8943 helix: 0.22 (0.08), residues: 3919 sheet: -0.56 (0.14), residues: 1309 loop : -0.19 (0.10), residues: 3715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP 5 343 HIS 0.015 0.002 HIS Q1780 PHE 0.048 0.003 PHE X 565 TYR 0.034 0.003 TYR G 749 ARG 0.012 0.001 ARG F 491 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1121 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1095 time to evaluate : 6.623 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: 2 452 GLU cc_start: 0.7600 (tt0) cc_final: 0.7184 (tt0) REVERT: 2 501 MET cc_start: 0.8788 (mmm) cc_final: 0.8582 (mmm) REVERT: 2 783 MET cc_start: 0.8107 (mtt) cc_final: 0.7835 (mtp) REVERT: 3 158 LYS cc_start: 0.5740 (tptm) cc_final: 0.5525 (tptp) REVERT: 3 306 MET cc_start: 0.8830 (mmt) cc_final: 0.8600 (mmp) REVERT: 4 280 MET cc_start: 0.9138 (mmt) cc_final: 0.8921 (mmt) REVERT: 4 316 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8177 (mt-10) REVERT: 4 356 MET cc_start: 0.8458 (ptp) cc_final: 0.8002 (ptp) REVERT: 4 398 LYS cc_start: 0.8425 (tttp) cc_final: 0.8218 (tttm) REVERT: 4 580 TYR cc_start: 0.8575 (m-80) cc_final: 0.8366 (m-80) REVERT: 4 698 LEU cc_start: 0.9131 (tp) cc_final: 0.8931 (tp) REVERT: 4 770 LEU cc_start: 0.9592 (mt) cc_final: 0.9338 (mt) REVERT: 5 158 LYS cc_start: 0.9044 (mmtt) cc_final: 0.8796 (mmmm) REVERT: 5 257 LYS cc_start: 0.8321 (mtpt) cc_final: 0.7990 (mttm) REVERT: 5 334 GLN cc_start: 0.7493 (tt0) cc_final: 0.7251 (tm-30) REVERT: 5 484 LYS cc_start: 0.9190 (mttp) cc_final: 0.8907 (mptt) REVERT: 5 487 ASP cc_start: 0.8538 (p0) cc_final: 0.8309 (p0) REVERT: 5 574 ASN cc_start: 0.9093 (m-40) cc_final: 0.8864 (m-40) REVERT: 5 599 MET cc_start: 0.8895 (ttt) cc_final: 0.8663 (ttt) REVERT: 5 633 LEU cc_start: 0.9084 (tp) cc_final: 0.8870 (tt) REVERT: 6 168 MET cc_start: 0.8590 (tmm) cc_final: 0.8302 (tmm) REVERT: 6 543 VAL cc_start: 0.8513 (t) cc_final: 0.8182 (t) REVERT: 6 711 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8939 (pp) REVERT: 7 132 ILE cc_start: 0.5532 (OUTLIER) cc_final: 0.5059 (tt) REVERT: 7 457 CYS cc_start: 0.8537 (t) cc_final: 0.8306 (t) REVERT: 7 459 MET cc_start: 0.8872 (mtm) cc_final: 0.8449 (mtm) REVERT: 7 543 GLN cc_start: 0.8275 (mp10) cc_final: 0.7897 (mp10) REVERT: 7 646 LYS cc_start: 0.9611 (mttm) cc_final: 0.9351 (mmmt) REVERT: 7 706 ASP cc_start: 0.8573 (t70) cc_final: 0.8355 (t0) REVERT: A 2 TYR cc_start: 0.8637 (m-80) cc_final: 0.8394 (m-80) REVERT: A 15 ARG cc_start: 0.8311 (ttp80) cc_final: 0.7695 (ttp80) REVERT: A 53 TYR cc_start: 0.8961 (t80) cc_final: 0.8686 (t80) REVERT: A 129 GLU cc_start: 0.8436 (pp20) cc_final: 0.8159 (pp20) REVERT: A 174 ILE cc_start: 0.7848 (pt) cc_final: 0.7251 (pt) REVERT: A 193 GLN cc_start: 0.8997 (tt0) cc_final: 0.8684 (tt0) REVERT: A 201 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8523 (mm-40) REVERT: B 47 HIS cc_start: 0.6564 (t70) cc_final: 0.6270 (t-90) REVERT: C 5 ASP cc_start: 0.8855 (t0) cc_final: 0.8513 (t0) REVERT: C 8 ASP cc_start: 0.9199 (t70) cc_final: 0.8923 (t70) REVERT: C 45 ASN cc_start: 0.5818 (m-40) cc_final: 0.5600 (m-40) REVERT: C 91 ASP cc_start: 0.8494 (t0) cc_final: 0.8269 (t0) REVERT: C 96 ASP cc_start: 0.8204 (t0) cc_final: 0.7767 (t0) REVERT: C 172 MET cc_start: 0.8295 (tmm) cc_final: 0.8078 (tmm) REVERT: D 84 MET cc_start: 0.9263 (mmm) cc_final: 0.9046 (tpp) REVERT: D 96 GLN cc_start: 0.8500 (tp40) cc_final: 0.8075 (tp40) REVERT: D 130 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8239 (mm-30) REVERT: D 189 ILE cc_start: 0.9220 (mm) cc_final: 0.8850 (mm) REVERT: D 251 PHE cc_start: 0.9021 (m-80) cc_final: 0.8789 (m-80) REVERT: D 253 LYS cc_start: 0.9029 (ptpt) cc_final: 0.8828 (ptpp) REVERT: E 2 TYR cc_start: 0.5511 (OUTLIER) cc_final: 0.5310 (m-80) REVERT: H 723 ASP cc_start: 0.8025 (t0) cc_final: 0.7760 (t0) REVERT: L 629 SER cc_start: 0.8525 (t) cc_final: 0.8264 (t) REVERT: Q 1535 MET cc_start: 0.7588 (tpp) cc_final: 0.7301 (tpp) REVERT: R 390 LEU cc_start: 0.8867 (tp) cc_final: 0.8644 (tp) REVERT: R 481 MET cc_start: 0.8182 (mpp) cc_final: 0.7622 (mmt) REVERT: R 617 ASP cc_start: 0.8104 (p0) cc_final: 0.7898 (p0) REVERT: X 81 TYR cc_start: 0.8263 (m-80) cc_final: 0.7732 (m-80) REVERT: X 200 MET cc_start: 0.8677 (ttp) cc_final: 0.8317 (tmm) REVERT: X 384 ASP cc_start: 0.7928 (m-30) cc_final: 0.7468 (m-30) REVERT: X 718 LEU cc_start: 0.9537 (tp) cc_final: 0.9263 (tp) REVERT: X 723 LEU cc_start: 0.8974 (mt) cc_final: 0.8764 (tp) REVERT: X 731 MET cc_start: 0.8664 (mmm) cc_final: 0.8084 (mmm) outliers start: 26 outliers final: 5 residues processed: 1115 average time/residue: 0.6995 time to fit residues: 1327.3647 Evaluate side-chains 674 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 666 time to evaluate : 6.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 711 LEU Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain E residue 2 TYR Chi-restraints excluded: chain G residue 757 VAL Chi-restraints excluded: chain H residue 530 ASP Chi-restraints excluded: chain X residue 414 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 909 random chunks: chunk 767 optimal weight: 0.6980 chunk 688 optimal weight: 0.6980 chunk 382 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 464 optimal weight: 0.7980 chunk 368 optimal weight: 7.9990 chunk 712 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 433 optimal weight: 0.6980 chunk 530 optimal weight: 6.9990 chunk 825 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 424 ASN 4 217 ASN 4 413 HIS 4 646 HIS 4 723 HIS 5 652 GLN 6 458 HIS A 33 HIS A 57 GLN C 21 GLN C 33 ASN D 96 GLN D 231 HIS D 247 GLN E 57 GLN E 402 GLN ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 439 ASN L 727 ASN Q1352 HIS ** Q1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 291 ASN ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 HIS X 159 HIS ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 76233 Z= 0.176 Angle : 0.602 11.129 103358 Z= 0.314 Chirality : 0.042 0.193 11785 Planarity : 0.004 0.053 12920 Dihedral : 11.383 80.812 10678 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.84 % Allowed : 7.84 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.48 (0.09), residues: 8943 helix: 0.99 (0.08), residues: 3900 sheet: -0.46 (0.14), residues: 1365 loop : 0.06 (0.11), residues: 3678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 5 343 HIS 0.007 0.001 HIS 2 779 PHE 0.024 0.002 PHE X 565 TYR 0.023 0.001 TYR Q1486 ARG 0.008 0.000 ARG X 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 755 time to evaluate : 6.625 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: 2 276 MET cc_start: 0.8422 (tpp) cc_final: 0.7993 (tpt) REVERT: 2 452 GLU cc_start: 0.7680 (tt0) cc_final: 0.7227 (tt0) REVERT: 2 624 MET cc_start: 0.8966 (ttp) cc_final: 0.8669 (ttp) REVERT: 2 857 LEU cc_start: 0.9517 (mt) cc_final: 0.9282 (mt) REVERT: 4 316 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8176 (mt-10) REVERT: 4 538 LYS cc_start: 0.9199 (mttt) cc_final: 0.8886 (mtmm) REVERT: 4 579 GLN cc_start: 0.8903 (mt0) cc_final: 0.8506 (mt0) REVERT: 4 636 LYS cc_start: 0.9213 (tttp) cc_final: 0.8839 (tttp) REVERT: 4 715 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8568 (tppt) REVERT: 4 749 MET cc_start: 0.8211 (tpt) cc_final: 0.7926 (tpp) REVERT: 4 750 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.8080 (t80) REVERT: 4 770 LEU cc_start: 0.9631 (mt) cc_final: 0.9382 (mt) REVERT: 5 158 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8769 (mmmm) REVERT: 5 370 LEU cc_start: 0.9613 (mt) cc_final: 0.9410 (mt) REVERT: 5 481 GLU cc_start: 0.8191 (tp30) cc_final: 0.7957 (mm-30) REVERT: 5 484 LYS cc_start: 0.9093 (mttp) cc_final: 0.8391 (mttp) REVERT: 5 574 ASN cc_start: 0.9091 (m-40) cc_final: 0.8676 (m-40) REVERT: 5 599 MET cc_start: 0.8853 (ttt) cc_final: 0.8478 (ttt) REVERT: 5 603 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8921 (mp) REVERT: 5 633 LEU cc_start: 0.9164 (tp) cc_final: 0.8930 (tt) REVERT: 6 257 GLU cc_start: 0.6188 (tm-30) cc_final: 0.5871 (tm-30) REVERT: 6 264 GLN cc_start: 0.7883 (mt0) cc_final: 0.7411 (mt0) REVERT: 6 543 VAL cc_start: 0.8313 (t) cc_final: 0.8102 (t) REVERT: 6 711 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8963 (pp) REVERT: 7 132 ILE cc_start: 0.5383 (OUTLIER) cc_final: 0.4806 (tt) REVERT: 7 459 MET cc_start: 0.8863 (mtm) cc_final: 0.8381 (mtm) REVERT: 7 538 HIS cc_start: 0.8718 (t70) cc_final: 0.8407 (t-90) REVERT: 7 543 GLN cc_start: 0.8146 (mp10) cc_final: 0.7939 (mp10) REVERT: 7 646 LYS cc_start: 0.9622 (mttm) cc_final: 0.9345 (mmmt) REVERT: 7 652 MET cc_start: 0.8291 (tpp) cc_final: 0.7628 (mmm) REVERT: 7 706 ASP cc_start: 0.8606 (t70) cc_final: 0.8386 (t0) REVERT: A 62 MET cc_start: 0.6001 (pmm) cc_final: 0.5668 (mpp) REVERT: A 193 GLN cc_start: 0.8946 (tt0) cc_final: 0.8678 (tt0) REVERT: A 197 GLU cc_start: 0.7641 (pm20) cc_final: 0.7437 (pm20) REVERT: B 114 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7255 (tm-30) REVERT: C 5 ASP cc_start: 0.8884 (t0) cc_final: 0.8461 (t0) REVERT: C 8 ASP cc_start: 0.9172 (t70) cc_final: 0.8769 (t0) REVERT: C 91 ASP cc_start: 0.8628 (t0) cc_final: 0.8175 (t70) REVERT: C 96 ASP cc_start: 0.8376 (t0) cc_final: 0.7927 (t0) REVERT: D 96 GLN cc_start: 0.8452 (tp-100) cc_final: 0.8165 (tp40) REVERT: D 130 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8261 (mm-30) REVERT: D 189 ILE cc_start: 0.9137 (mm) cc_final: 0.8908 (mt) REVERT: E 2 TYR cc_start: 0.5449 (OUTLIER) cc_final: 0.4935 (m-80) REVERT: K 124 LEU cc_start: 0.8644 (mt) cc_final: 0.8421 (mt) REVERT: Q 1535 MET cc_start: 0.7476 (tpp) cc_final: 0.7171 (tpp) REVERT: Q 1594 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8444 (p) REVERT: Q 1780 HIS cc_start: 0.6950 (m90) cc_final: 0.6604 (m-70) REVERT: Q 2174 TYR cc_start: 0.8532 (m-80) cc_final: 0.8220 (m-80) REVERT: R 481 MET cc_start: 0.7953 (mpp) cc_final: 0.7596 (mmp) REVERT: X 81 TYR cc_start: 0.8507 (m-80) cc_final: 0.7348 (m-80) REVERT: X 152 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9030 (mm) REVERT: X 165 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8928 (tptt) REVERT: X 200 MET cc_start: 0.8617 (ttp) cc_final: 0.8142 (tmm) REVERT: X 384 ASP cc_start: 0.7953 (m-30) cc_final: 0.7655 (m-30) REVERT: X 533 MET cc_start: 0.8381 (ttm) cc_final: 0.7821 (ttp) REVERT: X 588 MET cc_start: 0.8867 (mtt) cc_final: 0.8634 (mtm) outliers start: 69 outliers final: 24 residues processed: 806 average time/residue: 0.6844 time to fit residues: 957.3065 Evaluate side-chains 659 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 627 time to evaluate : 6.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 750 TYR Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 603 ILE Chi-restraints excluded: chain 6 residue 711 LEU Chi-restraints excluded: chain 6 residue 803 MET Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 2 TYR Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain G residue 841 LEU Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 616 LEU Chi-restraints excluded: chain L residue 642 VAL Chi-restraints excluded: chain L residue 727 ASN Chi-restraints excluded: chain Q residue 1408 LEU Chi-restraints excluded: chain Q residue 1594 SER Chi-restraints excluded: chain R residue 272 LYS Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 165 LYS Chi-restraints excluded: chain X residue 249 SER Chi-restraints excluded: chain X residue 287 LEU Chi-restraints excluded: chain X residue 414 LEU Chi-restraints excluded: chain Y residue 60 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 909 random chunks: chunk 458 optimal weight: 0.9980 chunk 256 optimal weight: 20.0000 chunk 687 optimal weight: 3.9990 chunk 562 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 826 optimal weight: 0.9990 chunk 893 optimal weight: 4.9990 chunk 736 optimal weight: 6.9990 chunk 820 optimal weight: 2.9990 chunk 281 optimal weight: 0.8980 chunk 663 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 538 HIS 7 622 HIS D 247 GLN ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 601 HIS ** L 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2001 ASN ** R 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 93 GLN ** Y 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 76233 Z= 0.175 Angle : 0.549 12.099 103358 Z= 0.285 Chirality : 0.041 0.204 11785 Planarity : 0.004 0.050 12920 Dihedral : 10.929 79.123 10674 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.14 % Allowed : 9.05 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.75 (0.09), residues: 8943 helix: 1.28 (0.08), residues: 3908 sheet: -0.41 (0.13), residues: 1376 loop : 0.17 (0.11), residues: 3659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP Q1798 HIS 0.008 0.001 HIS E 22 PHE 0.024 0.001 PHE F 870 TYR 0.026 0.001 TYR 4 580 ARG 0.021 0.000 ARG K 186 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 676 time to evaluate : 6.678 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: 2 276 MET cc_start: 0.8505 (tpp) cc_final: 0.8116 (tpt) REVERT: 2 452 GLU cc_start: 0.7753 (tt0) cc_final: 0.7523 (tt0) REVERT: 2 781 MET cc_start: 0.7782 (mmm) cc_final: 0.7444 (tmm) REVERT: 4 316 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8234 (mt-10) REVERT: 4 398 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8019 (tttm) REVERT: 4 538 LYS cc_start: 0.9204 (mttt) cc_final: 0.8955 (ttmm) REVERT: 4 579 GLN cc_start: 0.8883 (mt0) cc_final: 0.8519 (mt0) REVERT: 4 580 TYR cc_start: 0.8360 (m-80) cc_final: 0.8084 (m-80) REVERT: 4 715 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8637 (tppt) REVERT: 4 749 MET cc_start: 0.8276 (tpt) cc_final: 0.7978 (tpp) REVERT: 4 750 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.8184 (t80) REVERT: 4 770 LEU cc_start: 0.9620 (mt) cc_final: 0.9388 (mt) REVERT: 5 160 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8477 (m) REVERT: 5 257 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7927 (mttm) REVERT: 5 370 LEU cc_start: 0.9625 (mt) cc_final: 0.9403 (mt) REVERT: 5 481 GLU cc_start: 0.8262 (tp30) cc_final: 0.7937 (mm-30) REVERT: 5 484 LYS cc_start: 0.9080 (mttp) cc_final: 0.8217 (mttp) REVERT: 5 574 ASN cc_start: 0.9072 (m-40) cc_final: 0.8800 (t0) REVERT: 5 583 MET cc_start: 0.8826 (tpp) cc_final: 0.8603 (tpp) REVERT: 5 599 MET cc_start: 0.8863 (ttt) cc_final: 0.8428 (ttt) REVERT: 5 603 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8943 (mp) REVERT: 5 633 LEU cc_start: 0.9189 (tp) cc_final: 0.8951 (tt) REVERT: 5 761 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8038 (mt) REVERT: 6 257 GLU cc_start: 0.6137 (tm-30) cc_final: 0.5702 (tm-30) REVERT: 6 264 GLN cc_start: 0.8001 (mt0) cc_final: 0.7783 (mt0) REVERT: 6 305 TYR cc_start: 0.8715 (t80) cc_final: 0.8510 (t80) REVERT: 6 711 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9021 (pp) REVERT: 7 132 ILE cc_start: 0.5559 (OUTLIER) cc_final: 0.4957 (tt) REVERT: 7 459 MET cc_start: 0.8771 (mtm) cc_final: 0.8459 (mtm) REVERT: 7 538 HIS cc_start: 0.8577 (t-90) cc_final: 0.8300 (t-90) REVERT: 7 550 LYS cc_start: 0.9313 (mttp) cc_final: 0.9100 (mttp) REVERT: 7 652 MET cc_start: 0.8248 (tpp) cc_final: 0.7654 (mmm) REVERT: A 1 MET cc_start: 0.8777 (tmm) cc_final: 0.7994 (tmm) REVERT: A 62 MET cc_start: 0.5936 (pmm) cc_final: 0.5640 (mpp) REVERT: A 181 PHE cc_start: 0.8568 (m-10) cc_final: 0.8357 (m-10) REVERT: A 193 GLN cc_start: 0.8964 (tt0) cc_final: 0.8571 (tt0) REVERT: A 197 GLU cc_start: 0.7816 (pm20) cc_final: 0.7542 (pm20) REVERT: C 5 ASP cc_start: 0.8888 (t0) cc_final: 0.8461 (t0) REVERT: C 8 ASP cc_start: 0.9248 (t70) cc_final: 0.8923 (t0) REVERT: C 91 ASP cc_start: 0.8662 (t0) cc_final: 0.8127 (t0) REVERT: C 96 ASP cc_start: 0.8409 (t0) cc_final: 0.7919 (t0) REVERT: C 117 GLU cc_start: 0.7558 (tt0) cc_final: 0.6974 (tt0) REVERT: C 182 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7800 (tm-30) REVERT: E 2 TYR cc_start: 0.5384 (OUTLIER) cc_final: 0.4741 (m-80) REVERT: E 426 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7516 (mm-30) REVERT: K 124 LEU cc_start: 0.8591 (mt) cc_final: 0.8308 (mt) REVERT: L 482 ASP cc_start: 0.7542 (t0) cc_final: 0.7327 (t0) REVERT: Q 1535 MET cc_start: 0.7494 (tpp) cc_final: 0.7148 (tpp) REVERT: Q 1780 HIS cc_start: 0.6977 (m90) cc_final: 0.6604 (m-70) REVERT: Q 2045 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8589 (pp) REVERT: X 80 GLU cc_start: 0.8002 (pt0) cc_final: 0.7111 (pt0) REVERT: X 81 TYR cc_start: 0.8131 (m-80) cc_final: 0.7883 (m-80) REVERT: X 165 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8885 (tptt) REVERT: X 200 MET cc_start: 0.8625 (ttp) cc_final: 0.8144 (tmm) REVERT: X 293 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.8928 (t80) REVERT: X 384 ASP cc_start: 0.7929 (m-30) cc_final: 0.7648 (m-30) REVERT: X 533 MET cc_start: 0.8330 (ttm) cc_final: 0.8025 (ttp) REVERT: X 588 MET cc_start: 0.8879 (mtt) cc_final: 0.8625 (mtm) REVERT: X 731 MET cc_start: 0.8799 (mmm) cc_final: 0.8268 (mmm) outliers start: 93 outliers final: 38 residues processed: 745 average time/residue: 0.6704 time to fit residues: 871.1052 Evaluate side-chains 646 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 597 time to evaluate : 6.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 316 SER Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 750 TYR Chi-restraints excluded: chain 5 residue 22 ASP Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 593 GLU Chi-restraints excluded: chain 5 residue 603 ILE Chi-restraints excluded: chain 5 residue 614 LEU Chi-restraints excluded: chain 5 residue 761 ILE Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 6 residue 644 MET Chi-restraints excluded: chain 6 residue 711 LEU Chi-restraints excluded: chain 6 residue 803 MET Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 493 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain E residue 2 TYR Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain G residue 841 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 616 LEU Chi-restraints excluded: chain L residue 642 VAL Chi-restraints excluded: chain Q residue 1408 LEU Chi-restraints excluded: chain Q residue 2045 LEU Chi-restraints excluded: chain Q residue 2072 ILE Chi-restraints excluded: chain R residue 272 LYS Chi-restraints excluded: chain R residue 344 MET Chi-restraints excluded: chain X residue 93 ILE Chi-restraints excluded: chain X residue 94 ASP Chi-restraints excluded: chain X residue 141 VAL Chi-restraints excluded: chain X residue 165 LYS Chi-restraints excluded: chain X residue 293 PHE Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain Y residue 60 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 909 random chunks: chunk 817 optimal weight: 3.9990 chunk 621 optimal weight: 10.0000 chunk 429 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 394 optimal weight: 10.0000 chunk 555 optimal weight: 9.9990 chunk 829 optimal weight: 6.9990 chunk 878 optimal weight: 9.9990 chunk 433 optimal weight: 4.9990 chunk 786 optimal weight: 40.0000 chunk 236 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN 2 703 HIS ** 2 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 164 HIS 3 210 HIS 3 239 ASN 4 327 ASN 5 560 HIS 7 271 GLN C 33 ASN ** F 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 ASN G 527 HIS L 325 GLN L 439 ASN ** L 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2001 ASN Q2060 HIS ** R 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 611 HIS ** X 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 93 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 76233 Z= 0.438 Angle : 0.647 10.412 103358 Z= 0.335 Chirality : 0.044 0.192 11785 Planarity : 0.004 0.053 12920 Dihedral : 10.927 83.410 10672 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.75 % Favored : 97.24 % Rotamer: Outliers : 1.92 % Allowed : 9.97 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.63 (0.09), residues: 8943 helix: 1.27 (0.08), residues: 3897 sheet: -0.59 (0.13), residues: 1404 loop : 0.06 (0.11), residues: 3642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP Q1798 HIS 0.009 0.001 HIS G 527 PHE 0.039 0.002 PHE R 458 TYR 0.022 0.002 TYR 4 580 ARG 0.010 0.001 ARG E 398 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 584 time to evaluate : 6.671 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: 2 276 MET cc_start: 0.8622 (tpp) cc_final: 0.8255 (tpt) REVERT: 2 452 GLU cc_start: 0.7917 (tt0) cc_final: 0.7409 (tt0) REVERT: 2 627 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8315 (mm-40) REVERT: 2 778 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8185 (mm) REVERT: 2 781 MET cc_start: 0.7868 (mmm) cc_final: 0.7352 (tmm) REVERT: 4 316 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8258 (mt-10) REVERT: 4 398 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8168 (tttm) REVERT: 4 538 LYS cc_start: 0.9143 (mttt) cc_final: 0.8863 (mtmm) REVERT: 4 580 TYR cc_start: 0.8391 (m-80) cc_final: 0.7965 (m-80) REVERT: 4 636 LYS cc_start: 0.9228 (tttp) cc_final: 0.8985 (tttt) REVERT: 4 749 MET cc_start: 0.8187 (tpt) cc_final: 0.7875 (tpp) REVERT: 5 160 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8502 (m) REVERT: 5 257 LYS cc_start: 0.8338 (mtpt) cc_final: 0.8008 (mttm) REVERT: 5 370 LEU cc_start: 0.9656 (mt) cc_final: 0.9455 (mt) REVERT: 5 574 ASN cc_start: 0.9099 (m-40) cc_final: 0.8795 (t0) REVERT: 5 583 MET cc_start: 0.8887 (tpp) cc_final: 0.8546 (tpp) REVERT: 5 599 MET cc_start: 0.8879 (ttt) cc_final: 0.8394 (ttt) REVERT: 6 257 GLU cc_start: 0.6299 (tm-30) cc_final: 0.5893 (tm-30) REVERT: 6 711 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9169 (pp) REVERT: 7 132 ILE cc_start: 0.5578 (OUTLIER) cc_final: 0.5008 (tt) REVERT: 7 459 MET cc_start: 0.8855 (mtm) cc_final: 0.8603 (mtm) REVERT: 7 706 ASP cc_start: 0.8591 (t70) cc_final: 0.8324 (t0) REVERT: 7 707 MET cc_start: 0.8118 (tpp) cc_final: 0.7859 (tpp) REVERT: A 1 MET cc_start: 0.8644 (tmm) cc_final: 0.8134 (tmm) REVERT: A 33 HIS cc_start: 0.7691 (m-70) cc_final: 0.7039 (m-70) REVERT: A 62 MET cc_start: 0.5872 (pmm) cc_final: 0.5390 (mpp) REVERT: A 79 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8936 (mtm) REVERT: A 94 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8669 (m) REVERT: A 193 GLN cc_start: 0.9024 (tt0) cc_final: 0.8651 (tt0) REVERT: A 197 GLU cc_start: 0.7984 (pm20) cc_final: 0.7661 (pm20) REVERT: B 114 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7471 (tm-30) REVERT: C 5 ASP cc_start: 0.8968 (t0) cc_final: 0.8533 (t0) REVERT: C 8 ASP cc_start: 0.9298 (t70) cc_final: 0.8998 (t0) REVERT: C 91 ASP cc_start: 0.8692 (t0) cc_final: 0.8290 (t0) REVERT: C 96 ASP cc_start: 0.8533 (t0) cc_final: 0.8041 (t0) REVERT: D 130 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8276 (mm-30) REVERT: D 202 MET cc_start: 0.9215 (mmm) cc_final: 0.8555 (mmm) REVERT: E 2 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.5665 (m-80) REVERT: E 426 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7847 (mm-30) REVERT: F 738 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8321 (p) REVERT: G 726 MET cc_start: 0.8851 (tpp) cc_final: 0.8619 (tpp) REVERT: G 824 GLU cc_start: 0.8691 (tt0) cc_final: 0.8449 (tm-30) REVERT: H 723 ASP cc_start: 0.8029 (t0) cc_final: 0.7803 (t0) REVERT: K 175 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6841 (p0) REVERT: L 482 ASP cc_start: 0.7733 (t0) cc_final: 0.7531 (t0) REVERT: Q 1535 MET cc_start: 0.7860 (tpp) cc_final: 0.7542 (tpp) REVERT: Q 1702 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7409 (pp30) REVERT: Q 1780 HIS cc_start: 0.7103 (m90) cc_final: 0.6740 (m-70) REVERT: Q 2045 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8785 (pp) REVERT: X 80 GLU cc_start: 0.8085 (pt0) cc_final: 0.7402 (pt0) REVERT: X 81 TYR cc_start: 0.8307 (m-80) cc_final: 0.8066 (m-80) REVERT: X 152 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9135 (mm) REVERT: X 165 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8864 (tptt) REVERT: X 200 MET cc_start: 0.8701 (ttp) cc_final: 0.8251 (tmm) REVERT: X 293 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8906 (t80) REVERT: X 384 ASP cc_start: 0.7974 (m-30) cc_final: 0.7695 (m-30) REVERT: X 588 MET cc_start: 0.8922 (mtt) cc_final: 0.8686 (mtm) outliers start: 157 outliers final: 87 residues processed: 693 average time/residue: 0.6744 time to fit residues: 822.2162 Evaluate side-chains 653 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 550 time to evaluate : 6.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 281 LEU Chi-restraints excluded: chain 2 residue 316 SER Chi-restraints excluded: chain 2 residue 455 SER Chi-restraints excluded: chain 2 residue 627 GLN Chi-restraints excluded: chain 2 residue 778 LEU Chi-restraints excluded: chain 3 residue 233 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 382 MET Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 461 VAL Chi-restraints excluded: chain 4 residue 637 MET Chi-restraints excluded: chain 5 residue 22 ASP Chi-restraints excluded: chain 5 residue 153 SER Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 323 ILE Chi-restraints excluded: chain 5 residue 391 LEU Chi-restraints excluded: chain 5 residue 593 GLU Chi-restraints excluded: chain 5 residue 650 ILE Chi-restraints excluded: chain 5 residue 761 ILE Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 551 MET Chi-restraints excluded: chain 6 residue 711 LEU Chi-restraints excluded: chain 6 residue 803 MET Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 251 PHE Chi-restraints excluded: chain E residue 2 TYR Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain F residue 562 ILE Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain G residue 527 HIS Chi-restraints excluded: chain G residue 629 HIS Chi-restraints excluded: chain G residue 841 LEU Chi-restraints excluded: chain H residue 527 HIS Chi-restraints excluded: chain H residue 563 HIS Chi-restraints excluded: chain H residue 855 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 175 ASP Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 491 ASN Chi-restraints excluded: chain L residue 510 LYS Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain L residue 616 LEU Chi-restraints excluded: chain L residue 642 VAL Chi-restraints excluded: chain L residue 645 LEU Chi-restraints excluded: chain L residue 659 ILE Chi-restraints excluded: chain L residue 660 THR Chi-restraints excluded: chain L residue 662 ILE Chi-restraints excluded: chain Q residue 1408 LEU Chi-restraints excluded: chain Q residue 1432 THR Chi-restraints excluded: chain Q residue 1482 MET Chi-restraints excluded: chain Q residue 1550 VAL Chi-restraints excluded: chain Q residue 1594 SER Chi-restraints excluded: chain Q residue 1702 GLN Chi-restraints excluded: chain Q residue 1730 VAL Chi-restraints excluded: chain Q residue 1808 THR Chi-restraints excluded: chain Q residue 1848 VAL Chi-restraints excluded: chain Q residue 2034 ASP Chi-restraints excluded: chain Q residue 2039 VAL Chi-restraints excluded: chain Q residue 2045 LEU Chi-restraints excluded: chain Q residue 2068 THR Chi-restraints excluded: chain Q residue 2072 ILE Chi-restraints excluded: chain R residue 272 LYS Chi-restraints excluded: chain R residue 344 MET Chi-restraints excluded: chain R residue 456 THR Chi-restraints excluded: chain R residue 673 MET Chi-restraints excluded: chain X residue 94 ASP Chi-restraints excluded: chain X residue 141 VAL Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 165 LYS Chi-restraints excluded: chain X residue 249 SER Chi-restraints excluded: chain X residue 293 PHE Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 414 LEU Chi-restraints excluded: chain X residue 473 VAL Chi-restraints excluded: chain X residue 542 LEU Chi-restraints excluded: chain X residue 666 TYR Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 86 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 909 random chunks: chunk 731 optimal weight: 2.9990 chunk 498 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 654 optimal weight: 2.9990 chunk 362 optimal weight: 0.0470 chunk 749 optimal weight: 7.9990 chunk 607 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 448 optimal weight: 5.9990 chunk 788 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN F 507 ASN G 527 HIS L 439 ASN ** L 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 258 HIS ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 76233 Z= 0.195 Angle : 0.541 11.576 103358 Z= 0.278 Chirality : 0.041 0.246 11785 Planarity : 0.004 0.053 12920 Dihedral : 10.704 79.412 10672 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.37 % Favored : 97.62 % Rotamer: Outliers : 1.57 % Allowed : 11.02 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.86 (0.09), residues: 8943 helix: 1.50 (0.08), residues: 3902 sheet: -0.52 (0.13), residues: 1414 loop : 0.15 (0.11), residues: 3627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP Q1798 HIS 0.015 0.001 HIS G 527 PHE 0.026 0.001 PHE 6 142 TYR 0.035 0.001 TYR Q1486 ARG 0.010 0.000 ARG 2 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 630 time to evaluate : 6.577 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: 2 267 MET cc_start: 0.8658 (tpp) cc_final: 0.8457 (mmm) REVERT: 2 276 MET cc_start: 0.8627 (tpp) cc_final: 0.8246 (tpt) REVERT: 2 627 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8071 (mm-40) REVERT: 2 781 MET cc_start: 0.7670 (mmm) cc_final: 0.7272 (tpp) REVERT: 3 290 ASP cc_start: 0.7734 (m-30) cc_final: 0.7359 (m-30) REVERT: 4 316 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8254 (mt-10) REVERT: 4 398 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8133 (tttm) REVERT: 4 538 LYS cc_start: 0.9126 (mttt) cc_final: 0.8707 (mtpt) REVERT: 4 580 TYR cc_start: 0.8391 (m-80) cc_final: 0.8069 (m-80) REVERT: 4 636 LYS cc_start: 0.9291 (tttp) cc_final: 0.8886 (ttmt) REVERT: 4 749 MET cc_start: 0.8238 (tpt) cc_final: 0.7908 (tpp) REVERT: 4 824 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8781 (tp30) REVERT: 5 160 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8647 (m) REVERT: 5 257 LYS cc_start: 0.8236 (mtpt) cc_final: 0.7959 (mttm) REVERT: 5 348 MET cc_start: 0.6433 (ppp) cc_final: 0.6014 (ppp) REVERT: 5 370 LEU cc_start: 0.9622 (mt) cc_final: 0.9408 (mt) REVERT: 5 574 ASN cc_start: 0.9088 (m-40) cc_final: 0.8788 (t0) REVERT: 5 583 MET cc_start: 0.8913 (tpp) cc_final: 0.8560 (tpp) REVERT: 5 598 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8869 (ttmm) REVERT: 5 599 MET cc_start: 0.8824 (ttt) cc_final: 0.8390 (ttt) REVERT: 5 603 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8992 (mp) REVERT: 5 761 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8057 (mt) REVERT: 6 257 GLU cc_start: 0.6144 (tm-30) cc_final: 0.5720 (tm-30) REVERT: 6 711 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9170 (pp) REVERT: 7 132 ILE cc_start: 0.5593 (OUTLIER) cc_final: 0.4994 (tt) REVERT: 7 459 MET cc_start: 0.8650 (mtm) cc_final: 0.8425 (mtm) REVERT: 7 706 ASP cc_start: 0.8699 (t70) cc_final: 0.8476 (t0) REVERT: A 1 MET cc_start: 0.8542 (tmm) cc_final: 0.8050 (tmm) REVERT: A 33 HIS cc_start: 0.7852 (m-70) cc_final: 0.7347 (m-70) REVERT: A 62 MET cc_start: 0.5847 (pmm) cc_final: 0.5477 (mpp) REVERT: A 73 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8233 (t80) REVERT: A 94 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8630 (m) REVERT: A 193 GLN cc_start: 0.8993 (tt0) cc_final: 0.8596 (tt0) REVERT: A 197 GLU cc_start: 0.7980 (pm20) cc_final: 0.7637 (pm20) REVERT: B 23 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8143 (mm-30) REVERT: B 49 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7036 (mmm160) REVERT: B 114 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7244 (tm-30) REVERT: B 164 ASN cc_start: 0.8411 (m-40) cc_final: 0.8118 (m-40) REVERT: B 190 ASP cc_start: 0.8251 (m-30) cc_final: 0.8039 (m-30) REVERT: C 5 ASP cc_start: 0.8948 (t0) cc_final: 0.8497 (t0) REVERT: C 8 ASP cc_start: 0.9324 (t70) cc_final: 0.8861 (t0) REVERT: C 91 ASP cc_start: 0.8729 (t0) cc_final: 0.8284 (t0) REVERT: C 96 ASP cc_start: 0.8539 (t0) cc_final: 0.8039 (t0) REVERT: D 218 MET cc_start: 0.8398 (mtp) cc_final: 0.8194 (ttm) REVERT: E 2 TYR cc_start: 0.5894 (OUTLIER) cc_final: 0.5238 (m-80) REVERT: F 738 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8385 (p) REVERT: G 726 MET cc_start: 0.8863 (tpp) cc_final: 0.8625 (tpp) REVERT: G 835 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8113 (mm-30) REVERT: H 723 ASP cc_start: 0.8036 (t0) cc_final: 0.7772 (t0) REVERT: L 482 ASP cc_start: 0.7620 (t0) cc_final: 0.7293 (t0) REVERT: Q 1535 MET cc_start: 0.7690 (tpp) cc_final: 0.7158 (tpp) REVERT: Q 1610 MET cc_start: 0.8902 (pmm) cc_final: 0.8586 (pmm) REVERT: Q 1780 HIS cc_start: 0.7112 (m90) cc_final: 0.6737 (m-70) REVERT: Q 2045 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8630 (pp) REVERT: X 80 GLU cc_start: 0.8040 (pt0) cc_final: 0.7316 (pt0) REVERT: X 165 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8780 (tptt) REVERT: X 200 MET cc_start: 0.8619 (ttp) cc_final: 0.8125 (tmm) REVERT: X 293 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8991 (t80) REVERT: X 384 ASP cc_start: 0.7937 (m-30) cc_final: 0.7659 (m-30) REVERT: X 391 LYS cc_start: 0.9229 (tttp) cc_final: 0.8986 (tptp) REVERT: X 588 MET cc_start: 0.8873 (mtt) cc_final: 0.8644 (mtm) outliers start: 128 outliers final: 69 residues processed: 718 average time/residue: 0.6627 time to fit residues: 833.7289 Evaluate side-chains 668 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 584 time to evaluate : 6.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 281 LEU Chi-restraints excluded: chain 2 residue 316 SER Chi-restraints excluded: chain 2 residue 627 GLN Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 3 residue 698 THR Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 637 MET Chi-restraints excluded: chain 4 residue 824 GLU Chi-restraints excluded: chain 5 residue 22 ASP Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 182 MET Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 556 VAL Chi-restraints excluded: chain 5 residue 593 GLU Chi-restraints excluded: chain 5 residue 603 ILE Chi-restraints excluded: chain 5 residue 614 LEU Chi-restraints excluded: chain 5 residue 761 ILE Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 551 MET Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 711 LEU Chi-restraints excluded: chain 6 residue 803 MET Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 340 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain E residue 2 TYR Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 567 MET Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 527 HIS Chi-restraints excluded: chain G residue 629 HIS Chi-restraints excluded: chain G residue 778 MET Chi-restraints excluded: chain G residue 841 LEU Chi-restraints excluded: chain H residue 563 HIS Chi-restraints excluded: chain H residue 600 PHE Chi-restraints excluded: chain H residue 782 VAL Chi-restraints excluded: chain H residue 847 MET Chi-restraints excluded: chain H residue 855 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 491 ASN Chi-restraints excluded: chain L residue 510 LYS Chi-restraints excluded: chain L residue 616 LEU Chi-restraints excluded: chain L residue 645 LEU Chi-restraints excluded: chain L residue 662 ILE Chi-restraints excluded: chain Q residue 1408 LEU Chi-restraints excluded: chain Q residue 1482 MET Chi-restraints excluded: chain Q residue 1489 HIS Chi-restraints excluded: chain Q residue 1550 VAL Chi-restraints excluded: chain Q residue 1594 SER Chi-restraints excluded: chain Q residue 2045 LEU Chi-restraints excluded: chain Q residue 2072 ILE Chi-restraints excluded: chain R residue 272 LYS Chi-restraints excluded: chain R residue 344 MET Chi-restraints excluded: chain X residue 94 ASP Chi-restraints excluded: chain X residue 141 VAL Chi-restraints excluded: chain X residue 165 LYS Chi-restraints excluded: chain X residue 238 THR Chi-restraints excluded: chain X residue 293 PHE Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 383 VAL Chi-restraints excluded: chain X residue 403 ILE Chi-restraints excluded: chain X residue 414 LEU Chi-restraints excluded: chain X residue 666 TYR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Y residue 65 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 909 random chunks: chunk 295 optimal weight: 8.9990 chunk 791 optimal weight: 0.5980 chunk 173 optimal weight: 8.9990 chunk 515 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 879 optimal weight: 9.9990 chunk 730 optimal weight: 4.9990 chunk 407 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 461 optimal weight: 0.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 264 GLN F 507 ASN G 527 HIS ** L 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 76233 Z= 0.255 Angle : 0.551 12.755 103358 Z= 0.281 Chirality : 0.041 0.163 11785 Planarity : 0.004 0.056 12920 Dihedral : 10.604 81.664 10672 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.71 % Favored : 97.28 % Rotamer: Outliers : 1.79 % Allowed : 11.70 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.93 (0.09), residues: 8943 helix: 1.56 (0.08), residues: 3914 sheet: -0.49 (0.13), residues: 1414 loop : 0.18 (0.11), residues: 3615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP Q1798 HIS 0.019 0.001 HIS G 527 PHE 0.027 0.001 PHE 6 142 TYR 0.019 0.001 TYR G 526 ARG 0.012 0.000 ARG 2 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 606 time to evaluate : 6.762 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: 2 276 MET cc_start: 0.8631 (tpp) cc_final: 0.8329 (tpt) REVERT: 2 627 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8072 (mm-40) REVERT: 2 781 MET cc_start: 0.7635 (mmm) cc_final: 0.7324 (tmm) REVERT: 3 290 ASP cc_start: 0.7704 (m-30) cc_final: 0.7339 (m-30) REVERT: 4 316 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8284 (mt-10) REVERT: 4 398 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8158 (tttm) REVERT: 4 538 LYS cc_start: 0.9108 (mttt) cc_final: 0.8665 (mtpt) REVERT: 4 580 TYR cc_start: 0.8409 (m-80) cc_final: 0.8145 (m-80) REVERT: 4 749 MET cc_start: 0.8234 (tpt) cc_final: 0.7926 (tpp) REVERT: 4 824 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8818 (tp30) REVERT: 5 160 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8712 (m) REVERT: 5 257 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7992 (mttm) REVERT: 5 348 MET cc_start: 0.6510 (ppp) cc_final: 0.6075 (ppp) REVERT: 5 574 ASN cc_start: 0.9118 (m-40) cc_final: 0.8800 (t0) REVERT: 5 583 MET cc_start: 0.8932 (tpp) cc_final: 0.8559 (tpp) REVERT: 5 599 MET cc_start: 0.8830 (ttt) cc_final: 0.8425 (ttt) REVERT: 5 761 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8044 (mt) REVERT: 6 257 GLU cc_start: 0.6126 (tm-30) cc_final: 0.5711 (tm-30) REVERT: 6 711 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9205 (pp) REVERT: 7 132 ILE cc_start: 0.5621 (OUTLIER) cc_final: 0.5020 (tt) REVERT: 7 459 MET cc_start: 0.8709 (mtm) cc_final: 0.8495 (mtm) REVERT: 7 646 LYS cc_start: 0.9361 (mmtt) cc_final: 0.9062 (mmmt) REVERT: A 1 MET cc_start: 0.8459 (tmm) cc_final: 0.7976 (tmm) REVERT: A 33 HIS cc_start: 0.7767 (m-70) cc_final: 0.7165 (m-70) REVERT: A 62 MET cc_start: 0.5983 (pmm) cc_final: 0.5678 (mpp) REVERT: A 73 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8266 (t80) REVERT: A 79 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8926 (mtm) REVERT: A 94 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8647 (m) REVERT: A 164 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8508 (p0) REVERT: A 193 GLN cc_start: 0.9011 (tt0) cc_final: 0.8621 (tt0) REVERT: A 197 GLU cc_start: 0.8014 (pm20) cc_final: 0.7645 (pm20) REVERT: B 23 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8173 (mm-30) REVERT: B 114 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7249 (tm-30) REVERT: B 164 ASN cc_start: 0.8442 (m-40) cc_final: 0.8174 (m-40) REVERT: C 5 ASP cc_start: 0.8938 (t0) cc_final: 0.8488 (t0) REVERT: C 8 ASP cc_start: 0.9341 (t70) cc_final: 0.8875 (t0) REVERT: C 91 ASP cc_start: 0.8718 (t0) cc_final: 0.8310 (t0) REVERT: C 96 ASP cc_start: 0.8619 (t0) cc_final: 0.8149 (t0) REVERT: C 172 MET cc_start: 0.8006 (ttp) cc_final: 0.7700 (tmm) REVERT: D 129 MET cc_start: 0.8133 (mmm) cc_final: 0.7716 (mmm) REVERT: D 202 MET cc_start: 0.9267 (mmm) cc_final: 0.8613 (mmm) REVERT: E 2 TYR cc_start: 0.5991 (OUTLIER) cc_final: 0.5386 (m-80) REVERT: E 332 SER cc_start: 0.8859 (m) cc_final: 0.8579 (p) REVERT: E 426 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7617 (mm-30) REVERT: F 738 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8417 (p) REVERT: G 726 MET cc_start: 0.8863 (tpp) cc_final: 0.8615 (tpp) REVERT: G 835 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8149 (mm-30) REVERT: H 723 ASP cc_start: 0.8187 (t0) cc_final: 0.7915 (t0) REVERT: L 482 ASP cc_start: 0.7612 (t0) cc_final: 0.7294 (t0) REVERT: Q 1535 MET cc_start: 0.7726 (tpp) cc_final: 0.7212 (tpp) REVERT: Q 1610 MET cc_start: 0.8999 (pmm) cc_final: 0.8689 (pmm) REVERT: Q 1702 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7347 (pp30) REVERT: Q 1780 HIS cc_start: 0.7139 (m90) cc_final: 0.6771 (m-70) REVERT: Q 2045 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8617 (pp) REVERT: Q 2133 CYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7171 (p) REVERT: X 165 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8809 (tptt) REVERT: X 200 MET cc_start: 0.8625 (ttp) cc_final: 0.8134 (tmm) REVERT: X 293 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8999 (t80) REVERT: X 391 LYS cc_start: 0.9213 (tttp) cc_final: 0.9013 (tptp) REVERT: X 588 MET cc_start: 0.8924 (mtt) cc_final: 0.8687 (mtm) outliers start: 146 outliers final: 92 residues processed: 712 average time/residue: 0.6709 time to fit residues: 841.3853 Evaluate side-chains 684 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 574 time to evaluate : 6.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 2 residue 281 LEU Chi-restraints excluded: chain 2 residue 316 SER Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 627 GLN Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 3 residue 698 THR Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 693 ASP Chi-restraints excluded: chain 4 residue 824 GLU Chi-restraints excluded: chain 5 residue 22 ASP Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 182 MET Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain 5 residue 391 LEU Chi-restraints excluded: chain 5 residue 459 THR Chi-restraints excluded: chain 5 residue 556 VAL Chi-restraints excluded: chain 5 residue 593 GLU Chi-restraints excluded: chain 5 residue 614 LEU Chi-restraints excluded: chain 5 residue 761 ILE Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 6 residue 264 GLN Chi-restraints excluded: chain 6 residue 279 ILE Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 551 MET Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 711 LEU Chi-restraints excluded: chain 6 residue 803 MET Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 340 VAL Chi-restraints excluded: chain 7 residue 548 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain E residue 2 TYR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 567 MET Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain F residue 731 MET Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 527 HIS Chi-restraints excluded: chain G residue 629 HIS Chi-restraints excluded: chain G residue 778 MET Chi-restraints excluded: chain G residue 841 LEU Chi-restraints excluded: chain H residue 527 HIS Chi-restraints excluded: chain H residue 563 HIS Chi-restraints excluded: chain H residue 600 PHE Chi-restraints excluded: chain H residue 782 VAL Chi-restraints excluded: chain H residue 855 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 460 THR Chi-restraints excluded: chain L residue 491 ASN Chi-restraints excluded: chain L residue 510 LYS Chi-restraints excluded: chain L residue 616 LEU Chi-restraints excluded: chain L residue 627 LEU Chi-restraints excluded: chain L residue 642 VAL Chi-restraints excluded: chain L residue 645 LEU Chi-restraints excluded: chain L residue 659 ILE Chi-restraints excluded: chain L residue 662 ILE Chi-restraints excluded: chain Q residue 1408 LEU Chi-restraints excluded: chain Q residue 1432 THR Chi-restraints excluded: chain Q residue 1482 MET Chi-restraints excluded: chain Q residue 1489 HIS Chi-restraints excluded: chain Q residue 1550 VAL Chi-restraints excluded: chain Q residue 1570 TYR Chi-restraints excluded: chain Q residue 1594 SER Chi-restraints excluded: chain Q residue 1702 GLN Chi-restraints excluded: chain Q residue 2039 VAL Chi-restraints excluded: chain Q residue 2045 LEU Chi-restraints excluded: chain Q residue 2068 THR Chi-restraints excluded: chain Q residue 2072 ILE Chi-restraints excluded: chain Q residue 2133 CYS Chi-restraints excluded: chain R residue 272 LYS Chi-restraints excluded: chain R residue 344 MET Chi-restraints excluded: chain R residue 673 MET Chi-restraints excluded: chain X residue 94 ASP Chi-restraints excluded: chain X residue 141 VAL Chi-restraints excluded: chain X residue 165 LYS Chi-restraints excluded: chain X residue 238 THR Chi-restraints excluded: chain X residue 293 PHE Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 383 VAL Chi-restraints excluded: chain X residue 403 ILE Chi-restraints excluded: chain X residue 414 LEU Chi-restraints excluded: chain X residue 666 TYR Chi-restraints excluded: chain Y residue 65 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 909 random chunks: chunk 847 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 501 optimal weight: 5.9990 chunk 642 optimal weight: 10.0000 chunk 497 optimal weight: 0.9990 chunk 740 optimal weight: 6.9990 chunk 491 optimal weight: 0.0470 chunk 876 optimal weight: 0.7980 chunk 548 optimal weight: 10.0000 chunk 534 optimal weight: 9.9990 chunk 404 optimal weight: 4.9990 overall best weight: 2.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 554 ASN G 527 HIS ** L 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 76233 Z= 0.254 Angle : 0.550 11.905 103358 Z= 0.280 Chirality : 0.041 0.171 11785 Planarity : 0.004 0.055 12920 Dihedral : 10.532 82.844 10672 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.71 % Favored : 97.28 % Rotamer: Outliers : 1.85 % Allowed : 12.17 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 0.95 (0.09), residues: 8943 helix: 1.59 (0.09), residues: 3910 sheet: -0.50 (0.14), residues: 1410 loop : 0.18 (0.11), residues: 3623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Q1798 HIS 0.016 0.001 HIS G 527 PHE 0.031 0.001 PHE 7 192 TYR 0.023 0.001 TYR Q1486 ARG 0.013 0.000 ARG 2 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 596 time to evaluate : 6.658 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: 2 276 MET cc_start: 0.8648 (tpp) cc_final: 0.8320 (tpt) REVERT: 2 627 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8011 (mm-40) REVERT: 2 781 MET cc_start: 0.7846 (mmm) cc_final: 0.7476 (tmm) REVERT: 3 290 ASP cc_start: 0.7691 (m-30) cc_final: 0.7372 (m-30) REVERT: 3 306 MET cc_start: 0.8670 (mmp) cc_final: 0.8445 (mmm) REVERT: 4 316 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8302 (mt-10) REVERT: 4 398 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8118 (tttm) REVERT: 4 538 LYS cc_start: 0.9103 (mttt) cc_final: 0.8671 (mtpt) REVERT: 4 580 TYR cc_start: 0.8367 (m-80) cc_final: 0.8111 (m-80) REVERT: 4 636 LYS cc_start: 0.9341 (ttmt) cc_final: 0.9084 (tttt) REVERT: 4 749 MET cc_start: 0.8167 (tpt) cc_final: 0.7839 (tpp) REVERT: 4 824 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8860 (tp30) REVERT: 5 160 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8637 (m) REVERT: 5 257 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7990 (mttm) REVERT: 5 348 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.6117 (ppp) REVERT: 5 404 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8232 (ttm) REVERT: 5 574 ASN cc_start: 0.9119 (m-40) cc_final: 0.8790 (t0) REVERT: 5 583 MET cc_start: 0.8962 (tpp) cc_final: 0.8556 (tpp) REVERT: 5 599 MET cc_start: 0.8869 (ttt) cc_final: 0.8522 (ttt) REVERT: 5 761 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8046 (mt) REVERT: 6 257 GLU cc_start: 0.6052 (tm-30) cc_final: 0.5707 (tm-30) REVERT: 6 711 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9204 (pp) REVERT: 7 81 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7344 (t70) REVERT: 7 132 ILE cc_start: 0.5395 (OUTLIER) cc_final: 0.4888 (tt) REVERT: A 22 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7874 (ttm-80) REVERT: A 33 HIS cc_start: 0.7773 (m-70) cc_final: 0.7177 (m-70) REVERT: A 62 MET cc_start: 0.6009 (pmm) cc_final: 0.5744 (mpp) REVERT: A 73 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8277 (t80) REVERT: A 79 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8924 (mtm) REVERT: A 94 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8658 (m) REVERT: A 164 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8518 (p0) REVERT: A 193 GLN cc_start: 0.9016 (tt0) cc_final: 0.8629 (tt0) REVERT: A 197 GLU cc_start: 0.8048 (pm20) cc_final: 0.7675 (pm20) REVERT: B 23 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8169 (mm-30) REVERT: B 114 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7241 (tm-30) REVERT: B 164 ASN cc_start: 0.8457 (m-40) cc_final: 0.8185 (m-40) REVERT: C 5 ASP cc_start: 0.8931 (t0) cc_final: 0.8477 (t0) REVERT: C 8 ASP cc_start: 0.9338 (t70) cc_final: 0.8870 (t0) REVERT: C 91 ASP cc_start: 0.8722 (t0) cc_final: 0.8313 (t0) REVERT: C 96 ASP cc_start: 0.8634 (t0) cc_final: 0.8164 (t0) REVERT: C 172 MET cc_start: 0.8000 (ttp) cc_final: 0.7668 (tmm) REVERT: D 202 MET cc_start: 0.9262 (mmm) cc_final: 0.8617 (mmm) REVERT: E 2 TYR cc_start: 0.6029 (OUTLIER) cc_final: 0.5413 (m-80) REVERT: E 332 SER cc_start: 0.8919 (m) cc_final: 0.8639 (p) REVERT: E 426 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7596 (mm-30) REVERT: F 738 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8418 (p) REVERT: G 726 MET cc_start: 0.8860 (tpp) cc_final: 0.8601 (tpp) REVERT: G 835 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8140 (mm-30) REVERT: H 723 ASP cc_start: 0.8190 (t0) cc_final: 0.7907 (t0) REVERT: L 482 ASP cc_start: 0.7586 (t0) cc_final: 0.7244 (t0) REVERT: Q 1535 MET cc_start: 0.7731 (tpp) cc_final: 0.7210 (tpp) REVERT: Q 1610 MET cc_start: 0.9011 (pmm) cc_final: 0.8744 (pmm) REVERT: Q 1702 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7379 (pp30) REVERT: Q 1780 HIS cc_start: 0.7141 (m90) cc_final: 0.6778 (m-70) REVERT: Q 2045 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8585 (pp) REVERT: Q 2133 CYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7178 (p) REVERT: X 165 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8776 (tptt) REVERT: X 200 MET cc_start: 0.8612 (ttp) cc_final: 0.8119 (tmm) REVERT: X 293 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8995 (t80) REVERT: X 391 LYS cc_start: 0.9213 (tttp) cc_final: 0.8992 (tptp) REVERT: X 588 MET cc_start: 0.8910 (mtt) cc_final: 0.8662 (mtm) outliers start: 151 outliers final: 102 residues processed: 704 average time/residue: 0.6658 time to fit residues: 825.2090 Evaluate side-chains 702 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 579 time to evaluate : 6.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 281 LEU Chi-restraints excluded: chain 2 residue 316 SER Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 455 SER Chi-restraints excluded: chain 2 residue 627 GLN Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 233 THR Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 3 residue 698 THR Chi-restraints excluded: chain 4 residue 308 VAL Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 637 MET Chi-restraints excluded: chain 4 residue 693 ASP Chi-restraints excluded: chain 4 residue 824 GLU Chi-restraints excluded: chain 5 residue 22 ASP Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 182 MET Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain 5 residue 348 MET Chi-restraints excluded: chain 5 residue 391 LEU Chi-restraints excluded: chain 5 residue 404 MET Chi-restraints excluded: chain 5 residue 459 THR Chi-restraints excluded: chain 5 residue 556 VAL Chi-restraints excluded: chain 5 residue 579 ASN Chi-restraints excluded: chain 5 residue 593 GLU Chi-restraints excluded: chain 5 residue 614 LEU Chi-restraints excluded: chain 5 residue 760 THR Chi-restraints excluded: chain 5 residue 761 ILE Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 551 MET Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 711 LEU Chi-restraints excluded: chain 6 residue 803 MET Chi-restraints excluded: chain 7 residue 81 ASP Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 335 VAL Chi-restraints excluded: chain 7 residue 340 VAL Chi-restraints excluded: chain 7 residue 432 LEU Chi-restraints excluded: chain 7 residue 548 ILE Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain E residue 2 TYR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 466 LEU Chi-restraints excluded: chain E residue 468 ASN Chi-restraints excluded: chain E residue 567 MET Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 527 HIS Chi-restraints excluded: chain G residue 629 HIS Chi-restraints excluded: chain G residue 778 MET Chi-restraints excluded: chain G residue 841 LEU Chi-restraints excluded: chain H residue 527 HIS Chi-restraints excluded: chain H residue 600 PHE Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 782 VAL Chi-restraints excluded: chain H residue 855 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 367 LEU Chi-restraints excluded: chain L residue 460 THR Chi-restraints excluded: chain L residue 491 ASN Chi-restraints excluded: chain L residue 510 LYS Chi-restraints excluded: chain L residue 616 LEU Chi-restraints excluded: chain L residue 642 VAL Chi-restraints excluded: chain L residue 645 LEU Chi-restraints excluded: chain L residue 659 ILE Chi-restraints excluded: chain L residue 662 ILE Chi-restraints excluded: chain Q residue 1322 TRP Chi-restraints excluded: chain Q residue 1402 LEU Chi-restraints excluded: chain Q residue 1408 LEU Chi-restraints excluded: chain Q residue 1482 MET Chi-restraints excluded: chain Q residue 1489 HIS Chi-restraints excluded: chain Q residue 1550 VAL Chi-restraints excluded: chain Q residue 1570 TYR Chi-restraints excluded: chain Q residue 1594 SER Chi-restraints excluded: chain Q residue 1702 GLN Chi-restraints excluded: chain Q residue 2039 VAL Chi-restraints excluded: chain Q residue 2045 LEU Chi-restraints excluded: chain Q residue 2072 ILE Chi-restraints excluded: chain Q residue 2133 CYS Chi-restraints excluded: chain R residue 272 LYS Chi-restraints excluded: chain R residue 344 MET Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 673 MET Chi-restraints excluded: chain X residue 94 ASP Chi-restraints excluded: chain X residue 141 VAL Chi-restraints excluded: chain X residue 165 LYS Chi-restraints excluded: chain X residue 238 THR Chi-restraints excluded: chain X residue 293 PHE Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 383 VAL Chi-restraints excluded: chain X residue 403 ILE Chi-restraints excluded: chain X residue 414 LEU Chi-restraints excluded: chain X residue 666 TYR Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Y residue 65 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 909 random chunks: chunk 542 optimal weight: 7.9990 chunk 349 optimal weight: 30.0000 chunk 523 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 557 optimal weight: 0.7980 chunk 596 optimal weight: 8.9990 chunk 433 optimal weight: 0.9990 chunk 81 optimal weight: 0.0170 chunk 688 optimal weight: 0.9980 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN 6 409 GLN 6 550 GLN 7 554 ASN D 4 ASN E 254 GLN L 694 GLN ** Q1489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 76233 Z= 0.161 Angle : 0.526 12.719 103358 Z= 0.266 Chirality : 0.040 0.166 11785 Planarity : 0.004 0.061 12920 Dihedral : 10.394 83.904 10672 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.50 % Favored : 97.48 % Rotamer: Outliers : 1.57 % Allowed : 12.69 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 1.04 (0.09), residues: 8943 helix: 1.69 (0.09), residues: 3899 sheet: -0.45 (0.13), residues: 1439 loop : 0.21 (0.11), residues: 3605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Q1798 HIS 0.029 0.001 HIS G 527 PHE 0.025 0.001 PHE E 62 TYR 0.022 0.001 TYR G 526 ARG 0.013 0.000 ARG 2 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 623 time to evaluate : 6.827 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: 2 276 MET cc_start: 0.8624 (tpp) cc_final: 0.8299 (tpt) REVERT: 2 452 GLU cc_start: 0.7848 (tt0) cc_final: 0.7425 (tt0) REVERT: 2 592 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7321 (mm-30) REVERT: 2 627 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7897 (mm-40) REVERT: 2 781 MET cc_start: 0.7706 (mmm) cc_final: 0.7316 (tmm) REVERT: 3 290 ASP cc_start: 0.7641 (m-30) cc_final: 0.7353 (m-30) REVERT: 3 306 MET cc_start: 0.8720 (mmp) cc_final: 0.8353 (mmm) REVERT: 3 307 ASN cc_start: 0.8415 (p0) cc_final: 0.7934 (p0) REVERT: 4 316 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8302 (mt-10) REVERT: 4 398 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8063 (tttm) REVERT: 4 538 LYS cc_start: 0.9057 (mttt) cc_final: 0.8588 (mtmt) REVERT: 4 580 TYR cc_start: 0.8400 (m-80) cc_final: 0.8142 (m-80) REVERT: 4 636 LYS cc_start: 0.9314 (ttmt) cc_final: 0.9037 (tttt) REVERT: 4 749 MET cc_start: 0.8192 (tpt) cc_final: 0.7863 (tpp) REVERT: 4 824 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8536 (tp30) REVERT: 5 257 LYS cc_start: 0.8216 (mtpt) cc_final: 0.8005 (mttp) REVERT: 5 348 MET cc_start: 0.6555 (ppp) cc_final: 0.6214 (ppp) REVERT: 5 404 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8203 (ttm) REVERT: 5 599 MET cc_start: 0.8878 (ttt) cc_final: 0.8438 (ttt) REVERT: 5 761 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8048 (mt) REVERT: 6 257 GLU cc_start: 0.5879 (tm-30) cc_final: 0.5539 (tm-30) REVERT: 6 711 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9135 (pp) REVERT: 7 81 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7389 (t70) REVERT: 7 132 ILE cc_start: 0.5380 (OUTLIER) cc_final: 0.4849 (tt) REVERT: 7 506 MET cc_start: 0.8563 (ttt) cc_final: 0.8299 (ttp) REVERT: 7 529 MET cc_start: 0.8554 (ptp) cc_final: 0.8185 (ptm) REVERT: 7 539 GLU cc_start: 0.8731 (tt0) cc_final: 0.8528 (tt0) REVERT: 7 550 LYS cc_start: 0.9272 (mttp) cc_final: 0.9011 (mttp) REVERT: 7 646 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.9079 (mmmt) REVERT: A 22 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7837 (ttm-80) REVERT: A 33 HIS cc_start: 0.7897 (m-70) cc_final: 0.7416 (m-70) REVERT: A 62 MET cc_start: 0.5997 (pmm) cc_final: 0.5742 (mpp) REVERT: A 73 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8225 (t80) REVERT: A 94 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8602 (m) REVERT: A 164 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8501 (p0) REVERT: A 193 GLN cc_start: 0.8962 (tt0) cc_final: 0.8557 (tt0) REVERT: A 197 GLU cc_start: 0.8014 (pm20) cc_final: 0.7618 (pm20) REVERT: B 114 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7179 (tm-30) REVERT: C 5 ASP cc_start: 0.8916 (t0) cc_final: 0.8457 (t0) REVERT: C 8 ASP cc_start: 0.9334 (t70) cc_final: 0.8862 (t0) REVERT: C 91 ASP cc_start: 0.8683 (t0) cc_final: 0.8270 (t0) REVERT: C 96 ASP cc_start: 0.8645 (t0) cc_final: 0.8227 (t0) REVERT: C 172 MET cc_start: 0.7962 (ttp) cc_final: 0.7588 (tmm) REVERT: E 2 TYR cc_start: 0.5479 (OUTLIER) cc_final: 0.4974 (m-80) REVERT: E 332 SER cc_start: 0.8870 (m) cc_final: 0.8602 (p) REVERT: E 426 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7481 (mm-30) REVERT: F 738 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8387 (p) REVERT: G 707 LEU cc_start: 0.9448 (tp) cc_final: 0.9207 (tp) REVERT: G 726 MET cc_start: 0.8862 (tpp) cc_final: 0.8604 (tpp) REVERT: G 835 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8189 (mm-30) REVERT: H 616 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8886 (m) REVERT: H 723 ASP cc_start: 0.8185 (t0) cc_final: 0.7895 (t0) REVERT: L 265 MET cc_start: 0.7114 (tpp) cc_final: 0.6759 (tmm) REVERT: L 482 ASP cc_start: 0.7512 (t0) cc_final: 0.7128 (t0) REVERT: Q 1535 MET cc_start: 0.7668 (tpp) cc_final: 0.7133 (tpp) REVERT: Q 1610 MET cc_start: 0.9022 (pmm) cc_final: 0.8781 (pmm) REVERT: Q 1780 HIS cc_start: 0.7085 (m90) cc_final: 0.6746 (m-70) REVERT: Q 2045 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8472 (pp) REVERT: X 165 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8686 (tptt) REVERT: X 200 MET cc_start: 0.8591 (ttp) cc_final: 0.8111 (tmm) REVERT: X 293 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8951 (t80) REVERT: X 588 MET cc_start: 0.8828 (mtt) cc_final: 0.8577 (mtm) outliers start: 128 outliers final: 79 residues processed: 719 average time/residue: 0.6829 time to fit residues: 862.3723 Evaluate side-chains 687 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 590 time to evaluate : 6.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 2 residue 316 SER Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 455 SER Chi-restraints excluded: chain 2 residue 627 GLN Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 4 residue 308 VAL Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 398 LYS Chi-restraints excluded: chain 4 residue 637 MET Chi-restraints excluded: chain 4 residue 824 GLU Chi-restraints excluded: chain 5 residue 22 ASP Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain 5 residue 391 LEU Chi-restraints excluded: chain 5 residue 404 MET Chi-restraints excluded: chain 5 residue 556 VAL Chi-restraints excluded: chain 5 residue 579 ASN Chi-restraints excluded: chain 5 residue 593 GLU Chi-restraints excluded: chain 5 residue 614 LEU Chi-restraints excluded: chain 5 residue 760 THR Chi-restraints excluded: chain 5 residue 761 ILE Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 6 residue 264 GLN Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 711 LEU Chi-restraints excluded: chain 6 residue 803 MET Chi-restraints excluded: chain 7 residue 81 ASP Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 340 VAL Chi-restraints excluded: chain 7 residue 432 LEU Chi-restraints excluded: chain 7 residue 548 ILE Chi-restraints excluded: chain 7 residue 554 ASN Chi-restraints excluded: chain 7 residue 646 LYS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain E residue 2 TYR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 567 MET Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 629 HIS Chi-restraints excluded: chain G residue 778 MET Chi-restraints excluded: chain H residue 527 HIS Chi-restraints excluded: chain H residue 600 PHE Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 782 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 460 THR Chi-restraints excluded: chain L residue 491 ASN Chi-restraints excluded: chain L residue 616 LEU Chi-restraints excluded: chain L residue 645 LEU Chi-restraints excluded: chain L residue 662 ILE Chi-restraints excluded: chain Q residue 1402 LEU Chi-restraints excluded: chain Q residue 1408 LEU Chi-restraints excluded: chain Q residue 1482 MET Chi-restraints excluded: chain Q residue 1550 VAL Chi-restraints excluded: chain Q residue 1570 TYR Chi-restraints excluded: chain Q residue 1594 SER Chi-restraints excluded: chain Q residue 2039 VAL Chi-restraints excluded: chain Q residue 2045 LEU Chi-restraints excluded: chain Q residue 2072 ILE Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 272 LYS Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain X residue 94 ASP Chi-restraints excluded: chain X residue 141 VAL Chi-restraints excluded: chain X residue 165 LYS Chi-restraints excluded: chain X residue 238 THR Chi-restraints excluded: chain X residue 293 PHE Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 383 VAL Chi-restraints excluded: chain X residue 403 ILE Chi-restraints excluded: chain X residue 414 LEU Chi-restraints excluded: chain X residue 666 TYR Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 93 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 909 random chunks: chunk 796 optimal weight: 6.9990 chunk 839 optimal weight: 9.9990 chunk 765 optimal weight: 2.9990 chunk 816 optimal weight: 3.9990 chunk 491 optimal weight: 2.9990 chunk 355 optimal weight: 1.9990 chunk 641 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 737 optimal weight: 0.5980 chunk 772 optimal weight: 3.9990 chunk 813 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 334 HIS 7 554 ASN G 527 HIS L 626 HIS ** Q1489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 76233 Z= 0.254 Angle : 0.556 14.563 103358 Z= 0.281 Chirality : 0.041 0.165 11785 Planarity : 0.004 0.061 12920 Dihedral : 10.371 84.775 10672 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.71 % Favored : 97.28 % Rotamer: Outliers : 1.57 % Allowed : 13.03 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % 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: 1.03 (0.09), residues: 8943 helix: 1.69 (0.09), residues: 3894 sheet: -0.47 (0.13), residues: 1441 loop : 0.20 (0.11), residues: 3608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q1798 HIS 0.006 0.001 HIS E 22 PHE 0.030 0.001 PHE 7 192 TYR 0.017 0.001 TYR 6 146 ARG 0.014 0.000 ARG 2 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 590 time to evaluate : 6.698 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: 2 276 MET cc_start: 0.8630 (tpp) cc_final: 0.8317 (tpt) REVERT: 2 413 ASP cc_start: 0.8642 (t0) cc_final: 0.8242 (t0) REVERT: 2 452 GLU cc_start: 0.7954 (tt0) cc_final: 0.7543 (tt0) REVERT: 2 592 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7232 (mm-30) REVERT: 2 627 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7942 (mm-40) REVERT: 2 781 MET cc_start: 0.7756 (mmm) cc_final: 0.7328 (tmm) REVERT: 3 290 ASP cc_start: 0.7643 (m-30) cc_final: 0.7344 (m-30) REVERT: 3 306 MET cc_start: 0.8727 (mmp) cc_final: 0.8358 (mmm) REVERT: 3 307 ASN cc_start: 0.8406 (p0) cc_final: 0.7924 (p0) REVERT: 4 316 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8303 (mt-10) REVERT: 4 538 LYS cc_start: 0.9053 (mttt) cc_final: 0.8628 (mtpt) REVERT: 4 559 ARG cc_start: 0.7136 (mtt90) cc_final: 0.6605 (mtt90) REVERT: 4 580 TYR cc_start: 0.8391 (m-80) cc_final: 0.8141 (m-80) REVERT: 4 636 LYS cc_start: 0.9323 (ttmt) cc_final: 0.8895 (ttmt) REVERT: 4 749 MET cc_start: 0.8192 (tpt) cc_final: 0.7862 (tpp) REVERT: 4 824 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8755 (tp30) REVERT: 5 257 LYS cc_start: 0.8273 (mtpt) cc_final: 0.8042 (mttp) REVERT: 5 348 MET cc_start: 0.6594 (ppp) cc_final: 0.6390 (ppp) REVERT: 5 404 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8227 (ttm) REVERT: 5 599 MET cc_start: 0.8796 (ttt) cc_final: 0.8447 (ttt) REVERT: 5 761 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8097 (mt) REVERT: 6 257 GLU cc_start: 0.5809 (tm-30) cc_final: 0.5548 (tm-30) REVERT: 6 711 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9130 (pp) REVERT: 7 81 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7358 (t70) REVERT: 7 132 ILE cc_start: 0.5440 (OUTLIER) cc_final: 0.4924 (tt) REVERT: 7 506 MET cc_start: 0.8620 (ttt) cc_final: 0.8412 (ttp) REVERT: 7 521 CYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8352 (t) REVERT: 7 539 GLU cc_start: 0.8732 (tt0) cc_final: 0.8525 (tt0) REVERT: 7 550 LYS cc_start: 0.9302 (mttp) cc_final: 0.8947 (mttp) REVERT: A 22 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.7867 (ttm-80) REVERT: A 33 HIS cc_start: 0.7732 (m-70) cc_final: 0.7099 (m-70) REVERT: A 62 MET cc_start: 0.5959 (pmm) cc_final: 0.5702 (mpp) REVERT: A 73 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8262 (t80) REVERT: A 79 MET cc_start: 0.9132 (mtm) cc_final: 0.8919 (mtm) REVERT: A 94 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8606 (m) REVERT: A 164 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8543 (p0) REVERT: A 193 GLN cc_start: 0.8987 (tt0) cc_final: 0.8596 (tt0) REVERT: A 197 GLU cc_start: 0.8047 (pm20) cc_final: 0.7644 (pm20) REVERT: B 114 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7205 (tm-30) REVERT: C 5 ASP cc_start: 0.8932 (t0) cc_final: 0.8467 (t0) REVERT: C 8 ASP cc_start: 0.9336 (t70) cc_final: 0.8845 (t0) REVERT: C 91 ASP cc_start: 0.8710 (t0) cc_final: 0.8291 (t0) REVERT: C 96 ASP cc_start: 0.8684 (t0) cc_final: 0.8289 (t0) REVERT: C 172 MET cc_start: 0.8024 (ttp) cc_final: 0.7622 (tmm) REVERT: D 93 MET cc_start: 0.7992 (mmp) cc_final: 0.7720 (mpp) REVERT: D 202 MET cc_start: 0.9260 (mmm) cc_final: 0.8652 (mmm) REVERT: E 2 TYR cc_start: 0.5924 (OUTLIER) cc_final: 0.5318 (m-80) REVERT: E 332 SER cc_start: 0.8972 (m) cc_final: 0.8741 (p) REVERT: E 426 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7616 (mm-30) REVERT: F 738 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8439 (p) REVERT: G 726 MET cc_start: 0.8858 (tpp) cc_final: 0.8593 (tpp) REVERT: G 835 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8127 (mm-30) REVERT: H 723 ASP cc_start: 0.8168 (t0) cc_final: 0.7872 (t0) REVERT: L 265 MET cc_start: 0.7037 (tpp) cc_final: 0.6745 (tmm) REVERT: L 482 ASP cc_start: 0.7564 (t0) cc_final: 0.7213 (t0) REVERT: Q 1535 MET cc_start: 0.7728 (tpp) cc_final: 0.7191 (tpp) REVERT: Q 1610 MET cc_start: 0.9053 (pmm) cc_final: 0.8792 (pmm) REVERT: Q 1702 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7384 (pp30) REVERT: Q 1780 HIS cc_start: 0.7079 (m90) cc_final: 0.6757 (m-70) REVERT: Q 2045 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8514 (pp) REVERT: Q 2133 CYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7271 (p) REVERT: X 165 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8724 (tptt) REVERT: X 200 MET cc_start: 0.8619 (ttp) cc_final: 0.8150 (tmm) REVERT: X 293 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8984 (t80) outliers start: 128 outliers final: 95 residues processed: 691 average time/residue: 0.6729 time to fit residues: 821.7752 Evaluate side-chains 689 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 576 time to evaluate : 6.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 2 residue 271 PHE Chi-restraints excluded: chain 2 residue 281 LEU Chi-restraints excluded: chain 2 residue 316 SER Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 455 SER Chi-restraints excluded: chain 2 residue 627 GLN Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 4 residue 308 VAL Chi-restraints excluded: chain 4 residue 314 MET Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 637 MET Chi-restraints excluded: chain 4 residue 693 ASP Chi-restraints excluded: chain 4 residue 824 GLU Chi-restraints excluded: chain 5 residue 22 ASP Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain 5 residue 391 LEU Chi-restraints excluded: chain 5 residue 404 MET Chi-restraints excluded: chain 5 residue 556 VAL Chi-restraints excluded: chain 5 residue 593 GLU Chi-restraints excluded: chain 5 residue 614 LEU Chi-restraints excluded: chain 5 residue 760 THR Chi-restraints excluded: chain 5 residue 761 ILE Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 711 LEU Chi-restraints excluded: chain 6 residue 803 MET Chi-restraints excluded: chain 7 residue 81 ASP Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 340 VAL Chi-restraints excluded: chain 7 residue 432 LEU Chi-restraints excluded: chain 7 residue 521 CYS Chi-restraints excluded: chain 7 residue 548 ILE Chi-restraints excluded: chain 7 residue 555 THR Chi-restraints excluded: chain 7 residue 646 LYS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain E residue 2 TYR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 567 MET Chi-restraints excluded: chain E residue 641 LEU Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 527 HIS Chi-restraints excluded: chain G residue 629 HIS Chi-restraints excluded: chain G residue 778 MET Chi-restraints excluded: chain H residue 527 HIS Chi-restraints excluded: chain H residue 600 PHE Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 782 VAL Chi-restraints excluded: chain H residue 855 LEU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 367 LEU Chi-restraints excluded: chain L residue 460 THR Chi-restraints excluded: chain L residue 491 ASN Chi-restraints excluded: chain L residue 563 ILE Chi-restraints excluded: chain L residue 616 LEU Chi-restraints excluded: chain L residue 627 LEU Chi-restraints excluded: chain L residue 645 LEU Chi-restraints excluded: chain L residue 662 ILE Chi-restraints excluded: chain Q residue 1402 LEU Chi-restraints excluded: chain Q residue 1408 LEU Chi-restraints excluded: chain Q residue 1426 VAL Chi-restraints excluded: chain Q residue 1432 THR Chi-restraints excluded: chain Q residue 1482 MET Chi-restraints excluded: chain Q residue 1550 VAL Chi-restraints excluded: chain Q residue 1570 TYR Chi-restraints excluded: chain Q residue 1594 SER Chi-restraints excluded: chain Q residue 1702 GLN Chi-restraints excluded: chain Q residue 1730 VAL Chi-restraints excluded: chain Q residue 2039 VAL Chi-restraints excluded: chain Q residue 2045 LEU Chi-restraints excluded: chain Q residue 2068 THR Chi-restraints excluded: chain Q residue 2072 ILE Chi-restraints excluded: chain Q residue 2133 CYS Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 272 LYS Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 490 LEU Chi-restraints excluded: chain R residue 673 MET Chi-restraints excluded: chain X residue 94 ASP Chi-restraints excluded: chain X residue 141 VAL Chi-restraints excluded: chain X residue 165 LYS Chi-restraints excluded: chain X residue 238 THR Chi-restraints excluded: chain X residue 249 SER Chi-restraints excluded: chain X residue 293 PHE Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 383 VAL Chi-restraints excluded: chain X residue 403 ILE Chi-restraints excluded: chain X residue 414 LEU Chi-restraints excluded: chain X residue 666 TYR Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 93 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 909 random chunks: chunk 536 optimal weight: 0.4980 chunk 863 optimal weight: 4.9990 chunk 526 optimal weight: 1.9990 chunk 409 optimal weight: 0.9990 chunk 600 optimal weight: 20.0000 chunk 905 optimal weight: 7.9990 chunk 833 optimal weight: 9.9990 chunk 721 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 557 optimal weight: 0.0060 chunk 442 optimal weight: 9.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 264 GLN E 254 GLN ** G 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 76233 Z= 0.152 Angle : 0.548 16.944 103358 Z= 0.273 Chirality : 0.040 0.221 11785 Planarity : 0.004 0.059 12920 Dihedral : 10.275 84.595 10672 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.34 % Favored : 97.65 % Rotamer: Outliers : 1.17 % Allowed : 13.54 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.09), residues: 8943 helix: 1.71 (0.09), residues: 3898 sheet: -0.41 (0.14), residues: 1446 loop : 0.21 (0.11), residues: 3599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Q1798 HIS 0.012 0.001 HIS G 527 PHE 0.028 0.001 PHE 7 192 TYR 0.027 0.001 TYR G 526 ARG 0.013 0.000 ARG 2 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17886 Ramachandran restraints generated. 8943 Oldfield, 0 Emsley, 8943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 631 time to evaluate : 6.948 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: 2 276 MET cc_start: 0.8624 (tpp) cc_final: 0.8303 (tpt) REVERT: 2 413 ASP cc_start: 0.8632 (t0) cc_final: 0.8243 (t0) REVERT: 2 452 GLU cc_start: 0.7850 (tt0) cc_final: 0.7470 (tt0) REVERT: 2 592 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7179 (mm-30) REVERT: 2 627 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7826 (mm-40) REVERT: 2 781 MET cc_start: 0.7679 (mmm) cc_final: 0.7236 (tmm) REVERT: 3 306 MET cc_start: 0.8719 (mmp) cc_final: 0.8493 (mmm) REVERT: 4 316 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8321 (mt-10) REVERT: 4 559 ARG cc_start: 0.7075 (mtt90) cc_final: 0.6567 (mtt90) REVERT: 4 580 TYR cc_start: 0.8368 (m-80) cc_final: 0.8113 (m-80) REVERT: 4 636 LYS cc_start: 0.9297 (ttmt) cc_final: 0.8871 (ttmt) REVERT: 4 749 MET cc_start: 0.8212 (tpt) cc_final: 0.7883 (tpp) REVERT: 5 599 MET cc_start: 0.8832 (ttt) cc_final: 0.8501 (ttt) REVERT: 5 625 ASN cc_start: 0.9086 (t0) cc_final: 0.8873 (t0) REVERT: 5 761 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8057 (mt) REVERT: 6 257 GLU cc_start: 0.5781 (tm-30) cc_final: 0.5493 (tm-30) REVERT: 7 81 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7333 (t70) REVERT: 7 132 ILE cc_start: 0.5397 (OUTLIER) cc_final: 0.4859 (tt) REVERT: 7 521 CYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8272 (t) REVERT: 7 550 LYS cc_start: 0.9238 (mttp) cc_final: 0.8859 (mttp) REVERT: 7 646 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9056 (mmmt) REVERT: A 22 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.7857 (ttm-80) REVERT: A 33 HIS cc_start: 0.7847 (m-70) cc_final: 0.7397 (m-70) REVERT: A 62 MET cc_start: 0.5864 (pmm) cc_final: 0.5583 (mpp) REVERT: A 73 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8221 (t80) REVERT: A 94 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8554 (m) REVERT: A 193 GLN cc_start: 0.8984 (tt0) cc_final: 0.8603 (tt0) REVERT: A 197 GLU cc_start: 0.8006 (pm20) cc_final: 0.7591 (pm20) REVERT: B 114 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7338 (tm-30) REVERT: C 5 ASP cc_start: 0.8903 (t0) cc_final: 0.8452 (t0) REVERT: C 8 ASP cc_start: 0.9330 (t70) cc_final: 0.8872 (t0) REVERT: C 91 ASP cc_start: 0.8670 (t0) cc_final: 0.8245 (t0) REVERT: C 96 ASP cc_start: 0.8705 (t0) cc_final: 0.8333 (t0) REVERT: D 93 MET cc_start: 0.8026 (mmp) cc_final: 0.7747 (mpp) REVERT: E 2 TYR cc_start: 0.5379 (OUTLIER) cc_final: 0.4895 (m-80) REVERT: E 264 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7437 (mm-30) REVERT: E 426 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7488 (mm-30) REVERT: F 738 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8394 (p) REVERT: G 707 LEU cc_start: 0.9079 (tp) cc_final: 0.8768 (tp) REVERT: G 726 MET cc_start: 0.8851 (tpp) cc_final: 0.8589 (tpp) REVERT: G 835 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8198 (mm-30) REVERT: H 565 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8004 (m-40) REVERT: H 616 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8881 (m) REVERT: H 723 ASP cc_start: 0.8133 (t0) cc_final: 0.7840 (t0) REVERT: H 726 MET cc_start: 0.8694 (tpp) cc_final: 0.8288 (tpp) REVERT: L 265 MET cc_start: 0.6989 (tpp) cc_final: 0.6749 (tmm) REVERT: L 482 ASP cc_start: 0.7563 (t0) cc_final: 0.7079 (t0) REVERT: Q 1535 MET cc_start: 0.7593 (tpp) cc_final: 0.7070 (tpp) REVERT: Q 1610 MET cc_start: 0.9030 (pmm) cc_final: 0.8815 (pmm) REVERT: Q 1780 HIS cc_start: 0.7072 (m90) cc_final: 0.6768 (m-70) REVERT: Q 2045 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8477 (pp) REVERT: X 200 MET cc_start: 0.8620 (ttp) cc_final: 0.8126 (tmm) REVERT: X 765 PHE cc_start: 0.8268 (m-80) cc_final: 0.7860 (m-80) outliers start: 96 outliers final: 64 residues processed: 703 average time/residue: 0.6617 time to fit residues: 817.1550 Evaluate side-chains 667 residues out of total 8233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 590 time to evaluate : 6.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 234 LEU Chi-restraints excluded: chain 2 residue 281 LEU Chi-restraints excluded: chain 2 residue 316 SER Chi-restraints excluded: chain 2 residue 397 VAL Chi-restraints excluded: chain 2 residue 627 GLN Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 4 residue 308 VAL Chi-restraints excluded: chain 4 residue 393 ASP Chi-restraints excluded: chain 4 residue 637 MET Chi-restraints excluded: chain 4 residue 693 ASP Chi-restraints excluded: chain 5 residue 22 ASP Chi-restraints excluded: chain 5 residue 252 ASP Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain 5 residue 391 LEU Chi-restraints excluded: chain 5 residue 614 LEU Chi-restraints excluded: chain 5 residue 761 ILE Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 6 residue 264 GLN Chi-restraints excluded: chain 6 residue 404 VAL Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 803 MET Chi-restraints excluded: chain 7 residue 81 ASP Chi-restraints excluded: chain 7 residue 132 ILE Chi-restraints excluded: chain 7 residue 255 VAL Chi-restraints excluded: chain 7 residue 313 CYS Chi-restraints excluded: chain 7 residue 340 VAL Chi-restraints excluded: chain 7 residue 521 CYS Chi-restraints excluded: chain 7 residue 548 ILE Chi-restraints excluded: chain 7 residue 646 LYS Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain E residue 2 TYR Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 567 MET Chi-restraints excluded: chain F residue 738 THR Chi-restraints excluded: chain G residue 505 VAL Chi-restraints excluded: chain G residue 629 HIS Chi-restraints excluded: chain H residue 527 HIS Chi-restraints excluded: chain H residue 565 ASN Chi-restraints excluded: chain H residue 600 PHE Chi-restraints excluded: chain H residue 616 VAL Chi-restraints excluded: chain H residue 782 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 491 ASN Chi-restraints excluded: chain L residue 616 LEU Chi-restraints excluded: chain L residue 662 ILE Chi-restraints excluded: chain Q residue 1402 LEU Chi-restraints excluded: chain Q residue 1408 LEU Chi-restraints excluded: chain Q residue 1482 MET Chi-restraints excluded: chain Q residue 1550 VAL Chi-restraints excluded: chain Q residue 1570 TYR Chi-restraints excluded: chain Q residue 2045 LEU Chi-restraints excluded: chain Q residue 2072 ILE Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 272 LYS Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain X residue 141 VAL Chi-restraints excluded: chain X residue 238 THR Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 383 VAL Chi-restraints excluded: chain X residue 403 ILE Chi-restraints excluded: chain X residue 414 LEU Chi-restraints excluded: chain X residue 666 TYR Chi-restraints excluded: chain Y residue 60 LEU Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 93 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 909 random chunks: chunk 572 optimal weight: 8.9990 chunk 768 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 chunk 664 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 722 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 741 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 264 GLN ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 382 HIS F 507 ASN ** Q1489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 611 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.131180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100901 restraints weight = 211579.529| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.74 r_work: 0.3234 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 76233 Z= 0.168 Angle : 0.548 15.477 103358 Z= 0.273 Chirality : 0.040 0.165 11785 Planarity : 0.004 0.056 12920 Dihedral : 10.218 85.102 10670 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.36 % Favored : 97.63 % Rotamer: Outliers : 1.14 % Allowed : 13.82 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.09), residues: 8943 helix: 1.70 (0.09), residues: 3906 sheet: -0.38 (0.14), residues: 1446 loop : 0.22 (0.11), residues: 3591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.001 TRP G 718 HIS 0.006 0.001 HIS E 22 PHE 0.028 0.001 PHE 7 192 TYR 0.019 0.001 TYR 6 146 ARG 0.013 0.000 ARG E 386 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16855.89 seconds wall clock time: 297 minutes 52.33 seconds (17872.33 seconds total)