Starting phenix.real_space_refine on Sat Sep 28 00:26:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt7_13620/09_2024/7pt7_13620_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt7_13620/09_2024/7pt7_13620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt7_13620/09_2024/7pt7_13620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt7_13620/09_2024/7pt7_13620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt7_13620/09_2024/7pt7_13620_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt7_13620/09_2024/7pt7_13620_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 9 Type Number sf(0) Gaussians Zn 12 6.06 5 P 26 5.49 5 Mg 14 5.21 5 S 306 5.16 5 Be 7 3.05 5 C 42410 2.51 5 N 11715 2.21 5 O 12909 1.98 5 F 21 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 67420 Number of models: 1 Model: "" Number of chains: 29 Chain: "1" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 20 Classifications: {'peptide': 4} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4960 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 25, 'TRANS': 600} Chain breaks: 3 Chain: "3" Number of atoms: 4986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 4986 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 30, 'TRANS': 604} Chain breaks: 6 Chain: "4" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5323 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 24, 'TRANS': 643} Chain breaks: 1 Chain: "5" Number of atoms: 4927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4927 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 28, 'TRANS': 599} Chain breaks: 4 Chain: "6" Number of atoms: 4889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4889 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 22, 'TRANS': 594} Chain breaks: 4 Chain: "7" Number of atoms: 5370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5370 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 30, 'TRANS': 652} Chain breaks: 3 Chain: "8" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3292 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 3 Chain: "9" Number of atoms: 2813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2813 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain breaks: 4 Chain: "B" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4960 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 25, 'TRANS': 600} Chain breaks: 3 Chain: "C" Number of atoms: 4966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4966 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 30, 'TRANS': 602} Chain breaks: 6 Chain: "D" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5323 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 24, 'TRANS': 643} Chain breaks: 1 Chain: "E" Number of atoms: 4927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4927 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 28, 'TRANS': 599} Chain breaks: 4 Chain: "F" Number of atoms: 4889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4889 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 22, 'TRANS': 594} Chain breaks: 4 Chain: "G" Number of atoms: 5370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5370 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 30, 'TRANS': 652} Chain breaks: 3 Chain: "2" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "5" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "8" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1322 SG CYS 2 341 103.958 108.489 69.291 1.00130.39 S ATOM 1345 SG CYS 2 344 105.352 111.758 68.030 1.00119.74 S ATOM 1503 SG CYS 2 364 105.964 108.449 66.041 1.00124.72 S ATOM 1524 SG CYS 2 367 107.733 109.287 69.253 1.00127.42 S ATOM 11402 SG CYS 4 349 115.516 69.576 55.479 1.00139.18 S ATOM 11423 SG CYS 4 352 116.781 67.007 53.309 1.00133.09 S ATOM 11570 SG CYS 4 371 117.725 66.806 56.985 1.00140.97 S ATOM 11612 SG CYS 4 376 119.356 69.481 54.959 1.00147.55 S ATOM 16575 SG CYS 5 183 107.564 102.645 94.129 1.00 53.82 S ATOM 16600 SG CYS 5 186 111.052 104.275 94.888 1.00 51.93 S ATOM 16790 SG CYS 5 211 108.578 106.186 92.928 1.00 60.63 S ATOM 16825 SG CYS 5 236 110.287 103.176 91.493 1.00 65.31 S ATOM 21452 SG CYS 6 311 109.362 88.722 54.371 1.00131.25 S ATOM 21474 SG CYS 6 314 112.203 90.765 52.062 1.00111.17 S ATOM 21631 SG CYS 6 333 112.028 86.893 52.482 1.00123.08 S ATOM 21665 SG CYS 6 338 112.921 89.093 55.128 1.00118.83 S ATOM 26860 SG CYS 7 262 118.063 58.293 80.157 1.00 95.13 S ATOM 26883 SG CYS 7 265 120.779 57.575 82.649 1.00 85.37 S ATOM 27037 SG CYS 7 284 118.438 60.430 83.272 1.00100.39 S ATOM 27074 SG CYS 7 289 121.031 60.702 80.517 1.00104.26 S ATOM 32051 SG CYS 8 223 97.802 165.276 44.630 1.00105.22 S ATOM 32064 SG CYS 8 225 98.850 161.987 46.671 1.00111.15 S ATOM 32426 SG CYS 8 293 95.984 164.019 47.629 1.00 79.93 S ATOM 36248 SG CYS 9 661 109.585 178.711 73.411 1.00 49.17 S ATOM 36271 SG CYS 9 664 113.398 179.299 74.054 1.00 48.13 S ATOM 37882 SG CYS B 341 119.163 83.168 72.434 1.00149.96 S ATOM 37905 SG CYS B 344 120.113 79.825 70.663 1.00148.82 S ATOM 38063 SG CYS B 364 118.573 82.782 68.729 1.00149.47 S ATOM 38084 SG CYS B 367 116.732 80.374 71.166 1.00147.09 S ATOM 47942 SG CYS D 349 110.054 122.108 54.984 1.00114.78 S ATOM 47963 SG CYS D 352 107.564 123.946 52.744 1.00118.11 S ATOM 48110 SG CYS D 371 106.917 123.511 56.422 1.00118.78 S ATOM 48152 SG CYS D 376 106.547 120.568 54.131 1.00132.42 S ATOM 53115 SG CYS E 183 113.394 85.834 94.530 1.00 42.40 S ATOM 53140 SG CYS E 186 109.441 85.690 94.638 1.00 38.81 S ATOM 53330 SG CYS E 211 111.509 83.123 92.781 1.00 60.57 S ATOM 53365 SG CYS E 236 111.272 86.930 91.733 1.00 57.91 S ATOM 57992 SG CYS F 311 116.244 100.869 54.834 1.00118.68 S ATOM 58014 SG CYS F 314 113.852 98.293 52.669 1.00106.96 S ATOM 58171 SG CYS F 333 114.524 101.836 51.773 1.00121.75 S ATOM 58205 SG CYS F 338 112.560 101.103 54.739 1.00113.64 S ATOM 63400 SG CYS G 262 103.950 132.021 79.189 1.00 60.76 S ATOM 63423 SG CYS G 265 101.146 133.067 81.372 1.00 60.57 S ATOM 63577 SG CYS G 284 103.100 129.854 82.067 1.00 69.23 S ATOM 63614 SG CYS G 289 100.622 129.774 79.437 1.00 82.77 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="ZN ZN 61103 " occ=0.50 residue: pdb="ZN ZN F1103 " occ=0.50 Time building chain proxies: 31.36, per 1000 atoms: 0.47 Number of scatterers: 67420 At special positions: 0 Unit cell: (224.048, 219.76, 161.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 12 29.99 S 306 16.00 P 26 15.00 Mg 14 11.99 F 21 9.00 O 12909 8.00 N 11715 7.00 C 42410 6.00 Be 7 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.08 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 2 903 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 2 903 " - pdb=" SG CYS 2 364 " pdb=" ZN 41101 " pdb="ZN ZN 41101 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41101 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41101 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41101 " - pdb=" SG CYS 4 376 " pdb=" ZN 5 803 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 5 803 " - pdb=" SG CYS 5 183 " pdb=" ZN 61103 " pdb="ZN ZN 61103 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61103 " - pdb=" SG CYS 6 333 " pdb="ZN ZN 61103 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61103 " - pdb=" SG CYS 6 314 " pdb=" ZN 71101 " pdb="ZN ZN 71101 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 71101 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 71101 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 71101 " - pdb=" SG CYS 7 289 " pdb=" ZN 81005 " pdb="ZN ZN 81005 " - pdb=" ND1 HIS 8 348 " pdb="ZN ZN 81005 " - pdb=" SG CYS 8 293 " pdb="ZN ZN 81005 " - pdb=" SG CYS 8 225 " pdb="ZN ZN 81005 " - pdb=" SG CYS 8 223 " pdb=" ZN 91101 " pdb="ZN ZN 91101 " - pdb=" NE2 HIS 9 674 " pdb="ZN ZN 91101 " - pdb=" ND1 HIS 9 680 " pdb="ZN ZN 91101 " - pdb=" SG CYS 9 664 " pdb="ZN ZN 91101 " - pdb=" SG CYS 9 661 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 344 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 367 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 364 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 341 " pdb=" ZN D1101 " pdb="ZN ZN D1101 " - pdb=" SG CYS D 371 " pdb="ZN ZN D1101 " - pdb=" SG CYS D 352 " pdb="ZN ZN D1101 " - pdb=" SG CYS D 349 " pdb="ZN ZN D1101 " - pdb=" SG CYS D 376 " pdb=" ZN E 804 " pdb="ZN ZN E 804 " - pdb=" SG CYS E 236 " pdb="ZN ZN E 804 " - pdb=" SG CYS E 186 " pdb="ZN ZN E 804 " - pdb=" SG CYS E 183 " pdb="ZN ZN E 804 " - pdb=" SG CYS E 211 " pdb=" ZN F1103 " pdb="ZN ZN F1103 " - pdb=" SG CYS F 333 " pdb="ZN ZN F1103 " - pdb=" SG CYS F 338 " pdb="ZN ZN F1103 " - pdb=" SG CYS F 311 " pdb="ZN ZN F1103 " - pdb=" SG CYS F 314 " pdb=" ZN G1101 " pdb="ZN ZN G1101 " - pdb=" SG CYS G 284 " pdb="ZN ZN G1101 " - pdb=" SG CYS G 265 " pdb="ZN ZN G1101 " - pdb=" SG CYS G 262 " pdb="ZN ZN G1101 " - pdb=" SG CYS G 289 " Number of angles added : 64 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16088 Finding SS restraints... Secondary structure from input PDB file: 321 helices and 87 sheets defined 44.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.61 Creating SS restraints... Processing helix chain '2' and resid 182 through 188 removed outlier: 3.767A pdb=" N LEU 2 186 " --> pdb=" O THR 2 182 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER 2 187 " --> pdb=" O LEU 2 183 " (cutoff:3.500A) Processing helix chain '2' and resid 193 through 199 Processing helix chain '2' and resid 200 through 218 Processing helix chain '2' and resid 225 through 238 Processing helix chain '2' and resid 245 through 253 removed outlier: 3.788A pdb=" N LEU 2 249 " --> pdb=" O ASN 2 245 " (cutoff:3.500A) Processing helix chain '2' and resid 253 through 263 Processing helix chain '2' and resid 263 through 283 removed outlier: 3.921A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU 2 268 " --> pdb=" O PRO 2 264 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) Processing helix chain '2' and resid 305 through 309 Processing helix chain '2' and resid 413 through 415 No H-bonds generated for 'chain '2' and resid 413 through 415' Processing helix chain '2' and resid 477 through 490 removed outlier: 4.154A pdb=" N ARG 2 482 " --> pdb=" O GLU 2 478 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU 2 483 " --> pdb=" O GLU 2 479 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 501 Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 560 removed outlier: 3.511A pdb=" N ALA 2 560 " --> pdb=" O VAL 2 556 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 599 Processing helix chain '2' and resid 613 through 627 Processing helix chain '2' and resid 652 through 656 removed outlier: 4.215A pdb=" N ARG 2 656 " --> pdb=" O ASN 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 667 removed outlier: 3.582A pdb=" N VAL 2 667 " --> pdb=" O LEU 2 663 " (cutoff:3.500A) Processing helix chain '2' and resid 670 through 677 removed outlier: 3.974A pdb=" N PHE 2 677 " --> pdb=" O ILE 2 673 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 706 Processing helix chain '2' and resid 759 through 774 removed outlier: 4.003A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 782 through 801 removed outlier: 4.068A pdb=" N VAL 2 786 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER 2 787 " --> pdb=" O MET 2 783 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 3.656A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 848 Processing helix chain '2' and resid 854 through 859 removed outlier: 3.944A pdb=" N ARG 2 858 " --> pdb=" O ARG 2 854 " (cutoff:3.500A) Processing helix chain '2' and resid 860 through 864 removed outlier: 3.694A pdb=" N ILE 2 863 " --> pdb=" O SER 2 860 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 35 Processing helix chain '3' and resid 35 through 56 removed outlier: 4.284A pdb=" N ARG 3 39 " --> pdb=" O PHE 3 35 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 107 Processing helix chain '3' and resid 107 through 117 Processing helix chain '3' and resid 117 through 137 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 161 through 163 No H-bonds generated for 'chain '3' and resid 161 through 163' Processing helix chain '3' and resid 172 through 176 Processing helix chain '3' and resid 281 through 283 No H-bonds generated for 'chain '3' and resid 281 through 283' Processing helix chain '3' and resid 343 through 354 Processing helix chain '3' and resid 358 through 367 Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 426 Processing helix chain '3' and resid 460 through 465 Processing helix chain '3' and resid 475 through 478 Processing helix chain '3' and resid 479 through 485 removed outlier: 3.618A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) Processing helix chain '3' and resid 485 through 492 removed outlier: 4.574A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 534 Processing helix chain '3' and resid 536 through 543 Processing helix chain '3' and resid 554 through 570 Processing helix chain '3' and resid 652 through 667 removed outlier: 3.552A pdb=" N GLU 3 665 " --> pdb=" O GLN 3 661 " (cutoff:3.500A) Processing helix chain '3' and resid 672 through 689 removed outlier: 3.532A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 716 removed outlier: 3.745A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 Processing helix chain '4' and resid 186 through 200 Processing helix chain '4' and resid 202 through 210 removed outlier: 3.834A pdb=" N ARG 4 206 " --> pdb=" O LYS 4 202 " (cutoff:3.500A) Processing helix chain '4' and resid 217 through 222 removed outlier: 3.697A pdb=" N GLU 4 222 " --> pdb=" O ASN 4 218 " (cutoff:3.500A) Processing helix chain '4' and resid 224 through 237 Processing helix chain '4' and resid 244 through 251 removed outlier: 3.526A pdb=" N LEU 4 248 " --> pdb=" O ASP 4 244 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR 4 251 " --> pdb=" O ASN 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 removed outlier: 3.627A pdb=" N TYR 4 258 " --> pdb=" O THR 4 254 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 288 Processing helix chain '4' and resid 292 through 298 removed outlier: 4.348A pdb=" N ILE 4 296 " --> pdb=" O ASP 4 292 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR 4 298 " --> pdb=" O ASP 4 294 " (cutoff:3.500A) Processing helix chain '4' and resid 318 through 322 removed outlier: 3.513A pdb=" N ILE 4 322 " --> pdb=" O PRO 4 319 " (cutoff:3.500A) Processing helix chain '4' and resid 422 through 424 No H-bonds generated for 'chain '4' and resid 422 through 424' Processing helix chain '4' and resid 481 through 492 removed outlier: 3.874A pdb=" N MET 4 486 " --> pdb=" O GLU 4 482 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN 4 487 " --> pdb=" O GLN 4 483 " (cutoff:3.500A) Processing helix chain '4' and resid 502 through 514 Processing helix chain '4' and resid 517 through 525 Processing helix chain '4' and resid 533 through 546 Processing helix chain '4' and resid 573 through 585 Processing helix chain '4' and resid 594 through 596 No H-bonds generated for 'chain '4' and resid 594 through 596' Processing helix chain '4' and resid 619 through 624 Processing helix chain '4' and resid 638 through 644 removed outlier: 4.371A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) Processing helix chain '4' and resid 644 through 651 removed outlier: 4.093A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 Processing helix chain '4' and resid 695 through 702 removed outlier: 3.506A pdb=" N ARG 4 701 " --> pdb=" O PRO 4 697 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE 4 702 " --> pdb=" O LEU 4 698 " (cutoff:3.500A) Processing helix chain '4' and resid 713 through 727 Processing helix chain '4' and resid 743 through 758 Processing helix chain '4' and resid 763 through 778 Processing helix chain '4' and resid 794 through 812 Processing helix chain '4' and resid 818 through 833 removed outlier: 3.664A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) Processing helix chain '5' and resid 23 through 38 Processing helix chain '5' and resid 44 through 56 Processing helix chain '5' and resid 65 through 72 removed outlier: 3.856A pdb=" N ILE 5 69 " --> pdb=" O MET 5 65 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY 5 70 " --> pdb=" O GLU 5 66 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR 5 71 " --> pdb=" O HIS 5 67 " (cutoff:3.500A) Processing helix chain '5' and resid 72 through 82 Processing helix chain '5' and resid 82 through 107 removed outlier: 3.517A pdb=" N ILE 5 86 " --> pdb=" O GLU 5 82 " (cutoff:3.500A) Proline residue: 5 88 - end of helix removed outlier: 4.269A pdb=" N ALA 5 107 " --> pdb=" O ILE 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 151 removed outlier: 3.533A pdb=" N LEU 5 151 " --> pdb=" O LEU 5 148 " (cutoff:3.500A) Processing helix chain '5' and resid 279 through 283 Processing helix chain '5' and resid 350 through 362 removed outlier: 3.511A pdb=" N ARG 5 362 " --> pdb=" O LEU 5 358 " (cutoff:3.500A) Processing helix chain '5' and resid 365 through 374 Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 421 through 433 Processing helix chain '5' and resid 467 through 472 Processing helix chain '5' and resid 486 through 499 removed outlier: 3.830A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU 5 495 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) Processing helix chain '5' and resid 535 through 540 removed outlier: 3.788A pdb=" N ILE 5 540 " --> pdb=" O PRO 5 536 " (cutoff:3.500A) Processing helix chain '5' and resid 543 through 550 Processing helix chain '5' and resid 561 through 576 Processing helix chain '5' and resid 595 through 610 Processing helix chain '5' and resid 615 through 640 removed outlier: 3.540A pdb=" N ALA 5 619 " --> pdb=" O SER 5 615 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU 5 620 " --> pdb=" O PRO 5 616 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS 5 621 " --> pdb=" O GLN 5 617 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER 5 640 " --> pdb=" O ASN 5 636 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 667 removed outlier: 3.867A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 688 Processing helix chain '6' and resid 105 through 121 removed outlier: 3.559A pdb=" N GLU 6 109 " --> pdb=" O ASP 6 105 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 146 removed outlier: 3.851A pdb=" N GLU 6 141 " --> pdb=" O ARG 6 137 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR 6 146 " --> pdb=" O PHE 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 161 removed outlier: 3.921A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 173 Processing helix chain '6' and resid 173 through 192 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 384 through 386 No H-bonds generated for 'chain '6' and resid 384 through 386' Processing helix chain '6' and resid 501 through 508 Processing helix chain '6' and resid 509 through 521 Processing helix chain '6' and resid 525 through 532 Processing helix chain '6' and resid 541 through 553 Processing helix chain '6' and resid 580 through 589 Processing helix chain '6' and resid 604 through 609 Processing helix chain '6' and resid 626 through 631 Processing helix chain '6' and resid 645 through 659 removed outlier: 3.575A pdb=" N GLN 6 658 " --> pdb=" O GLU 6 654 " (cutoff:3.500A) Processing helix chain '6' and resid 684 through 688 removed outlier: 3.998A pdb=" N ARG 6 688 " --> pdb=" O VAL 6 685 " (cutoff:3.500A) Processing helix chain '6' and resid 695 through 699 removed outlier: 3.501A pdb=" N LEU 6 699 " --> pdb=" O ARG 6 696 " (cutoff:3.500A) Processing helix chain '6' and resid 702 through 709 Processing helix chain '6' and resid 720 through 737 Processing helix chain '6' and resid 747 through 761 removed outlier: 3.593A pdb=" N PHE 6 761 " --> pdb=" O TYR 6 757 " (cutoff:3.500A) Processing helix chain '6' and resid 766 through 784 removed outlier: 3.621A pdb=" N ARG 6 770 " --> pdb=" O THR 6 766 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR 6 772 " --> pdb=" O GLU 6 768 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP 6 784 " --> pdb=" O LEU 6 780 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 814 removed outlier: 3.660A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA 6 809 " --> pdb=" O ARG 6 805 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 835 removed outlier: 3.502A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 27 removed outlier: 3.619A pdb=" N LEU 7 17 " --> pdb=" O ASP 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 Processing helix chain '7' and resid 82 through 96 removed outlier: 3.553A pdb=" N GLN 7 95 " --> pdb=" O GLU 7 91 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY 7 96 " --> pdb=" O LYS 7 92 " (cutoff:3.500A) Processing helix chain '7' and resid 101 through 124 removed outlier: 8.019A pdb=" N ASN 7 111 " --> pdb=" O GLN 7 107 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N HIS 7 112 " --> pdb=" O GLN 7 108 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE 7 113 " --> pdb=" O ASN 7 109 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 165 removed outlier: 3.723A pdb=" N ASN 7 165 " --> pdb=" O ILE 7 161 " (cutoff:3.500A) Processing helix chain '7' and resid 178 through 189 removed outlier: 4.476A pdb=" N GLU 7 183 " --> pdb=" O ASP 7 179 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL 7 184 " --> pdb=" O ALA 7 180 " (cutoff:3.500A) Processing helix chain '7' and resid 193 through 198 removed outlier: 3.920A pdb=" N ARG 7 198 " --> pdb=" O ASN 7 195 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 212 removed outlier: 3.557A pdb=" N ALA 7 212 " --> pdb=" O GLN 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 226 through 230 Processing helix chain '7' and resid 286 through 292 Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain '7' and resid 394 through 407 Processing helix chain '7' and resid 409 through 418 removed outlier: 3.516A pdb=" N ILE 7 418 " --> pdb=" O LEU 7 414 " (cutoff:3.500A) Processing helix chain '7' and resid 426 through 438 Processing helix chain '7' and resid 465 through 477 Processing helix chain '7' and resid 487 through 492 removed outlier: 4.092A pdb=" N VAL 7 491 " --> pdb=" O GLY 7 487 " (cutoff:3.500A) Processing helix chain '7' and resid 511 through 516 Processing helix chain '7' and resid 530 through 544 removed outlier: 3.633A pdb=" N ALA 7 536 " --> pdb=" O SER 7 532 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU 7 539 " --> pdb=" O THR 7 535 " (cutoff:3.500A) Processing helix chain '7' and resid 579 through 585 Processing helix chain '7' and resid 587 through 594 removed outlier: 3.767A pdb=" N ARG 7 593 " --> pdb=" O ALA 7 589 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE 7 594 " --> pdb=" O LEU 7 590 " (cutoff:3.500A) Processing helix chain '7' and resid 605 through 622 removed outlier: 3.751A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 648 removed outlier: 3.660A pdb=" N LYS 7 648 " --> pdb=" O TYR 7 644 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 674 Processing helix chain '7' and resid 685 through 704 removed outlier: 3.863A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 723 removed outlier: 3.645A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) Processing helix chain '7' and resid 724 through 728 removed outlier: 4.023A pdb=" N LEU 7 727 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR 7 728 " --> pdb=" O GLU 7 725 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 724 through 728' Processing helix chain '8' and resid 12 through 26 removed outlier: 4.419A pdb=" N GLU 8 18 " --> pdb=" O GLU 8 14 " (cutoff:3.500A) Processing helix chain '8' and resid 55 through 60 Processing helix chain '8' and resid 83 through 97 Processing helix chain '8' and resid 127 through 132 removed outlier: 3.911A pdb=" N PHE 8 131 " --> pdb=" O GLU 8 127 " (cutoff:3.500A) Processing helix chain '8' and resid 136 through 158 Processing helix chain '8' and resid 165 through 167 No H-bonds generated for 'chain '8' and resid 165 through 167' Processing helix chain '8' and resid 286 through 291 Processing helix chain '8' and resid 298 through 313 removed outlier: 3.965A pdb=" N ILE 8 302 " --> pdb=" O THR 8 298 " (cutoff:3.500A) Processing helix chain '8' and resid 324 through 336 Processing helix chain '8' and resid 337 through 348 Processing helix chain '8' and resid 368 through 384 removed outlier: 4.058A pdb=" N PHE 8 372 " --> pdb=" O GLY 8 368 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU 8 380 " --> pdb=" O LEU 8 376 " (cutoff:3.500A) Processing helix chain '8' and resid 391 through 403 removed outlier: 4.061A pdb=" N THR 8 395 " --> pdb=" O VAL 8 391 " (cutoff:3.500A) Processing helix chain '8' and resid 425 through 450 removed outlier: 3.647A pdb=" N GLN 8 448 " --> pdb=" O GLN 8 444 " (cutoff:3.500A) Processing helix chain '8' and resid 459 through 465 Processing helix chain '8' and resid 471 through 475 removed outlier: 3.748A pdb=" N GLU 8 474 " --> pdb=" O GLU 8 471 " (cutoff:3.500A) Processing helix chain '9' and resid 112 through 116 Processing helix chain '9' and resid 137 through 157 removed outlier: 3.672A pdb=" N PHE 9 155 " --> pdb=" O LEU 9 151 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR 9 157 " --> pdb=" O ARG 9 153 " (cutoff:3.500A) Processing helix chain '9' and resid 189 through 198 removed outlier: 4.306A pdb=" N LYS 9 195 " --> pdb=" O LEU 9 191 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS 9 196 " --> pdb=" O SER 9 192 " (cutoff:3.500A) Processing helix chain '9' and resid 203 through 215 removed outlier: 4.093A pdb=" N ASN 9 213 " --> pdb=" O ARG 9 209 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU 9 214 " --> pdb=" O PHE 9 210 " (cutoff:3.500A) Processing helix chain '9' and resid 233 through 242 Processing helix chain '9' and resid 285 through 289 Processing helix chain '9' and resid 319 through 333 Processing helix chain '9' and resid 333 through 344 Processing helix chain '9' and resid 373 through 385 Processing helix chain '9' and resid 521 through 530 removed outlier: 3.742A pdb=" N ARG 9 529 " --> pdb=" O LYS 9 525 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU 9 530 " --> pdb=" O SER 9 526 " (cutoff:3.500A) Processing helix chain '9' and resid 670 through 676 removed outlier: 3.848A pdb=" N VAL 9 676 " --> pdb=" O GLU 9 672 " (cutoff:3.500A) Processing helix chain '9' and resid 677 through 686 Processing helix chain '9' and resid 687 through 689 No H-bonds generated for 'chain '9' and resid 687 through 689' Processing helix chain '9' and resid 690 through 701 removed outlier: 3.530A pdb=" N LEU 9 696 " --> pdb=" O ALA 9 692 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG 9 701 " --> pdb=" O ILE 9 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 188 Processing helix chain 'B' and resid 193 through 200 removed outlier: 3.852A pdb=" N TRP B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 198 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 218 Processing helix chain 'B' and resid 225 through 238 Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 263 through 283 removed outlier: 3.523A pdb=" N LYS B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 289 removed outlier: 3.963A pdb=" N ARG B 288 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 removed outlier: 3.991A pdb=" N LEU B 309 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 594 through 599 Processing helix chain 'B' and resid 613 through 627 Processing helix chain 'B' and resid 652 through 656 removed outlier: 3.893A pdb=" N ARG B 656 " --> pdb=" O ASN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 667 Processing helix chain 'B' and resid 670 through 676 removed outlier: 3.984A pdb=" N ARG B 676 " --> pdb=" O PRO B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 Processing helix chain 'B' and resid 759 through 774 Processing helix chain 'B' and resid 782 through 801 removed outlier: 3.928A pdb=" N VAL B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 787 " --> pdb=" O MET B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 825 removed outlier: 3.535A pdb=" N ARG B 824 " --> pdb=" O PHE B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 849 Processing helix chain 'B' and resid 854 through 859 removed outlier: 3.956A pdb=" N ARG B 858 " --> pdb=" O ARG B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 864 Processing helix chain 'C' and resid 18 through 35 Processing helix chain 'C' and resid 35 through 56 removed outlier: 4.260A pdb=" N ARG C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR C 56 " --> pdb=" O ASN C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 107 through 117 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 121 through 137 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 172 through 176 Processing helix chain 'C' and resid 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 343 through 355 Processing helix chain 'C' and resid 358 through 366 Processing helix chain 'C' and resid 374 through 387 Processing helix chain 'C' and resid 414 through 426 Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 479 through 493 removed outlier: 4.653A pdb=" N GLU C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 534 Processing helix chain 'C' and resid 536 through 543 Processing helix chain 'C' and resid 554 through 570 Processing helix chain 'C' and resid 652 through 667 Processing helix chain 'C' and resid 672 through 688 Processing helix chain 'C' and resid 698 through 716 removed outlier: 3.804A pdb=" N LEU C 702 " --> pdb=" O THR C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 739 Processing helix chain 'D' and resid 186 through 200 Processing helix chain 'D' and resid 202 through 210 removed outlier: 4.059A pdb=" N ARG D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 216 Processing helix chain 'D' and resid 224 through 237 Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.734A pdb=" N HIS D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 288 Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 318 through 322 Processing helix chain 'D' and resid 378 through 380 No H-bonds generated for 'chain 'D' and resid 378 through 380' Processing helix chain 'D' and resid 422 through 424 No H-bonds generated for 'chain 'D' and resid 422 through 424' Processing helix chain 'D' and resid 481 through 492 removed outlier: 3.553A pdb=" N LEU D 485 " --> pdb=" O ILE D 481 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N MET D 486 " --> pdb=" O GLU D 482 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLN D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL D 490 " --> pdb=" O MET D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 514 Processing helix chain 'D' and resid 517 through 526 Processing helix chain 'D' and resid 533 through 546 Processing helix chain 'D' and resid 573 through 585 Processing helix chain 'D' and resid 594 through 596 No H-bonds generated for 'chain 'D' and resid 594 through 596' Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 638 through 643 Processing helix chain 'D' and resid 644 through 652 removed outlier: 3.684A pdb=" N VAL D 648 " --> pdb=" O VAL D 644 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 650 " --> pdb=" O HIS D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 681 removed outlier: 4.149A pdb=" N ARG D 681 " --> pdb=" O ILE D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 693 Processing helix chain 'D' and resid 695 through 702 removed outlier: 3.642A pdb=" N ARG D 701 " --> pdb=" O PRO D 697 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 702 " --> pdb=" O LEU D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 728 Processing helix chain 'D' and resid 743 through 758 Processing helix chain 'D' and resid 763 through 778 Processing helix chain 'D' and resid 794 through 812 Processing helix chain 'D' and resid 818 through 833 removed outlier: 3.641A pdb=" N VAL D 822 " --> pdb=" O GLU D 818 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 833 " --> pdb=" O ILE D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 838 removed outlier: 3.697A pdb=" N THR D 838 " --> pdb=" O ASP D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 851 removed outlier: 3.681A pdb=" N GLN D 851 " --> pdb=" O MET D 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 38 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 72 through 82 Processing helix chain 'E' and resid 82 through 106 removed outlier: 3.776A pdb=" N ILE E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.616A pdb=" N LEU E 151 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 350 through 362 removed outlier: 3.539A pdb=" N ARG E 362 " --> pdb=" O LEU E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 374 Processing helix chain 'E' and resid 381 through 394 Processing helix chain 'E' and resid 421 through 433 Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 482 through 485 Processing helix chain 'E' and resid 486 through 500 removed outlier: 3.813A pdb=" N ALA E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU E 495 " --> pdb=" O VAL E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 550 Processing helix chain 'E' and resid 561 through 576 Processing helix chain 'E' and resid 595 through 610 removed outlier: 3.607A pdb=" N CYS E 610 " --> pdb=" O CYS E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 640 removed outlier: 4.037A pdb=" N GLU E 620 " --> pdb=" O PRO E 616 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS E 621 " --> pdb=" O GLN E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 667 Processing helix chain 'E' and resid 673 through 688 Processing helix chain 'E' and resid 690 through 695 Processing helix chain 'F' and resid 105 through 122 removed outlier: 3.819A pdb=" N GLU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 147 Processing helix chain 'F' and resid 155 through 161 Processing helix chain 'F' and resid 164 through 173 Processing helix chain 'F' and resid 173 through 192 Proline residue: F 179 - end of helix Processing helix chain 'F' and resid 193 through 198 removed outlier: 3.930A pdb=" N LEU F 196 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN F 198 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 364 through 368 Processing helix chain 'F' and resid 501 through 507 Processing helix chain 'F' and resid 509 through 522 Processing helix chain 'F' and resid 524 through 533 Processing helix chain 'F' and resid 541 through 553 Processing helix chain 'F' and resid 580 through 589 removed outlier: 3.738A pdb=" N LEU F 585 " --> pdb=" O LYS F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 609 Processing helix chain 'F' and resid 626 through 631 Processing helix chain 'F' and resid 645 through 659 Processing helix chain 'F' and resid 694 through 699 Processing helix chain 'F' and resid 702 through 709 removed outlier: 3.667A pdb=" N PHE F 709 " --> pdb=" O ILE F 705 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 737 Processing helix chain 'F' and resid 747 through 761 removed outlier: 3.681A pdb=" N PHE F 761 " --> pdb=" O TYR F 757 " (cutoff:3.500A) Processing helix chain 'F' and resid 766 through 784 Processing helix chain 'F' and resid 796 through 814 removed outlier: 3.647A pdb=" N LEU F 800 " --> pdb=" O THR F 796 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 835 Processing helix chain 'G' and resid 13 through 27 Processing helix chain 'G' and resid 61 through 72 Processing helix chain 'G' and resid 82 through 95 Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 109 through 124 removed outlier: 3.836A pdb=" N PHE G 113 " --> pdb=" O ASN G 109 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 165 removed outlier: 3.815A pdb=" N ASN G 165 " --> pdb=" O ILE G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 189 Processing helix chain 'G' and resid 193 through 197 Processing helix chain 'G' and resid 231 through 235 removed outlier: 3.731A pdb=" N LEU G 235 " --> pdb=" O GLY G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 292 Processing helix chain 'G' and resid 338 through 340 No H-bonds generated for 'chain 'G' and resid 338 through 340' Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 394 through 408 removed outlier: 4.028A pdb=" N ARG G 400 " --> pdb=" O ASP G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 417 Processing helix chain 'G' and resid 425 through 438 Processing helix chain 'G' and resid 465 through 477 removed outlier: 3.647A pdb=" N LEU G 469 " --> pdb=" O ALA G 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 516 removed outlier: 3.632A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 543 removed outlier: 3.747A pdb=" N GLU G 539 " --> pdb=" O THR G 535 " (cutoff:3.500A) Processing helix chain 'G' and resid 579 through 585 removed outlier: 3.703A pdb=" N ASN G 585 " --> pdb=" O LEU G 581 " (cutoff:3.500A) Processing helix chain 'G' and resid 587 through 594 removed outlier: 3.930A pdb=" N ARG G 593 " --> pdb=" O ALA G 589 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE G 594 " --> pdb=" O LEU G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 622 removed outlier: 3.786A pdb=" N GLU G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 648 removed outlier: 3.775A pdb=" N LYS G 648 " --> pdb=" O TYR G 644 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 674 Processing helix chain 'G' and resid 685 through 703 removed outlier: 3.662A pdb=" N LEU G 689 " --> pdb=" O THR G 685 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 723 Processing helix chain 'G' and resid 724 through 728 Processing sheet with id=AA1, first strand: chain '2' and resid 241 through 242 Processing sheet with id=AA2, first strand: chain '2' and resid 455 through 458 removed outlier: 9.646A pdb=" N HIS 2 405 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ILE 2 451 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER 2 316 " --> pdb=" O TYR 2 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 347 through 352 removed outlier: 5.134A pdb=" N PHE 2 339 " --> pdb=" O LEU 2 348 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL 2 337 " --> pdb=" O PRO 2 350 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE 2 352 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS 2 335 " --> pdb=" O PHE 2 352 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 563 through 567 removed outlier: 6.533A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ASP 2 607 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA 2 566 " --> pdb=" O ASP 2 607 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL 2 683 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU 2 542 " --> pdb=" O VAL 2 683 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 579 through 582 Processing sheet with id=AA6, first strand: chain '2' and resid 628 through 631 Processing sheet with id=AA7, first strand: chain '3' and resid 95 through 99 Processing sheet with id=AA8, first strand: chain '3' and resid 165 through 166 removed outlier: 7.237A pdb=" N LEU 3 166 " --> pdb=" O GLU 3 183 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N ILE 3 185 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR 3 257 " --> pdb=" O THR 3 187 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR 3 189 " --> pdb=" O ARG 3 255 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG 3 255 " --> pdb=" O THR 3 189 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '3' and resid 273 through 279 current: chain '3' and resid 318 through 325 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 318 through 325 current: chain '3' and resid 589 through 590 Processing sheet with id=AA9, first strand: chain '3' and resid 195 through 203 removed outlier: 3.599A pdb=" N ARG 3 208 " --> pdb=" O ALA 3 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain '3' and resid 429 through 432 removed outlier: 6.760A pdb=" N ILE 3 430 " --> pdb=" O CYS 3 471 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ASP 3 473 " --> pdb=" O ILE 3 430 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR 3 432 " --> pdb=" O ASP 3 473 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 444 through 446 Processing sheet with id=AB4, first strand: chain '3' and resid 494 through 496 Processing sheet with id=AB5, first strand: chain '4' and resid 240 through 241 Processing sheet with id=AB6, first strand: chain '4' and resid 325 through 335 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 325 through 335 current: chain '4' and resid 390 through 401 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 414 through 420 current: chain '4' and resid 453 through 462 Processing sheet with id=AB7, first strand: chain '4' and resid 354 through 355 removed outlier: 3.763A pdb=" N HIS 4 354 " --> pdb=" O CYS 4 349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS 4 349 " --> pdb=" O HIS 4 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 591 through 592 removed outlier: 6.288A pdb=" N THR 4 591 " --> pdb=" O ASP 4 632 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE 4 564 " --> pdb=" O ALA 4 673 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA 4 675 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU 4 566 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 603 through 607 removed outlier: 3.779A pdb=" N TYR 4 604 " --> pdb=" O GLU 4 617 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 653 through 658 Processing sheet with id=AC2, first strand: chain '5' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 11 through 12 current: chain 'G' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 267 through 272 current: chain 'G' and resid 376 through 383 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain '5' and resid 60 through 64 removed outlier: 6.212A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASN 5 140 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL 5 63 " --> pdb=" O ASN 5 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '5' and resid 159 through 169 removed outlier: 6.765A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR 5 275 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE 5 330 " --> pdb=" O THR 5 277 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER 5 335 " --> pdb=" O ARG 5 291 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ARG 5 291 " --> pdb=" O SER 5 335 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '5' and resid 188 through 193 removed outlier: 3.691A pdb=" N HIS 5 188 " --> pdb=" O CYS 5 183 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE 5 192 " --> pdb=" O LEU 5 179 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU 5 179 " --> pdb=" O SER 5 247 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N SER 5 247 " --> pdb=" O LEU 5 179 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N ILE 5 181 " --> pdb=" O HIS 5 245 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N HIS 5 245 " --> pdb=" O ILE 5 181 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N CYS 5 183 " --> pdb=" O ILE 5 243 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N ILE 5 243 " --> pdb=" O CYS 5 183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 398 through 399 removed outlier: 3.805A pdb=" N LYS 5 398 " --> pdb=" O LEU 5 406 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 436 through 440 removed outlier: 3.527A pdb=" N VAL 5 437 " --> pdb=" O VAL 5 476 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY 5 416 " --> pdb=" O ALA 5 523 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU 5 413 " --> pdb=" O PHE 5 554 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL 5 556 " --> pdb=" O LEU 5 413 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU 5 415 " --> pdb=" O VAL 5 556 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '5' and resid 453 through 455 Processing sheet with id=AC9, first strand: chain '5' and resid 501 through 504 Processing sheet with id=AD1, first strand: chain '6' and resid 150 through 154 removed outlier: 3.751A pdb=" N ILE 6 153 " --> pdb=" O SER 6 266 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE 6 268 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 273 through 274 removed outlier: 3.923A pdb=" N SER 6 291 " --> pdb=" O HIS 6 274 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '6' and resid 287 through 297 current: chain '6' and resid 318 through 322 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 318 through 322 current: chain '6' and resid 376 through 382 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 376 through 382 current: chain '6' and resid 450 through 461 Processing sheet with id=AD3, first strand: chain '6' and resid 557 through 558 removed outlier: 3.875A pdb=" N LYS 6 557 " --> pdb=" O LEU 6 565 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 596 through 599 removed outlier: 6.518A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N CYS 6 636 " --> pdb=" O LEU 6 679 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ALA 6 681 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE 6 638 " --> pdb=" O ALA 6 681 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '6' and resid 611 through 614 Processing sheet with id=AD6, first strand: chain '6' and resid 660 through 662 Processing sheet with id=AD7, first strand: chain '6' and resid 764 through 765 removed outlier: 7.442A pdb=" N ILE 6 764 " --> pdb=" O ILE 6 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain '7' and resid 77 through 81 Processing sheet with id=AD9, first strand: chain '7' and resid 224 through 225 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 238 through 247 current: chain '7' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 267 through 272 current: chain '7' and resid 330 through 336 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 330 through 336 current: chain '7' and resid 372 through 383 Processing sheet with id=AE1, first strand: chain '7' and resid 442 through 443 removed outlier: 3.811A pdb=" N LYS 7 442 " --> pdb=" O ILE 7 450 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '7' and resid 523 through 524 Processing sheet with id=AE3, first strand: chain '7' and resid 545 through 547 Processing sheet with id=AE4, first strand: chain '8' and resid 33 through 41 removed outlier: 5.515A pdb=" N LEU 8 35 " --> pdb=" O LYS 8 51 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LYS 8 51 " --> pdb=" O LEU 8 35 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL 8 47 " --> pdb=" O ILE 8 39 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU 8 41 " --> pdb=" O SER 8 45 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N SER 8 45 " --> pdb=" O GLU 8 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE 8 78 " --> pdb=" O VAL 8 116 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL 8 116 " --> pdb=" O ILE 8 78 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP 8 108 " --> pdb=" O VAL 8 119 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '8' and resid 159 through 160 Processing sheet with id=AE6, first strand: chain '8' and resid 169 through 172 Processing sheet with id=AE7, first strand: chain '8' and resid 264 through 266 Processing sheet with id=AE8, first strand: chain '8' and resid 350 through 355 removed outlier: 3.935A pdb=" N ILE 9 279 " --> pdb=" O LEU 9 268 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '9' and resid 173 through 174 removed outlier: 7.327A pdb=" N VAL 9 173 " --> pdb=" O TRP 9 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain '9' and resid 659 through 661 Processing sheet with id=AF2, first strand: chain 'B' and resid 241 through 245 removed outlier: 6.269A pdb=" N LEU B 242 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N SER B 298 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 244 " --> pdb=" O SER B 298 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'B' and resid 317 through 327 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 317 through 327 current: chain 'B' and resid 351 through 352 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 351 through 352 current: chain 'B' and resid 405 through 411 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 405 through 411 current: chain 'B' and resid 449 through 452 No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'B' and resid 525 through 527 removed outlier: 4.055A pdb=" N LYS B 525 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 533 " --> pdb=" O LYS B 525 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 563 through 567 removed outlier: 6.065A pdb=" N CYS B 604 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA B 649 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 606 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 579 through 582 Processing sheet with id=AF7, first strand: chain 'B' and resid 630 through 633 Processing sheet with id=AF8, first strand: chain 'B' and resid 777 through 778 removed outlier: 7.420A pdb=" N LYS B 777 " --> pdb=" O VAL B 829 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'C' and resid 95 through 99 removed outlier: 5.906A pdb=" N ILE C 96 " --> pdb=" O SER C 156 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS C 158 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE C 98 " --> pdb=" O LYS C 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 165 through 166 removed outlier: 7.242A pdb=" N LEU C 166 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 9.550A pdb=" N ILE C 185 " --> pdb=" O LEU C 166 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 179 through 189 current: chain 'C' and resid 209 through 213 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 209 through 213 current: chain 'C' and resid 273 through 279 No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'C' and resid 300 through 301 Processing sheet with id=AG3, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.742A pdb=" N LYS C 391 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 429 through 433 removed outlier: 6.546A pdb=" N ILE C 430 " --> pdb=" O CYS C 471 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ASP C 473 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C 432 " --> pdb=" O ASP C 473 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL C 470 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA C 515 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE C 472 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE C 405 " --> pdb=" O ALA C 514 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALA C 516 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N MET C 407 " --> pdb=" O ALA C 516 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 444 through 446 Processing sheet with id=AG6, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AG7, first strand: chain 'D' and resid 240 through 244 removed outlier: 6.527A pdb=" N LEU D 241 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N TYR D 306 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU D 243 " --> pdb=" O TYR D 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'G' and resid 277 through 278 removed outlier: 4.666A pdb=" N ILE D 444 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU D 456 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE D 442 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS D 458 " --> pdb=" O ARG D 440 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG D 440 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR D 460 " --> pdb=" O THR D 438 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR D 438 " --> pdb=" O TYR D 460 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASP D 462 " --> pdb=" O THR D 436 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR D 436 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N VAL D 464 " --> pdb=" O GLU D 434 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N GLU D 434 " --> pdb=" O VAL D 464 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N VAL D 466 " --> pdb=" O ARG D 432 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N ARG D 432 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL D 332 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN D 400 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 334 " --> pdb=" O LYS D 398 " (cutoff:3.500A) removed outlier: 13.826A pdb=" N SER D 414 " --> pdb=" O TYR D 457 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N THR D 459 " --> pdb=" O SER D 414 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER D 416 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR D 420 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N HIS D 465 " --> pdb=" O TYR D 420 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 358 through 359 removed outlier: 6.836A pdb=" N SER D 390 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 347 through 349 removed outlier: 3.885A pdb=" N LYS D 348 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 365 through 366 Processing sheet with id=AH3, first strand: chain 'D' and resid 590 through 592 removed outlier: 6.530A pdb=" N THR D 591 " --> pdb=" O ASP D 632 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N CYS D 629 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N SER D 674 " --> pdb=" O CYS D 629 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE D 631 " --> pdb=" O SER D 674 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 568 " --> pdb=" O ALA D 675 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 603 through 608 Processing sheet with id=AH5, first strand: chain 'D' and resid 653 through 656 Processing sheet with id=AH6, first strand: chain 'D' and resid 761 through 762 removed outlier: 6.640A pdb=" N ILE D 761 " --> pdb=" O VAL D 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'E' and resid 60 through 64 Processing sheet with id=AH8, first strand: chain 'E' and resid 159 through 169 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 159 through 169 current: chain 'E' and resid 189 through 193 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 189 through 193 current: chain 'E' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 273 through 279 current: chain 'E' and resid 325 through 335 No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'E' and resid 398 through 399 removed outlier: 3.863A pdb=" N LYS E 398 " --> pdb=" O LEU E 406 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 438 through 439 removed outlier: 6.289A pdb=" N VAL E 477 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA E 522 " --> pdb=" O VAL E 477 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE E 479 " --> pdb=" O ALA E 522 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY E 416 " --> pdb=" O ALA E 523 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU E 413 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL E 556 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU E 415 " --> pdb=" O VAL E 556 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 452 through 455 removed outlier: 7.107A pdb=" N SER E 452 " --> pdb=" O GLU E 465 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 501 through 504 Processing sheet with id=AI4, first strand: chain 'F' and resid 124 through 125 removed outlier: 3.529A pdb=" N GLU F 133 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 150 through 154 removed outlier: 5.981A pdb=" N ILE F 151 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE F 268 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE F 153 " --> pdb=" O PHE F 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'F' and resid 317 through 322 removed outlier: 3.510A pdb=" N PHE F 309 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASN F 320 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA F 307 " --> pdb=" O ASN F 320 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLU F 322 " --> pdb=" O TYR F 305 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR F 305 " --> pdb=" O GLU F 322 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU F 303 " --> pdb=" O LEU F 354 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG F 352 " --> pdb=" O TYR F 305 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA F 307 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ARG F 350 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N PHE F 309 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL F 348 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 14.409A pdb=" N THR F 376 " --> pdb=" O TYR F 450 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ILE F 452 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASP F 378 " --> pdb=" O ILE F 452 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG F 382 " --> pdb=" O ALA F 456 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N HIS F 458 " --> pdb=" O ARG F 382 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ILE F 452 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL F 404 " --> pdb=" O ILE F 452 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE F 454 " --> pdb=" O ILE F 402 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE F 402 " --> pdb=" O PHE F 454 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA F 456 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL F 400 " --> pdb=" O ALA F 456 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG F 360 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR F 297 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LYS F 358 " --> pdb=" O THR F 297 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 557 through 558 Processing sheet with id=AI8, first strand: chain 'F' and resid 595 through 598 removed outlier: 3.551A pdb=" N VAL F 596 " --> pdb=" O ILE F 635 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY F 575 " --> pdb=" O ALA F 682 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS F 572 " --> pdb=" O PHE F 713 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE F 715 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL F 574 " --> pdb=" O ILE F 715 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 611 through 614 Processing sheet with id=AJ1, first strand: chain 'F' and resid 660 through 662 Processing sheet with id=AJ2, first strand: chain 'G' and resid 77 through 81 Processing sheet with id=AJ3, first strand: chain 'G' and resid 357 through 359 Processing sheet with id=AJ4, first strand: chain 'G' and resid 480 through 484 removed outlier: 5.822A pdb=" N VAL G 481 " --> pdb=" O CYS G 522 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP G 524 " --> pdb=" O VAL G 481 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR G 483 " --> pdb=" O ASP G 524 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'G' and resid 496 through 499 Processing sheet with id=AJ6, first strand: chain 'G' and resid 545 through 550 2696 hydrogen bonds defined for protein. 7794 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: 34.47 Time building geometry restraints manager: 15.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 12074 1.32 - 1.45: 16716 1.45 - 1.58: 39175 1.58 - 1.70: 52 1.70 - 1.83: 503 Bond restraints: 68520 Sorted by residual: bond pdb=" F1 BEF G1103 " pdb="BE BEF G1103 " ideal model delta sigma weight residual 1.476 1.774 -0.298 2.00e-02 2.50e+03 2.23e+02 bond pdb=" F1 BEF 31004 " pdb="BE BEF 31004 " ideal model delta sigma weight residual 1.476 1.774 -0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" F1 BEF 41103 " pdb="BE BEF 41103 " ideal model delta sigma weight residual 1.476 1.774 -0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" F1 BEF D1103 " pdb="BE BEF D1103 " ideal model delta sigma weight residual 1.476 1.774 -0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" F2 BEF 31002 " pdb="BE BEF 31002 " ideal model delta sigma weight residual 1.476 1.768 -0.292 2.00e-02 2.50e+03 2.13e+02 ... (remaining 68515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 92388 4.51 - 9.02: 248 9.02 - 13.53: 44 13.53 - 18.04: 7 18.04 - 22.55: 1 Bond angle restraints: 92688 Sorted by residual: angle pdb=" C ASP 3 280 " pdb=" CA ASP 3 280 " pdb=" CB ASP 3 280 " ideal model delta sigma weight residual 116.63 107.21 9.42 1.16e+00 7.43e-01 6.59e+01 angle pdb=" F2 BEF 81003 " pdb="BE BEF 81003 " pdb=" F3 BEF 81003 " ideal model delta sigma weight residual 119.96 97.41 22.55 3.00e+00 1.11e-01 5.65e+01 angle pdb=" N LEU D 601 " pdb=" CA LEU D 601 " pdb=" C LEU D 601 " ideal model delta sigma weight residual 110.53 101.62 8.91 1.29e+00 6.01e-01 4.77e+01 angle pdb=" N GLU 6 515 " pdb=" CA GLU 6 515 " pdb=" C GLU 6 515 " ideal model delta sigma weight residual 111.11 103.04 8.07 1.20e+00 6.94e-01 4.52e+01 angle pdb=" N PHE 8 183 " pdb=" CA PHE 8 183 " pdb=" C PHE 8 183 " ideal model delta sigma weight residual 112.30 103.15 9.15 1.36e+00 5.41e-01 4.52e+01 ... (remaining 92683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 41070 34.21 - 68.42: 918 68.42 - 102.64: 80 102.64 - 136.85: 12 136.85 - 171.06: 3 Dihedral angle restraints: 42083 sinusoidal: 17317 harmonic: 24766 Sorted by residual: dihedral pdb=" O1B ADP 31001 " pdb=" O3A ADP 31001 " pdb=" PB ADP 31001 " pdb=" PA ADP 31001 " ideal model delta sinusoidal sigma weight residual 300.00 128.94 171.06 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O1B ADP C1001 " pdb=" O3A ADP C1001 " pdb=" PB ADP C1001 " pdb=" PA ADP C1001 " ideal model delta sinusoidal sigma weight residual 300.00 128.98 171.02 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP 5 801 " pdb=" O3A ADP 5 801 " pdb=" PA ADP 5 801 " pdb=" PB ADP 5 801 " ideal model delta sinusoidal sigma weight residual 300.00 145.01 154.99 1 2.00e+01 2.50e-03 4.58e+01 ... (remaining 42080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 9574 0.080 - 0.160: 1003 0.160 - 0.240: 78 0.240 - 0.320: 19 0.320 - 0.401: 6 Chirality restraints: 10680 Sorted by residual: chirality pdb=" CA THR 6 127 " pdb=" N THR 6 127 " pdb=" C THR 6 127 " pdb=" CB THR 6 127 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CB VAL B 807 " pdb=" CA VAL B 807 " pdb=" CG1 VAL B 807 " pdb=" CG2 VAL B 807 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA ARG 6 752 " pdb=" N ARG 6 752 " pdb=" C ARG 6 752 " pdb=" CB ARG 6 752 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 10677 not shown) Planarity restraints: 11887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 504 " -0.012 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C PHE F 504 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE F 504 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU F 505 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS F 653 " -0.010 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C HIS F 653 " 0.037 2.00e-02 2.50e+03 pdb=" O HIS F 653 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU F 654 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN 8 172 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C ASN 8 172 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN 8 172 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU 8 173 " 0.012 2.00e-02 2.50e+03 ... (remaining 11884 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 426 2.47 - 3.08: 48351 3.08 - 3.69: 104465 3.69 - 4.29: 151322 4.29 - 4.90: 247736 Nonbonded interactions: 552300 Sorted by model distance: nonbonded pdb=" OG SER G 467 " pdb="MG MG G1104 " model vdw 1.865 2.170 nonbonded pdb=" OD2 ASP 8 182 " pdb="MG MG 81004 " model vdw 1.885 2.170 nonbonded pdb=" OG SER F 582 " pdb="MG MG F1102 " model vdw 1.958 2.170 nonbonded pdb=" O2B ADP B 901 " pdb="MG MG B 902 " model vdw 1.975 2.170 nonbonded pdb=" OG SER 6 582 " pdb="MG MG 61102 " model vdw 1.987 2.170 ... (remaining 552295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '2' selection = chain 'B' } ncs_group { reference = (chain '3' and (resid 16 through 449 or resid 454 through 742 or resid 1001)) selection = (chain 'C' and (resid 16 through 742 or resid 1001)) } ncs_group { reference = chain '4' selection = chain 'D' } ncs_group { reference = (chain '5' and resid 2 through 696) selection = (chain 'E' and resid 2 through 696) } ncs_group { reference = chain '6' selection = chain 'F' } ncs_group { reference = (chain '7' and (resid 2 through 728 or resid 1101 through 1102)) selection = (chain 'G' and (resid 2 through 728 or resid 1101 through 1102)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 54.760 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: 0.110 Extract box with map and model: 2.210 Check model and map are aligned: 0.400 Set scattering table: 0.510 Process input model: 141.510 Find NCS groups from input model: 4.820 Set up NCS constraints: 0.500 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: 0.030 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 0.298 68520 Z= 0.489 Angle : 0.745 22.554 92688 Z= 0.410 Chirality : 0.049 0.401 10680 Planarity : 0.004 0.053 11887 Dihedral : 14.968 171.060 25995 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.64 % Allowed : 1.00 % Favored : 98.36 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.09), residues: 8325 helix: 1.56 (0.09), residues: 3215 sheet: -0.38 (0.14), residues: 1336 loop : -0.31 (0.10), residues: 3774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 9 283 HIS 0.011 0.001 HIS 4 413 PHE 0.035 0.001 PHE F 115 TYR 0.024 0.001 TYR D 604 ARG 0.005 0.000 ARG D 642 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 387 time to evaluate : 6.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 276 MET cc_start: 0.7797 (tpp) cc_final: 0.7467 (tpp) REVERT: 4 484 GLU cc_start: 0.5178 (mm-30) cc_final: 0.4893 (mm-30) REVERT: 4 815 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7865 (t0) REVERT: 6 131 GLU cc_start: 0.5759 (OUTLIER) cc_final: 0.5220 (mt-10) REVERT: 6 515 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7457 (tp30) REVERT: 6 656 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6504 (mtp) REVERT: 8 174 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: B 206 THR cc_start: 0.6180 (m) cc_final: 0.5737 (m) REVERT: F 143 MET cc_start: 0.8106 (tpp) cc_final: 0.7496 (tpp) REVERT: F 762 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8305 (mmmm) outliers start: 48 outliers final: 14 residues processed: 430 average time/residue: 0.6455 time to fit residues: 477.4723 Evaluate side-chains 318 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 298 time to evaluate : 6.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 808 ARG Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 4 residue 536 VAL Chi-restraints excluded: chain 4 residue 573 SER Chi-restraints excluded: chain 4 residue 815 ASN Chi-restraints excluded: chain 5 residue 546 ILE Chi-restraints excluded: chain 6 residue 131 GLU Chi-restraints excluded: chain 6 residue 515 GLU Chi-restraints excluded: chain 6 residue 656 MET Chi-restraints excluded: chain 6 residue 801 GLU Chi-restraints excluded: chain 7 residue 507 ILE Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 7 residue 689 LEU Chi-restraints excluded: chain 7 residue 704 LEU Chi-restraints excluded: chain 8 residue 174 GLU Chi-restraints excluded: chain 9 residue 122 ARG Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 652 ILE Chi-restraints excluded: chain F residue 653 HIS Chi-restraints excluded: chain F residue 762 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 707 optimal weight: 0.9990 chunk 635 optimal weight: 1.9990 chunk 352 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 428 optimal weight: 30.0000 chunk 339 optimal weight: 6.9990 chunk 656 optimal weight: 6.9990 chunk 254 optimal weight: 6.9990 chunk 399 optimal weight: 2.9990 chunk 488 optimal weight: 3.9990 chunk 760 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 722 ASN ** 4 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 576 HIS ** 5 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 814 ASN ** 7 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 168 ASN 9 369 HIS 9 673 GLN B 384 ASN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 GLN D 488 ASN F 366 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 68520 Z= 0.233 Angle : 0.576 8.912 92688 Z= 0.294 Chirality : 0.043 0.189 10680 Planarity : 0.004 0.055 11887 Dihedral : 7.977 167.713 9420 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.49 % Allowed : 6.85 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 8325 helix: 1.65 (0.09), residues: 3311 sheet: -0.54 (0.14), residues: 1423 loop : -0.31 (0.10), residues: 3591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 3 111 HIS 0.009 0.001 HIS 9 239 PHE 0.020 0.001 PHE 3 421 TYR 0.022 0.001 TYR 4 519 ARG 0.004 0.000 ARG 8 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 332 time to evaluate : 6.401 Fit side-chains revert: symmetry clash REVERT: 2 276 MET cc_start: 0.7755 (tpp) cc_final: 0.7467 (tpp) REVERT: 4 356 MET cc_start: 0.1927 (mmt) cc_final: 0.1709 (mmt) REVERT: 4 484 GLU cc_start: 0.5073 (mm-30) cc_final: 0.4793 (mm-30) REVERT: 4 801 MET cc_start: 0.8032 (mtm) cc_final: 0.7786 (mtm) REVERT: 4 815 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8216 (m-40) REVERT: 6 656 MET cc_start: 0.7146 (ttm) cc_final: 0.6707 (mtp) REVERT: 8 174 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: 8 227 MET cc_start: 0.2077 (pmm) cc_final: 0.1478 (mmt) REVERT: 9 136 MET cc_start: 0.6682 (ttp) cc_final: 0.6447 (ttt) REVERT: B 818 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: C 576 TYR cc_start: 0.7343 (m-80) cc_final: 0.7131 (m-10) REVERT: F 143 MET cc_start: 0.8042 (tpp) cc_final: 0.7564 (tpp) REVERT: F 648 ASP cc_start: 0.8078 (m-30) cc_final: 0.7858 (m-30) REVERT: F 712 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.6670 (t80) outliers start: 37 outliers final: 21 residues processed: 355 average time/residue: 0.6407 time to fit residues: 401.3531 Evaluate side-chains 324 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 299 time to evaluate : 6.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 4 residue 815 ASN Chi-restraints excluded: chain 5 residue 270 MET Chi-restraints excluded: chain 5 residue 546 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 7 residue 628 LEU Chi-restraints excluded: chain 7 residue 689 LEU Chi-restraints excluded: chain 7 residue 707 MET Chi-restraints excluded: chain 8 residue 70 SER Chi-restraints excluded: chain 8 residue 174 GLU Chi-restraints excluded: chain 8 residue 181 VAL Chi-restraints excluded: chain 9 residue 244 TYR Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain F residue 653 HIS Chi-restraints excluded: chain F residue 712 PHE Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 621 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 422 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 633 optimal weight: 8.9990 chunk 518 optimal weight: 7.9990 chunk 209 optimal weight: 0.6980 chunk 762 optimal weight: 9.9990 chunk 823 optimal weight: 0.9980 chunk 678 optimal weight: 0.1980 chunk 756 optimal weight: 7.9990 chunk 259 optimal weight: 20.0000 chunk 611 optimal weight: 20.0000 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 808 HIS 5 494 HIS 7 334 HIS 9 673 GLN B 710 ASN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 GLN F 347 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 68520 Z= 0.254 Angle : 0.556 9.690 92688 Z= 0.282 Chirality : 0.042 0.197 10680 Planarity : 0.004 0.058 11887 Dihedral : 7.546 163.666 9384 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.93 % Allowed : 9.11 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 8325 helix: 1.67 (0.09), residues: 3317 sheet: -0.55 (0.14), residues: 1390 loop : -0.39 (0.10), residues: 3618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 8 338 HIS 0.008 0.001 HIS 9 239 PHE 0.021 0.001 PHE 3 421 TYR 0.020 0.001 TYR G 63 ARG 0.005 0.000 ARG F 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 321 time to evaluate : 6.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 276 MET cc_start: 0.7730 (tpp) cc_final: 0.7422 (tpp) REVERT: 4 356 MET cc_start: 0.2323 (mmt) cc_final: 0.1992 (mmt) REVERT: 4 484 GLU cc_start: 0.4903 (mm-30) cc_final: 0.4610 (mm-30) REVERT: 4 801 MET cc_start: 0.8045 (mtm) cc_final: 0.7826 (mtm) REVERT: 6 656 MET cc_start: 0.7017 (ttm) cc_final: 0.6713 (mtp) REVERT: 7 506 MET cc_start: 0.6474 (tpp) cc_final: 0.6221 (tpt) REVERT: 8 174 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: 8 227 MET cc_start: 0.1794 (pmm) cc_final: 0.1347 (mmt) REVERT: 9 136 MET cc_start: 0.6452 (ttp) cc_final: 0.6216 (ttt) REVERT: B 271 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6667 (t80) REVERT: B 818 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: E 552 MET cc_start: 0.7339 (ptp) cc_final: 0.7058 (mtm) REVERT: F 143 MET cc_start: 0.8045 (tpp) cc_final: 0.7624 (tpp) REVERT: F 648 ASP cc_start: 0.8093 (m-30) cc_final: 0.7844 (m-30) REVERT: F 712 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.6751 (t80) outliers start: 70 outliers final: 40 residues processed: 373 average time/residue: 0.6926 time to fit residues: 455.6741 Evaluate side-chains 341 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 297 time to evaluate : 6.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 251 GLU Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 295 VAL Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 5 residue 196 ASN Chi-restraints excluded: chain 5 residue 270 MET Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 546 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 300 VAL Chi-restraints excluded: chain 6 residue 654 GLU Chi-restraints excluded: chain 7 residue 547 SER Chi-restraints excluded: chain 7 residue 583 ASN Chi-restraints excluded: chain 7 residue 628 LEU Chi-restraints excluded: chain 7 residue 688 THR Chi-restraints excluded: chain 7 residue 689 LEU Chi-restraints excluded: chain 7 residue 707 MET Chi-restraints excluded: chain 8 residue 70 SER Chi-restraints excluded: chain 8 residue 174 GLU Chi-restraints excluded: chain 8 residue 181 VAL Chi-restraints excluded: chain 8 residue 265 TYR Chi-restraints excluded: chain 8 residue 302 ILE Chi-restraints excluded: chain 8 residue 338 TRP Chi-restraints excluded: chain 9 residue 166 PHE Chi-restraints excluded: chain 9 residue 244 TYR Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 563 GLU Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 653 HIS Chi-restraints excluded: chain F residue 712 PHE Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 529 MET Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 621 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 753 optimal weight: 0.0980 chunk 573 optimal weight: 0.9980 chunk 395 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 363 optimal weight: 7.9990 chunk 511 optimal weight: 10.0000 chunk 765 optimal weight: 10.0000 chunk 810 optimal weight: 5.9990 chunk 399 optimal weight: 7.9990 chunk 725 optimal weight: 30.0000 chunk 218 optimal weight: 3.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9 673 GLN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN F 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 68520 Z= 0.241 Angle : 0.548 10.529 92688 Z= 0.276 Chirality : 0.042 0.190 10680 Planarity : 0.004 0.060 11887 Dihedral : 7.354 159.616 9382 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.28 % Allowed : 10.72 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.09), residues: 8325 helix: 1.73 (0.09), residues: 3308 sheet: -0.57 (0.14), residues: 1376 loop : -0.38 (0.10), residues: 3641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 3 111 HIS 0.008 0.001 HIS 9 239 PHE 0.022 0.001 PHE 3 345 TYR 0.021 0.001 TYR D 291 ARG 0.003 0.000 ARG C 435 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 316 time to evaluate : 6.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 276 MET cc_start: 0.7678 (tpp) cc_final: 0.7351 (tpp) REVERT: 4 356 MET cc_start: 0.2305 (mmt) cc_final: 0.2025 (mmt) REVERT: 4 484 GLU cc_start: 0.4855 (mm-30) cc_final: 0.4525 (mm-30) REVERT: 4 801 MET cc_start: 0.8040 (mtm) cc_final: 0.7838 (mtm) REVERT: 7 181 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7908 (mm) REVERT: 8 174 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: 8 227 MET cc_start: 0.1690 (pmm) cc_final: 0.1445 (mmt) REVERT: 9 136 MET cc_start: 0.6510 (ttp) cc_final: 0.6223 (ttt) REVERT: 9 671 LEU cc_start: 0.8345 (tp) cc_final: 0.8117 (tt) REVERT: B 271 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6696 (t80) REVERT: C 386 MET cc_start: 0.8942 (tpp) cc_final: 0.8516 (tpp) REVERT: E 552 MET cc_start: 0.7364 (ptp) cc_final: 0.7076 (mtm) REVERT: F 143 MET cc_start: 0.8028 (tpp) cc_final: 0.7635 (tpp) REVERT: F 712 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.6954 (t80) outliers start: 96 outliers final: 54 residues processed: 395 average time/residue: 0.6179 time to fit residues: 431.3396 Evaluate side-chains 357 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 299 time to evaluate : 6.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 251 GLU Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 295 VAL Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 4 residue 815 ASN Chi-restraints excluded: chain 5 residue 196 ASN Chi-restraints excluded: chain 5 residue 270 MET Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 354 GLU Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 546 ILE Chi-restraints excluded: chain 5 residue 656 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 300 VAL Chi-restraints excluded: chain 6 residue 654 GLU Chi-restraints excluded: chain 7 residue 100 ASP Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 547 SER Chi-restraints excluded: chain 7 residue 583 ASN Chi-restraints excluded: chain 7 residue 628 LEU Chi-restraints excluded: chain 7 residue 688 THR Chi-restraints excluded: chain 7 residue 689 LEU Chi-restraints excluded: chain 7 residue 707 MET Chi-restraints excluded: chain 8 residue 70 SER Chi-restraints excluded: chain 8 residue 174 GLU Chi-restraints excluded: chain 8 residue 181 VAL Chi-restraints excluded: chain 8 residue 185 LEU Chi-restraints excluded: chain 8 residue 265 TYR Chi-restraints excluded: chain 8 residue 302 ILE Chi-restraints excluded: chain 8 residue 338 TRP Chi-restraints excluded: chain 9 residue 112 TRP Chi-restraints excluded: chain 9 residue 166 PHE Chi-restraints excluded: chain 9 residue 244 TYR Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 563 GLU Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 712 PHE Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 488 SER Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 529 MET Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 621 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 674 optimal weight: 8.9990 chunk 459 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 603 optimal weight: 3.9990 chunk 334 optimal weight: 8.9990 chunk 691 optimal weight: 4.9990 chunk 559 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 413 optimal weight: 0.7980 chunk 727 optimal weight: 30.0000 chunk 204 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 157 HIS 7 112 HIS 9 673 GLN B 353 GLN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 68520 Z= 0.312 Angle : 0.580 11.206 92688 Z= 0.292 Chirality : 0.042 0.210 10680 Planarity : 0.004 0.060 11887 Dihedral : 7.304 155.197 9380 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.43 % Allowed : 12.07 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.09), residues: 8325 helix: 1.67 (0.09), residues: 3317 sheet: -0.65 (0.14), residues: 1380 loop : -0.41 (0.10), residues: 3628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 9 116 HIS 0.008 0.001 HIS 9 239 PHE 0.023 0.001 PHE 3 421 TYR 0.024 0.001 TYR G 63 ARG 0.004 0.000 ARG G 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 302 time to evaluate : 6.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 276 MET cc_start: 0.7738 (tpp) cc_final: 0.7410 (tpp) REVERT: 4 356 MET cc_start: 0.2568 (mmt) cc_final: 0.2331 (mmt) REVERT: 4 413 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.8130 (t-170) REVERT: 4 484 GLU cc_start: 0.4972 (mm-30) cc_final: 0.4651 (mm-30) REVERT: 6 515 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6872 (tp30) REVERT: 7 181 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7929 (mm) REVERT: 7 506 MET cc_start: 0.6709 (tpp) cc_final: 0.6152 (tpt) REVERT: 8 76 LYS cc_start: 0.7793 (tppt) cc_final: 0.7590 (tptt) REVERT: 8 174 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: 8 227 MET cc_start: 0.1729 (pmm) cc_final: 0.1514 (mmt) REVERT: E 103 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8331 (mt) REVERT: E 346 VAL cc_start: 0.6508 (OUTLIER) cc_final: 0.6019 (p) REVERT: E 552 MET cc_start: 0.7496 (ptp) cc_final: 0.7190 (mtm) REVERT: F 143 MET cc_start: 0.8098 (tpp) cc_final: 0.7724 (tpp) REVERT: F 648 ASP cc_start: 0.8204 (m-30) cc_final: 0.7949 (m-30) REVERT: F 712 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.6846 (t80) REVERT: G 366 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5562 (tt) REVERT: G 428 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8683 (p) outliers start: 107 outliers final: 79 residues processed: 390 average time/residue: 0.6056 time to fit residues: 419.0760 Evaluate side-chains 379 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 291 time to evaluate : 6.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 251 GLU Chi-restraints excluded: chain 2 residue 359 ILE Chi-restraints excluded: chain 2 residue 564 VAL Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 295 VAL Chi-restraints excluded: chain 3 residue 432 THR Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 4 residue 413 HIS Chi-restraints excluded: chain 4 residue 502 THR Chi-restraints excluded: chain 4 residue 533 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 196 ASN Chi-restraints excluded: chain 5 residue 270 MET Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 354 GLU Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 546 ILE Chi-restraints excluded: chain 5 residue 656 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 300 VAL Chi-restraints excluded: chain 6 residue 343 PHE Chi-restraints excluded: chain 6 residue 515 GLU Chi-restraints excluded: chain 6 residue 556 HIS Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 654 GLU Chi-restraints excluded: chain 7 residue 100 ASP Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 504 ASP Chi-restraints excluded: chain 7 residue 547 SER Chi-restraints excluded: chain 7 residue 583 ASN Chi-restraints excluded: chain 7 residue 628 LEU Chi-restraints excluded: chain 7 residue 688 THR Chi-restraints excluded: chain 7 residue 689 LEU Chi-restraints excluded: chain 7 residue 707 MET Chi-restraints excluded: chain 8 residue 70 SER Chi-restraints excluded: chain 8 residue 173 LEU Chi-restraints excluded: chain 8 residue 174 GLU Chi-restraints excluded: chain 8 residue 181 VAL Chi-restraints excluded: chain 8 residue 185 LEU Chi-restraints excluded: chain 8 residue 265 TYR Chi-restraints excluded: chain 8 residue 338 TRP Chi-restraints excluded: chain 8 residue 444 GLN Chi-restraints excluded: chain 9 residue 112 TRP Chi-restraints excluded: chain 9 residue 166 PHE Chi-restraints excluded: chain 9 residue 244 TYR Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 563 GLU Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 598 THR Chi-restraints excluded: chain F residue 712 PHE Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain G residue 366 LEU Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain G residue 488 SER Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 507 ILE Chi-restraints excluded: chain G residue 529 MET Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 621 MET Chi-restraints excluded: chain G residue 704 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 272 optimal weight: 0.0170 chunk 729 optimal weight: 0.0670 chunk 160 optimal weight: 6.9990 chunk 475 optimal weight: 20.0000 chunk 199 optimal weight: 4.9990 chunk 810 optimal weight: 10.0000 chunk 673 optimal weight: 5.9990 chunk 375 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 268 optimal weight: 9.9990 chunk 425 optimal weight: 9.9990 overall best weight: 3.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 68520 Z= 0.251 Angle : 0.554 11.587 92688 Z= 0.278 Chirality : 0.042 0.192 10680 Planarity : 0.004 0.060 11887 Dihedral : 7.188 154.048 9380 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.55 % Allowed : 12.91 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.09), residues: 8325 helix: 1.71 (0.09), residues: 3317 sheet: -0.65 (0.14), residues: 1366 loop : -0.37 (0.10), residues: 3642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 3 111 HIS 0.008 0.001 HIS 9 239 PHE 0.023 0.001 PHE F 115 TYR 0.020 0.001 TYR G 63 ARG 0.004 0.000 ARG C 435 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 314 time to evaluate : 7.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 276 MET cc_start: 0.7703 (tpp) cc_final: 0.7362 (tpp) REVERT: 4 413 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.7924 (t-170) REVERT: 4 811 MET cc_start: 0.8455 (ttt) cc_final: 0.8186 (ttp) REVERT: 7 181 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.7943 (mm) REVERT: 7 638 MET cc_start: 0.7795 (mmm) cc_final: 0.7108 (mtt) REVERT: 8 76 LYS cc_start: 0.7796 (tppt) cc_final: 0.7568 (tptt) REVERT: 8 174 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: B 818 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: C 386 MET cc_start: 0.8894 (tpp) cc_final: 0.8458 (tpp) REVERT: D 612 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7357 (mppt) REVERT: E 103 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8347 (mt) REVERT: E 552 MET cc_start: 0.7518 (ptp) cc_final: 0.7206 (mtm) REVERT: F 143 MET cc_start: 0.8067 (tpp) cc_final: 0.7685 (tpp) REVERT: F 712 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.6905 (t80) REVERT: G 428 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8666 (p) outliers start: 116 outliers final: 84 residues processed: 415 average time/residue: 0.6204 time to fit residues: 460.3768 Evaluate side-chains 384 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 293 time to evaluate : 6.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 251 GLU Chi-restraints excluded: chain 2 residue 359 ILE Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 295 VAL Chi-restraints excluded: chain 3 residue 479 THR Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 4 residue 413 HIS Chi-restraints excluded: chain 4 residue 418 CYS Chi-restraints excluded: chain 4 residue 502 THR Chi-restraints excluded: chain 4 residue 815 ASN Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 196 ASN Chi-restraints excluded: chain 5 residue 270 MET Chi-restraints excluded: chain 5 residue 354 GLU Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 485 MET Chi-restraints excluded: chain 5 residue 546 ILE Chi-restraints excluded: chain 5 residue 656 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 300 VAL Chi-restraints excluded: chain 6 residue 515 GLU Chi-restraints excluded: chain 6 residue 556 HIS Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 654 GLU Chi-restraints excluded: chain 6 residue 775 GLU Chi-restraints excluded: chain 7 residue 100 ASP Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 547 SER Chi-restraints excluded: chain 7 residue 583 ASN Chi-restraints excluded: chain 7 residue 603 ILE Chi-restraints excluded: chain 7 residue 628 LEU Chi-restraints excluded: chain 7 residue 688 THR Chi-restraints excluded: chain 7 residue 689 LEU Chi-restraints excluded: chain 7 residue 707 MET Chi-restraints excluded: chain 8 residue 173 LEU Chi-restraints excluded: chain 8 residue 174 GLU Chi-restraints excluded: chain 8 residue 181 VAL Chi-restraints excluded: chain 8 residue 185 LEU Chi-restraints excluded: chain 8 residue 265 TYR Chi-restraints excluded: chain 8 residue 302 ILE Chi-restraints excluded: chain 8 residue 338 TRP Chi-restraints excluded: chain 8 residue 444 GLN Chi-restraints excluded: chain 9 residue 112 TRP Chi-restraints excluded: chain 9 residue 166 PHE Chi-restraints excluded: chain 9 residue 244 TYR Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 563 GLU Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 598 THR Chi-restraints excluded: chain F residue 712 PHE Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain G residue 488 SER Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 529 MET Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 621 MET Chi-restraints excluded: chain G residue 704 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 781 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 461 optimal weight: 4.9990 chunk 592 optimal weight: 10.0000 chunk 458 optimal weight: 5.9990 chunk 682 optimal weight: 6.9990 chunk 452 optimal weight: 6.9990 chunk 807 optimal weight: 0.0170 chunk 505 optimal weight: 20.0000 chunk 492 optimal weight: 5.9990 chunk 372 optimal weight: 10.0000 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 68520 Z= 0.273 Angle : 0.565 12.065 92688 Z= 0.283 Chirality : 0.042 0.190 10680 Planarity : 0.004 0.060 11887 Dihedral : 7.132 155.182 9380 Min Nonbonded Distance : 1.612 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.85 % Allowed : 13.54 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 8325 helix: 1.71 (0.09), residues: 3310 sheet: -0.66 (0.14), residues: 1370 loop : -0.38 (0.10), residues: 3645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 3 111 HIS 0.008 0.001 HIS 9 239 PHE 0.022 0.001 PHE 3 421 TYR 0.021 0.001 TYR G 63 ARG 0.004 0.000 ARG 4 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 310 time to evaluate : 6.190 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: 0.7703 (tpp) cc_final: 0.7360 (tpp) REVERT: 4 413 HIS cc_start: 0.8409 (OUTLIER) cc_final: 0.7939 (t-170) REVERT: 4 811 MET cc_start: 0.8468 (ttt) cc_final: 0.8206 (ttp) REVERT: 7 181 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.7919 (mm) REVERT: 8 174 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: D 612 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7344 (mppt) REVERT: E 103 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8388 (mt) REVERT: E 552 MET cc_start: 0.7538 (ptp) cc_final: 0.7212 (mtm) REVERT: F 128 ASP cc_start: 0.6586 (m-30) cc_final: 0.6383 (m-30) REVERT: F 143 MET cc_start: 0.8057 (tpp) cc_final: 0.7675 (tpp) REVERT: F 712 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.6987 (t80) REVERT: G 428 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8663 (p) outliers start: 139 outliers final: 102 residues processed: 431 average time/residue: 0.6052 time to fit residues: 464.9993 Evaluate side-chains 404 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 296 time to evaluate : 6.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 251 GLU Chi-restraints excluded: chain 2 residue 359 ILE Chi-restraints excluded: chain 2 residue 365 THR Chi-restraints excluded: chain 2 residue 561 HIS Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 295 VAL Chi-restraints excluded: chain 3 residue 479 THR Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 4 residue 328 LEU Chi-restraints excluded: chain 4 residue 413 HIS Chi-restraints excluded: chain 4 residue 418 CYS Chi-restraints excluded: chain 4 residue 502 THR Chi-restraints excluded: chain 4 residue 533 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 196 ASN Chi-restraints excluded: chain 5 residue 270 MET Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 354 GLU Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 485 MET Chi-restraints excluded: chain 5 residue 546 ILE Chi-restraints excluded: chain 5 residue 656 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 300 VAL Chi-restraints excluded: chain 6 residue 343 PHE Chi-restraints excluded: chain 6 residue 515 GLU Chi-restraints excluded: chain 6 residue 556 HIS Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 654 GLU Chi-restraints excluded: chain 6 residue 672 LEU Chi-restraints excluded: chain 6 residue 775 GLU Chi-restraints excluded: chain 7 residue 100 ASP Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 504 ASP Chi-restraints excluded: chain 7 residue 547 SER Chi-restraints excluded: chain 7 residue 583 ASN Chi-restraints excluded: chain 7 residue 603 ILE Chi-restraints excluded: chain 7 residue 628 LEU Chi-restraints excluded: chain 7 residue 688 THR Chi-restraints excluded: chain 7 residue 689 LEU Chi-restraints excluded: chain 7 residue 707 MET Chi-restraints excluded: chain 8 residue 173 LEU Chi-restraints excluded: chain 8 residue 174 GLU Chi-restraints excluded: chain 8 residue 181 VAL Chi-restraints excluded: chain 8 residue 185 LEU Chi-restraints excluded: chain 8 residue 265 TYR Chi-restraints excluded: chain 8 residue 302 ILE Chi-restraints excluded: chain 8 residue 312 LEU Chi-restraints excluded: chain 8 residue 338 TRP Chi-restraints excluded: chain 8 residue 444 GLN Chi-restraints excluded: chain 9 residue 112 TRP Chi-restraints excluded: chain 9 residue 166 PHE Chi-restraints excluded: chain 9 residue 244 TYR Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 563 GLU Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 598 THR Chi-restraints excluded: chain F residue 712 PHE Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 397 VAL Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain G residue 488 SER Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 507 ILE Chi-restraints excluded: chain G residue 529 MET Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 621 MET Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain G residue 704 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 499 optimal weight: 1.9990 chunk 322 optimal weight: 0.8980 chunk 482 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 513 optimal weight: 5.9990 chunk 550 optimal weight: 6.9990 chunk 399 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 634 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 454 GLN 6 409 GLN 7 297 GLN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 68520 Z= 0.182 Angle : 0.541 12.585 92688 Z= 0.269 Chirality : 0.041 0.200 10680 Planarity : 0.003 0.049 11887 Dihedral : 6.956 155.952 9380 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.53 % Allowed : 14.14 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.09), residues: 8325 helix: 1.80 (0.09), residues: 3315 sheet: -0.58 (0.14), residues: 1353 loop : -0.31 (0.10), residues: 3657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 202 HIS 0.008 0.001 HIS 9 239 PHE 0.018 0.001 PHE F 115 TYR 0.018 0.001 TYR G 63 ARG 0.005 0.000 ARG 4 451 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 320 time to evaluate : 6.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 276 MET cc_start: 0.7662 (tpp) cc_final: 0.7328 (tpp) REVERT: 4 413 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.7886 (t-170) REVERT: 4 811 MET cc_start: 0.8462 (ttt) cc_final: 0.8159 (ttp) REVERT: 7 181 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7874 (mm) REVERT: 8 174 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: B 271 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6711 (t80) REVERT: B 818 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7905 (pm20) REVERT: C 386 MET cc_start: 0.8869 (tpp) cc_final: 0.8486 (tpp) REVERT: D 612 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7236 (mppt) REVERT: E 103 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8160 (mt) REVERT: F 143 MET cc_start: 0.8030 (tpp) cc_final: 0.7695 (tpp) REVERT: F 712 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.6996 (t80) REVERT: G 428 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8637 (p) REVERT: G 541 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7941 (mtm) outliers start: 115 outliers final: 85 residues processed: 418 average time/residue: 0.6211 time to fit residues: 462.6666 Evaluate side-chains 391 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 297 time to evaluate : 6.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 251 GLU Chi-restraints excluded: chain 2 residue 359 ILE Chi-restraints excluded: chain 2 residue 365 THR Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 3 residue 136 MET Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 295 VAL Chi-restraints excluded: chain 3 residue 432 THR Chi-restraints excluded: chain 3 residue 479 THR Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 4 residue 413 HIS Chi-restraints excluded: chain 4 residue 418 CYS Chi-restraints excluded: chain 4 residue 502 THR Chi-restraints excluded: chain 4 residue 654 ILE Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 270 MET Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 485 MET Chi-restraints excluded: chain 5 residue 546 ILE Chi-restraints excluded: chain 5 residue 656 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 300 VAL Chi-restraints excluded: chain 6 residue 515 GLU Chi-restraints excluded: chain 6 residue 556 HIS Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 654 GLU Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 547 SER Chi-restraints excluded: chain 7 residue 583 ASN Chi-restraints excluded: chain 7 residue 603 ILE Chi-restraints excluded: chain 7 residue 628 LEU Chi-restraints excluded: chain 7 residue 688 THR Chi-restraints excluded: chain 7 residue 689 LEU Chi-restraints excluded: chain 7 residue 707 MET Chi-restraints excluded: chain 8 residue 173 LEU Chi-restraints excluded: chain 8 residue 174 GLU Chi-restraints excluded: chain 8 residue 181 VAL Chi-restraints excluded: chain 8 residue 185 LEU Chi-restraints excluded: chain 8 residue 338 TRP Chi-restraints excluded: chain 8 residue 444 GLN Chi-restraints excluded: chain 9 residue 112 TRP Chi-restraints excluded: chain 9 residue 166 PHE Chi-restraints excluded: chain 9 residue 244 TYR Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 563 GLU Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain F residue 173 GLN Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 598 THR Chi-restraints excluded: chain F residue 712 PHE Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain G residue 488 SER Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 529 MET Chi-restraints excluded: chain G residue 541 MET Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 621 MET Chi-restraints excluded: chain G residue 704 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 734 optimal weight: 8.9990 chunk 773 optimal weight: 5.9990 chunk 705 optimal weight: 4.9990 chunk 752 optimal weight: 6.9990 chunk 453 optimal weight: 8.9990 chunk 327 optimal weight: 9.9990 chunk 591 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 680 optimal weight: 5.9990 chunk 711 optimal weight: 40.0000 chunk 750 optimal weight: 0.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 68520 Z= 0.260 Angle : 0.567 12.869 92688 Z= 0.283 Chirality : 0.042 0.203 10680 Planarity : 0.004 0.051 11887 Dihedral : 6.957 155.867 9380 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.56 % Allowed : 14.22 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.09), residues: 8325 helix: 1.77 (0.09), residues: 3309 sheet: -0.60 (0.14), residues: 1378 loop : -0.34 (0.10), residues: 3638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 111 HIS 0.007 0.001 HIS 9 239 PHE 0.022 0.001 PHE 3 421 TYR 0.023 0.001 TYR D 519 ARG 0.005 0.000 ARG G 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 297 time to evaluate : 6.231 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: 0.7652 (tpp) cc_final: 0.7334 (tpp) REVERT: 4 413 HIS cc_start: 0.8342 (OUTLIER) cc_final: 0.7939 (t-170) REVERT: 4 451 ARG cc_start: 0.7101 (mpt180) cc_final: 0.6041 (mpp-170) REVERT: 4 811 MET cc_start: 0.8482 (ttt) cc_final: 0.8155 (ttp) REVERT: 7 181 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7836 (mm) REVERT: 9 520 MET cc_start: 0.7386 (tpp) cc_final: 0.6867 (tpp) REVERT: 9 531 MET cc_start: 0.8407 (mmm) cc_final: 0.8113 (mmm) REVERT: B 270 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7919 (mp) REVERT: B 271 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6712 (t80) REVERT: C 386 MET cc_start: 0.8881 (tpp) cc_final: 0.8427 (tpp) REVERT: D 612 LYS cc_start: 0.8010 (mmtt) cc_final: 0.7342 (mppt) REVERT: E 103 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8117 (mt) REVERT: E 301 TYR cc_start: 0.6372 (t80) cc_final: 0.6076 (t80) REVERT: F 143 MET cc_start: 0.8138 (tpp) cc_final: 0.7791 (tpp) REVERT: F 712 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7058 (t80) REVERT: G 428 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8670 (p) REVERT: G 541 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7996 (mtm) outliers start: 117 outliers final: 97 residues processed: 397 average time/residue: 0.6007 time to fit residues: 427.0786 Evaluate side-chains 399 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 294 time to evaluate : 6.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 251 GLU Chi-restraints excluded: chain 2 residue 359 ILE Chi-restraints excluded: chain 2 residue 365 THR Chi-restraints excluded: chain 2 residue 561 HIS Chi-restraints excluded: chain 2 residue 564 VAL Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 3 residue 136 MET Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 295 VAL Chi-restraints excluded: chain 3 residue 432 THR Chi-restraints excluded: chain 3 residue 479 THR Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 4 residue 328 LEU Chi-restraints excluded: chain 4 residue 413 HIS Chi-restraints excluded: chain 4 residue 418 CYS Chi-restraints excluded: chain 4 residue 502 THR Chi-restraints excluded: chain 4 residue 654 ILE Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 214 THR Chi-restraints excluded: chain 5 residue 270 MET Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 485 MET Chi-restraints excluded: chain 5 residue 546 ILE Chi-restraints excluded: chain 5 residue 573 ILE Chi-restraints excluded: chain 5 residue 656 ILE Chi-restraints excluded: chain 6 residue 129 THR Chi-restraints excluded: chain 6 residue 300 VAL Chi-restraints excluded: chain 6 residue 506 ASN Chi-restraints excluded: chain 6 residue 515 GLU Chi-restraints excluded: chain 6 residue 556 HIS Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 654 GLU Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 191 LEU Chi-restraints excluded: chain 7 residue 241 VAL Chi-restraints excluded: chain 7 residue 504 ASP Chi-restraints excluded: chain 7 residue 547 SER Chi-restraints excluded: chain 7 residue 583 ASN Chi-restraints excluded: chain 7 residue 603 ILE Chi-restraints excluded: chain 7 residue 628 LEU Chi-restraints excluded: chain 7 residue 688 THR Chi-restraints excluded: chain 7 residue 689 LEU Chi-restraints excluded: chain 7 residue 707 MET Chi-restraints excluded: chain 8 residue 173 LEU Chi-restraints excluded: chain 8 residue 181 VAL Chi-restraints excluded: chain 8 residue 185 LEU Chi-restraints excluded: chain 8 residue 338 TRP Chi-restraints excluded: chain 8 residue 444 GLN Chi-restraints excluded: chain 9 residue 112 TRP Chi-restraints excluded: chain 9 residue 166 PHE Chi-restraints excluded: chain 9 residue 244 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 563 GLU Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 598 THR Chi-restraints excluded: chain F residue 712 PHE Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain G residue 488 SER Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 529 MET Chi-restraints excluded: chain G residue 541 MET Chi-restraints excluded: chain G residue 545 THR Chi-restraints excluded: chain G residue 621 MET Chi-restraints excluded: chain G residue 704 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 494 optimal weight: 3.9990 chunk 795 optimal weight: 0.0570 chunk 485 optimal weight: 10.0000 chunk 377 optimal weight: 20.0000 chunk 553 optimal weight: 7.9990 chunk 834 optimal weight: 1.9990 chunk 768 optimal weight: 7.9990 chunk 664 optimal weight: 0.0570 chunk 69 optimal weight: 0.9980 chunk 513 optimal weight: 4.9990 chunk 407 optimal weight: 8.9990 overall best weight: 1.4220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 333 GLN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 68520 Z= 0.157 Angle : 0.541 12.536 92688 Z= 0.267 Chirality : 0.041 0.271 10680 Planarity : 0.003 0.049 11887 Dihedral : 6.760 155.686 9377 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.31 % Allowed : 14.54 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.09), residues: 8325 helix: 1.86 (0.09), residues: 3311 sheet: -0.55 (0.14), residues: 1389 loop : -0.27 (0.10), residues: 3625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 9 202 HIS 0.008 0.001 HIS 9 239 PHE 0.020 0.001 PHE D 215 TYR 0.022 0.001 TYR D 519 ARG 0.004 0.000 ARG G 182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16650 Ramachandran restraints generated. 8325 Oldfield, 0 Emsley, 8325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 320 time to evaluate : 6.135 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: 0.7671 (tpp) cc_final: 0.7362 (tpp) REVERT: 3 308 GLN cc_start: 0.6925 (mp10) cc_final: 0.6717 (mp10) REVERT: 4 285 VAL cc_start: 0.7974 (t) cc_final: 0.7743 (m) REVERT: 4 413 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.7968 (t-170) REVERT: 4 811 MET cc_start: 0.8510 (ttt) cc_final: 0.8197 (ttp) REVERT: 7 181 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7858 (mm) REVERT: 8 76 LYS cc_start: 0.7701 (tppt) cc_final: 0.7023 (tptt) REVERT: 9 531 MET cc_start: 0.8426 (mmm) cc_final: 0.8121 (mmm) REVERT: B 270 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7906 (mp) REVERT: B 271 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6708 (t80) REVERT: B 818 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: C 386 MET cc_start: 0.8849 (tpp) cc_final: 0.8496 (tpp) REVERT: D 612 LYS cc_start: 0.7904 (mmtt) cc_final: 0.7233 (mppt) REVERT: E 103 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8070 (mt) REVERT: F 143 MET cc_start: 0.8195 (tpp) cc_final: 0.7867 (tpp) REVERT: F 712 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7117 (t80) REVERT: G 428 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8624 (p) outliers start: 98 outliers final: 79 residues processed: 402 average time/residue: 0.6146 time to fit residues: 442.4288 Evaluate side-chains 393 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 306 time to evaluate : 6.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 251 GLU Chi-restraints excluded: chain 2 residue 337 VAL Chi-restraints excluded: chain 2 residue 359 ILE Chi-restraints excluded: chain 2 residue 365 THR Chi-restraints excluded: chain 2 residue 561 HIS Chi-restraints excluded: chain 2 residue 603 VAL Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 3 residue 281 ASP Chi-restraints excluded: chain 3 residue 432 THR Chi-restraints excluded: chain 3 residue 479 THR Chi-restraints excluded: chain 3 residue 484 VAL Chi-restraints excluded: chain 4 residue 328 LEU Chi-restraints excluded: chain 4 residue 413 HIS Chi-restraints excluded: chain 4 residue 418 CYS Chi-restraints excluded: chain 4 residue 502 THR Chi-restraints excluded: chain 5 residue 192 ILE Chi-restraints excluded: chain 5 residue 194 ILE Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 393 MET Chi-restraints excluded: chain 5 residue 485 MET Chi-restraints excluded: chain 5 residue 546 ILE Chi-restraints excluded: chain 5 residue 656 ILE Chi-restraints excluded: chain 6 residue 300 VAL Chi-restraints excluded: chain 6 residue 343 PHE Chi-restraints excluded: chain 6 residue 515 GLU Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 654 GLU Chi-restraints excluded: chain 7 residue 181 LEU Chi-restraints excluded: chain 7 residue 547 SER Chi-restraints excluded: chain 7 residue 583 ASN Chi-restraints excluded: chain 7 residue 603 ILE Chi-restraints excluded: chain 7 residue 628 LEU Chi-restraints excluded: chain 7 residue 688 THR Chi-restraints excluded: chain 7 residue 689 LEU Chi-restraints excluded: chain 7 residue 707 MET Chi-restraints excluded: chain 8 residue 94 LEU Chi-restraints excluded: chain 8 residue 173 LEU Chi-restraints excluded: chain 8 residue 181 VAL Chi-restraints excluded: chain 8 residue 338 TRP Chi-restraints excluded: chain 8 residue 444 GLN Chi-restraints excluded: chain 9 residue 112 TRP Chi-restraints excluded: chain 9 residue 166 PHE Chi-restraints excluded: chain 9 residue 244 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 796 GLU Chi-restraints excluded: chain B residue 818 GLU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 306 MET Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 563 GLU Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 65 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 430 GLU Chi-restraints excluded: chain F residue 118 PHE Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 598 THR Chi-restraints excluded: chain F residue 712 PHE Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain G residue 428 VAL Chi-restraints excluded: chain G residue 488 SER Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 621 MET Chi-restraints excluded: chain G residue 704 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 528 optimal weight: 8.9990 chunk 708 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 chunk 612 optimal weight: 30.0000 chunk 98 optimal weight: 4.9990 chunk 184 optimal weight: 0.0270 chunk 665 optimal weight: 2.9990 chunk 278 optimal weight: 0.7980 chunk 683 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 615 GLN 4 450 GLN 5 494 HIS ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.077395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.059027 restraints weight = 240848.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.058580 restraints weight = 148623.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.059256 restraints weight = 128031.170| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 68520 Z= 0.168 Angle : 0.541 12.375 92688 Z= 0.267 Chirality : 0.041 0.226 10680 Planarity : 0.003 0.048 11887 Dihedral : 6.642 155.869 9377 Min Nonbonded Distance : 1.548 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.28 % Allowed : 14.75 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.09), residues: 8325 helix: 1.95 (0.09), residues: 3287 sheet: -0.47 (0.14), residues: 1375 loop : -0.25 (0.10), residues: 3663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 202 HIS 0.008 0.001 HIS 9 239 PHE 0.049 0.001 PHE F 115 TYR 0.021 0.001 TYR D 519 ARG 0.005 0.000 ARG F 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9813.37 seconds wall clock time: 175 minutes 16.20 seconds (10516.20 seconds total)