Starting phenix.real_space_refine on Thu Nov 16 17:13:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt7_13620/11_2023/7pt7_13620_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt7_13620/11_2023/7pt7_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_13620/11_2023/7pt7_13620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt7_13620/11_2023/7pt7_13620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt7_13620/11_2023/7pt7_13620_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pt7_13620/11_2023/7pt7_13620_neut_updated.pdb" } 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 Residue "2 TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 221": "OE1" <-> "OE2" Residue "2 PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 524": "OD1" <-> "OD2" Residue "4 TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 647": "OE1" <-> "OE2" Residue "5 ASP 22": "OD1" <-> "OD2" Residue "5 ASP 279": "OD1" <-> "OD2" Residue "6 GLU 131": "OE1" <-> "OE2" Residue "6 GLU 303": "OE1" <-> "OE2" Residue "6 TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 524": "OD1" <-> "OD2" Residue "8 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 182": "OD1" <-> "OD2" Residue "8 PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 123": "OD1" <-> "OD2" Residue "9 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 452": "OE1" <-> "OE2" Residue "B GLU 480": "OE1" <-> "OE2" Residue "B ASP 600": "OD1" <-> "OD2" Residue "B ASP 782": "OD1" <-> "OD2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C ASP 619": "OD1" <-> "OD2" Residue "C GLU 623": "OE1" <-> "OE2" Residue "D ASP 278": "OD1" <-> "OD2" Residue "D TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 28.12, per 1000 atoms: 0.42 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.73 Conformation dependent library (CDL) restraints added in 9.1 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... running ksdssp... Secondary structure from input PDB file: 315 helices and 87 sheets defined 37.6% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.18 Creating SS restraints... Processing helix chain '2' and resid 183 through 187 removed outlier: 3.666A pdb=" N SER 2 187 " --> pdb=" O LEU 2 183 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 183 through 187' Processing helix chain '2' and resid 194 through 198 Processing helix chain '2' and resid 201 through 217 Processing helix chain '2' and resid 226 through 237 Processing helix chain '2' and resid 246 through 252 Processing helix chain '2' and resid 254 through 262 Processing helix chain '2' and resid 264 through 282 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 306 through 308 No H-bonds generated for 'chain '2' and resid 306 through 308' Processing helix chain '2' and resid 412 through 414 No H-bonds generated for 'chain '2' and resid 412 through 414' Processing helix chain '2' and resid 478 through 489 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 493 through 500 Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 549 through 559 Processing helix chain '2' and resid 595 through 598 No H-bonds generated for 'chain '2' and resid 595 through 598' Processing helix chain '2' and resid 614 through 626 Processing helix chain '2' and resid 653 through 655 No H-bonds generated for 'chain '2' and resid 653 through 655' Processing helix chain '2' and resid 663 through 666 No H-bonds generated for 'chain '2' and resid 663 through 666' Processing helix chain '2' and resid 671 through 676 Processing helix chain '2' and resid 689 through 705 Processing helix chain '2' and resid 760 through 773 removed outlier: 4.003A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 781 through 800 removed outlier: 3.879A pdb=" N ASP 2 784 " --> pdb=" O MET 2 781 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS 2 785 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL 2 786 " --> pdb=" O MET 2 783 " (cutoff:3.500A) Processing helix chain '2' and resid 807 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 831 through 847 Processing helix chain '2' and resid 855 through 858 No H-bonds generated for 'chain '2' and resid 855 through 858' Processing helix chain '2' and resid 861 through 863 No H-bonds generated for 'chain '2' and resid 861 through 863' Processing helix chain '3' and resid 19 through 34 Processing helix chain '3' and resid 36 through 55 Processing helix chain '3' and resid 100 through 106 Processing helix chain '3' and resid 108 through 116 Processing helix chain '3' and resid 118 through 136 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 162 through 164 No H-bonds generated for 'chain '3' and resid 162 through 164' Processing helix chain '3' and resid 173 through 175 No H-bonds generated for 'chain '3' and resid 173 through 175' Processing helix chain '3' and resid 280 through 282 No H-bonds generated for 'chain '3' and resid 280 through 282' Processing helix chain '3' and resid 344 through 355 removed outlier: 3.696A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) Processing helix chain '3' and resid 359 through 367 Processing helix chain '3' and resid 375 through 386 Processing helix chain '3' and resid 415 through 425 Processing helix chain '3' and resid 461 through 464 No H-bonds generated for 'chain '3' and resid 461 through 464' Processing helix chain '3' and resid 480 through 484 Processing helix chain '3' and resid 486 through 491 Processing helix chain '3' and resid 529 through 533 Processing helix chain '3' and resid 537 through 542 Processing helix chain '3' and resid 555 through 569 Processing helix chain '3' and resid 653 through 666 removed outlier: 3.552A pdb=" N GLU 3 665 " --> pdb=" O GLN 3 661 " (cutoff:3.500A) Processing helix chain '3' and resid 673 through 688 removed outlier: 3.532A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 699 through 715 Processing helix chain '3' and resid 723 through 737 Processing helix chain '4' and resid 187 through 199 Processing helix chain '4' and resid 203 through 209 Processing helix chain '4' and resid 218 through 221 No H-bonds generated for 'chain '4' and resid 218 through 221' Processing helix chain '4' and resid 225 through 236 Processing helix chain '4' and resid 245 through 250 Processing helix chain '4' and resid 252 through 263 removed outlier: 4.892A pdb=" N ASP 4 256 " --> pdb=" O GLN 4 253 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN 4 263 " --> pdb=" O GLN 4 260 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 287 Processing helix chain '4' and resid 293 through 297 Processing helix chain '4' and resid 319 through 321 No H-bonds generated for 'chain '4' and resid 319 through 321' Processing helix chain '4' and resid 421 through 423 No H-bonds generated for 'chain '4' and resid 421 through 423' Processing helix chain '4' and resid 482 through 491 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 503 through 513 Processing helix chain '4' and resid 518 through 525 Processing helix chain '4' and resid 534 through 545 Processing helix chain '4' and resid 574 through 584 Processing helix chain '4' and resid 593 through 595 No H-bonds generated for 'chain '4' and resid 593 through 595' Processing helix chain '4' and resid 620 through 623 No H-bonds generated for 'chain '4' and resid 620 through 623' Processing helix chain '4' and resid 639 through 650 removed outlier: 4.371A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU 4 645 " --> pdb=" O THR 4 641 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N HIS 4 646 " --> pdb=" O ARG 4 642 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 688 through 692 Processing helix chain '4' and resid 696 through 701 removed outlier: 3.506A pdb=" N ARG 4 701 " --> pdb=" O PRO 4 697 " (cutoff:3.500A) Processing helix chain '4' and resid 714 through 728 removed outlier: 3.616A pdb=" N TYR 4 728 " --> pdb=" O LEU 4 724 " (cutoff:3.500A) Processing helix chain '4' and resid 744 through 757 Processing helix chain '4' and resid 764 through 777 Processing helix chain '4' and resid 795 through 811 Processing helix chain '4' and resid 819 through 832 Processing helix chain '5' and resid 24 through 37 Processing helix chain '5' and resid 45 through 55 Processing helix chain '5' and resid 66 through 71 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) No H-bonds generated for 'chain '5' and resid 66 through 71' Processing helix chain '5' and resid 73 through 81 Processing helix chain '5' and resid 83 through 106 Proline residue: 5 88 - end of helix Processing helix chain '5' and resid 148 through 150 No H-bonds generated for 'chain '5' and resid 148 through 150' Processing helix chain '5' and resid 245 through 247 No H-bonds generated for 'chain '5' and resid 245 through 247' Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '5' and resid 351 through 361 Processing helix chain '5' and resid 366 through 373 Processing helix chain '5' and resid 382 through 393 Processing helix chain '5' and resid 422 through 432 Processing helix chain '5' and resid 468 through 471 No H-bonds generated for 'chain '5' and resid 468 through 471' Processing helix chain '5' and resid 487 through 498 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 536 through 539 No H-bonds generated for 'chain '5' and resid 536 through 539' Processing helix chain '5' and resid 544 through 549 Processing helix chain '5' and resid 562 through 575 Processing helix chain '5' and resid 596 through 609 Processing helix chain '5' and resid 616 through 639 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) Processing helix chain '5' and resid 650 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 674 through 687 Processing helix chain '6' and resid 106 through 120 Processing helix chain '6' and resid 135 through 145 removed outlier: 3.851A pdb=" N GLU 6 141 " --> pdb=" O ARG 6 137 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 172 removed outlier: 3.921A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN 6 163 " --> pdb=" O SER 6 159 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY 6 164 " --> pdb=" O MET 6 160 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA 6 165 " --> pdb=" O ARG 6 161 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU 6 166 " --> pdb=" O GLU 6 162 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA 6 167 " --> pdb=" O ASN 6 163 " (cutoff:3.500A) Processing helix chain '6' and resid 174 through 191 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 383 through 385 No H-bonds generated for 'chain '6' and resid 383 through 385' Processing helix chain '6' and resid 501 through 507 Processing helix chain '6' and resid 510 through 520 Processing helix chain '6' and resid 526 through 531 Processing helix chain '6' and resid 542 through 552 Processing helix chain '6' and resid 581 through 588 Processing helix chain '6' and resid 605 through 608 No H-bonds generated for 'chain '6' and resid 605 through 608' Processing helix chain '6' and resid 627 through 631 Processing helix chain '6' and resid 646 through 658 removed outlier: 3.575A pdb=" N GLN 6 658 " --> pdb=" O GLU 6 654 " (cutoff:3.500A) Processing helix chain '6' and resid 685 through 687 No H-bonds generated for 'chain '6' and resid 685 through 687' Processing helix chain '6' and resid 696 through 698 No H-bonds generated for 'chain '6' and resid 696 through 698' Processing helix chain '6' and resid 703 through 708 Processing helix chain '6' and resid 721 through 736 Processing helix chain '6' and resid 748 through 760 Processing helix chain '6' and resid 767 through 783 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) Processing helix chain '6' and resid 797 through 813 removed outlier: 3.646A pdb=" N ALA 6 809 " --> pdb=" O ARG 6 805 " (cutoff:3.500A) Processing helix chain '6' and resid 821 through 834 Processing helix chain '7' and resid 14 through 26 Processing helix chain '7' and resid 62 through 71 Processing helix chain '7' and resid 82 through 95 removed outlier: 3.553A pdb=" N GLN 7 95 " --> pdb=" O GLU 7 91 " (cutoff:3.500A) Processing helix chain '7' and resid 102 through 108 Processing helix chain '7' and resid 110 through 124 removed outlier: 3.802A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 138 through 164 Processing helix chain '7' and resid 178 through 188 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 194 through 197 Processing helix chain '7' and resid 209 through 211 No H-bonds generated for 'chain '7' and resid 209 through 211' Processing helix chain '7' and resid 227 through 229 No H-bonds generated for 'chain '7' and resid 227 through 229' Processing helix chain '7' and resid 287 through 291 Processing helix chain '7' and resid 337 through 339 No H-bonds generated for 'chain '7' and resid 337 through 339' Processing helix chain '7' and resid 395 through 406 Processing helix chain '7' and resid 410 through 417 Processing helix chain '7' and resid 427 through 437 Processing helix chain '7' and resid 466 through 476 Processing helix chain '7' and resid 488 through 492 Processing helix chain '7' and resid 512 through 515 No H-bonds generated for 'chain '7' and resid 512 through 515' Processing helix chain '7' and resid 531 through 543 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 580 through 584 Processing helix chain '7' and resid 588 through 593 removed outlier: 3.767A pdb=" N ARG 7 593 " --> pdb=" O ALA 7 589 " (cutoff:3.500A) Processing helix chain '7' and resid 606 through 621 removed outlier: 3.751A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) Processing helix chain '7' and resid 635 through 647 Processing helix chain '7' and resid 654 through 673 Processing helix chain '7' and resid 686 through 703 Processing helix chain '7' and resid 710 through 727 removed outlier: 4.313A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU 7 725 " --> pdb=" O ARG 7 721 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER 7 726 " --> pdb=" O VAL 7 722 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) Processing helix chain '8' and resid 13 through 25 removed outlier: 4.419A pdb=" N GLU 8 18 " --> pdb=" O GLU 8 14 " (cutoff:3.500A) Processing helix chain '8' and resid 56 through 59 No H-bonds generated for 'chain '8' and resid 56 through 59' Processing helix chain '8' and resid 84 through 96 Processing helix chain '8' and resid 128 through 131 No H-bonds generated for 'chain '8' and resid 128 through 131' Processing helix chain '8' and resid 137 through 157 Processing helix chain '8' and resid 166 through 168 No H-bonds generated for 'chain '8' and resid 166 through 168' Processing helix chain '8' and resid 287 through 290 No H-bonds generated for 'chain '8' and resid 287 through 290' Processing helix chain '8' and resid 298 through 312 Processing helix chain '8' and resid 325 through 335 Processing helix chain '8' and resid 338 through 347 Processing helix chain '8' and resid 369 through 383 removed outlier: 3.508A pdb=" N GLU 8 380 " --> pdb=" O LEU 8 376 " (cutoff:3.500A) Processing helix chain '8' and resid 392 through 402 Processing helix chain '8' and resid 425 through 449 removed outlier: 3.647A pdb=" N GLN 8 448 " --> pdb=" O GLN 8 444 " (cutoff:3.500A) Processing helix chain '8' and resid 460 through 464 Processing helix chain '8' and resid 472 through 474 No H-bonds generated for 'chain '8' and resid 472 through 474' Processing helix chain '9' and resid 112 through 116 Processing helix chain '9' and resid 138 through 156 removed outlier: 3.672A pdb=" N PHE 9 155 " --> pdb=" O LEU 9 151 " (cutoff:3.500A) Processing helix chain '9' and resid 190 through 197 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 204 through 214 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 234 through 241 Processing helix chain '9' and resid 286 through 288 No H-bonds generated for 'chain '9' and resid 286 through 288' Processing helix chain '9' and resid 320 through 332 Processing helix chain '9' and resid 334 through 343 Processing helix chain '9' and resid 374 through 386 Processing helix chain '9' and resid 522 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 671 through 675 Processing helix chain '9' and resid 678 through 685 Processing helix chain '9' and resid 687 through 700 removed outlier: 3.852A pdb=" N GLU 9 691 " --> pdb=" O LEU 9 688 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ALA 9 692 " --> pdb=" O ASN 9 689 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU 9 698 " --> pdb=" O SER 9 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.891A pdb=" N ILE B 198 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 264 through 282 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 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 478 through 488 Processing helix chain 'B' and resid 493 through 500 Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 595 through 598 No H-bonds generated for 'chain 'B' and resid 595 through 598' Processing helix chain 'B' and resid 614 through 626 Processing helix chain 'B' and resid 653 through 655 No H-bonds generated for 'chain 'B' and resid 653 through 655' Processing helix chain 'B' and resid 663 through 666 No H-bonds generated for 'chain 'B' and resid 663 through 666' Processing helix chain 'B' and resid 671 through 675 Processing helix chain 'B' and resid 689 through 705 Processing helix chain 'B' and resid 760 through 773 Processing helix chain 'B' and resid 780 through 800 removed outlier: 4.816A pdb=" N ASP B 784 " --> pdb=" O MET B 781 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 786 " --> pdb=" O MET B 783 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 796 " --> pdb=" O LEU B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 824 removed outlier: 3.535A pdb=" N ARG B 824 " --> pdb=" O PHE B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 848 Processing helix chain 'B' and resid 855 through 858 No H-bonds generated for 'chain 'B' and resid 855 through 858' Processing helix chain 'B' and resid 861 through 863 No H-bonds generated for 'chain 'B' and resid 861 through 863' Processing helix chain 'C' and resid 19 through 34 Processing helix chain 'C' and resid 36 through 55 Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 108 through 116 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 122 through 136 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 344 through 354 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 375 through 386 Processing helix chain 'C' and resid 415 through 425 Processing helix chain 'C' and resid 461 through 464 No H-bonds generated for 'chain 'C' and resid 461 through 464' Processing helix chain 'C' and resid 480 through 491 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 529 through 533 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 555 through 569 Processing helix chain 'C' and resid 653 through 666 Processing helix chain 'C' and resid 673 through 687 Processing helix chain 'C' and resid 699 through 715 Processing helix chain 'C' and resid 723 through 738 Processing helix chain 'D' and resid 187 through 199 Processing helix chain 'D' and resid 203 through 209 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 225 through 236 Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 252 through 263 removed outlier: 5.130A pdb=" N ASP D 256 " --> pdb=" O GLN D 253 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN D 263 " --> pdb=" O GLN D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 287 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 421 through 423 No H-bonds generated for 'chain 'D' and resid 421 through 423' Processing helix chain 'D' and resid 482 through 491 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 503 through 513 Processing helix chain 'D' and resid 518 through 525 Processing helix chain 'D' and resid 534 through 545 Processing helix chain 'D' and resid 574 through 584 Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 620 through 623 No H-bonds generated for 'chain 'D' and resid 620 through 623' Processing helix chain 'D' and resid 639 through 651 removed outlier: 4.749A pdb=" N VAL D 644 " --> pdb=" O SER D 640 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU D 645 " --> pdb=" O THR D 641 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS D 646 " --> pdb=" O ARG D 642 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU D 647 " --> pdb=" O SER D 643 " (cutoff:3.500A) 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 678 through 680 No H-bonds generated for 'chain 'D' and resid 678 through 680' Processing helix chain 'D' and resid 688 through 692 Processing helix chain 'D' and resid 696 through 701 removed outlier: 3.642A pdb=" N ARG D 701 " --> pdb=" O PRO D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 727 Processing helix chain 'D' and resid 744 through 757 Processing helix chain 'D' and resid 764 through 777 Processing helix chain 'D' and resid 795 through 811 Processing helix chain 'D' and resid 819 through 832 Processing helix chain 'D' and resid 835 through 837 No H-bonds generated for 'chain 'D' and resid 835 through 837' Processing helix chain 'D' and resid 847 through 850 No H-bonds generated for 'chain 'D' and resid 847 through 850' Processing helix chain 'E' and resid 24 through 37 Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 65 through 71 Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 83 through 105 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 351 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 366 through 373 Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 422 through 432 Processing helix chain 'E' and resid 468 through 471 No H-bonds generated for 'chain 'E' and resid 468 through 471' Processing helix chain 'E' and resid 482 through 484 No H-bonds generated for 'chain 'E' and resid 482 through 484' Processing helix chain 'E' and resid 487 through 499 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 544 through 549 Processing helix chain 'E' and resid 562 through 575 Processing helix chain 'E' and resid 596 through 609 Processing helix chain 'E' and resid 616 through 639 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 650 through 666 Processing helix chain 'E' and resid 674 through 687 Processing helix chain 'E' and resid 691 through 694 No H-bonds generated for 'chain 'E' and resid 691 through 694' Processing helix chain 'F' and resid 106 through 121 removed outlier: 3.819A pdb=" N GLU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 146 Processing helix chain 'F' and resid 155 through 172 removed outlier: 5.191A pdb=" N GLU F 162 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY F 164 " --> pdb=" O MET F 160 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA F 167 " --> pdb=" O ASN F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 191 Proline residue: F 179 - end of helix Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 281 through 283 No H-bonds generated for 'chain 'F' and resid 281 through 283' Processing helix chain 'F' and resid 365 through 367 No H-bonds generated for 'chain 'F' and resid 365 through 367' Processing helix chain 'F' and resid 501 through 506 Processing helix chain 'F' and resid 510 through 521 Processing helix chain 'F' and resid 523 through 532 removed outlier: 4.250A pdb=" N TYR F 526 " --> pdb=" O GLU F 523 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS F 528 " --> pdb=" O ILE F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 552 Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.738A pdb=" N LEU F 585 " --> pdb=" O LYS F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 608 No H-bonds generated for 'chain 'F' and resid 605 through 608' Processing helix chain 'F' and resid 627 through 631 Processing helix chain 'F' and resid 646 through 658 Processing helix chain 'F' and resid 695 through 698 No H-bonds generated for 'chain 'F' and resid 695 through 698' Processing helix chain 'F' and resid 703 through 708 Processing helix chain 'F' and resid 721 through 736 Processing helix chain 'F' and resid 748 through 760 Processing helix chain 'F' and resid 767 through 783 Processing helix chain 'F' and resid 797 through 813 Processing helix chain 'F' and resid 821 through 834 Processing helix chain 'G' and resid 14 through 26 Processing helix chain 'G' and resid 62 through 71 Processing helix chain 'G' and resid 82 through 94 Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 110 through 123 removed outlier: 3.704A pdb=" N GLU G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 164 Processing helix chain 'G' and resid 178 through 188 Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 287 through 291 Processing helix chain 'G' and resid 337 through 339 No H-bonds generated for 'chain 'G' and resid 337 through 339' Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' Processing helix chain 'G' and resid 395 through 407 removed outlier: 4.028A pdb=" N ARG G 400 " --> pdb=" O ASP G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 416 Processing helix chain 'G' and resid 426 through 437 Processing helix chain 'G' and resid 466 through 476 Processing helix chain 'G' and resid 512 through 515 No H-bonds generated for 'chain 'G' and resid 512 through 515' Processing helix chain 'G' and resid 531 through 542 removed outlier: 3.747A pdb=" N GLU G 539 " --> pdb=" O THR G 535 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 584 Processing helix chain 'G' and resid 588 through 593 removed outlier: 3.930A pdb=" N ARG G 593 " --> pdb=" O ALA G 589 " (cutoff:3.500A) Processing helix chain 'G' and resid 606 through 621 removed outlier: 3.786A pdb=" N GLU G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 635 through 647 Processing helix chain 'G' and resid 654 through 673 Processing helix chain 'G' and resid 686 through 703 Processing helix chain 'G' and resid 710 through 727 removed outlier: 4.539A pdb=" N LYS G 724 " --> pdb=" O VAL G 720 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU G 725 " --> pdb=" O ARG G 721 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER G 726 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU G 727 " --> pdb=" O SER G 723 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 455 through 458 removed outlier: 3.995A pdb=" N SER 2 316 " --> pdb=" O TYR 2 430 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR 2 449 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU 2 407 " --> pdb=" O THR 2 449 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 350 through 352 removed outlier: 6.658A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 679 through 683 removed outlier: 3.656A pdb=" N LEU 2 542 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 579 through 582 Processing sheet with id= E, first strand: chain '2' and resid 628 through 633 Processing sheet with id= F, first strand: chain '3' and resid 95 through 99 removed outlier: 6.959A pdb=" N LYS 3 154 " --> pdb=" O ILE 3 96 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE 3 98 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER 3 156 " --> pdb=" O ILE 3 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain '3' and resid 165 through 167 removed outlier: 7.845A pdb=" N LEU 3 166 " --> pdb=" O LEU 3 179 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N SER 3 181 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL 3 297 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLY 3 323 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS 3 299 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE 3 321 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU 3 301 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR 3 319 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 208 through 213 removed outlier: 3.599A pdb=" N ARG 3 208 " --> pdb=" O ALA 3 203 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 273 through 279 removed outlier: 3.882A pdb=" N LYS 3 188 " --> pdb=" O THR 3 257 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN 3 259 " --> pdb=" O VAL 3 186 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL 3 186 " --> pdb=" O GLN 3 259 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 545 through 549 removed outlier: 3.562A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY 3 468 " --> pdb=" O SER 3 511 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE 3 513 " --> pdb=" O GLY 3 468 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL 3 470 " --> pdb=" O ILE 3 513 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ALA 3 515 " --> pdb=" O VAL 3 470 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE 3 472 " --> pdb=" O ALA 3 515 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 444 through 446 Processing sheet with id= L, first strand: chain '3' and resid 494 through 496 Processing sheet with id= M, first strand: chain '3' and resid 195 through 198 removed outlier: 6.822A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 433 through 438 removed outlier: 6.925A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER 4 335 " --> pdb=" O VAL 4 396 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL 4 396 " --> pdb=" O SER 4 335 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '4' and resid 347 through 349 Processing sheet with id= P, first strand: chain '4' and resid 439 through 442 Processing sheet with id= Q, first strand: chain '4' and resid 704 through 706 removed outlier: 6.266A pdb=" N VAL 4 589 " --> pdb=" O CYS 4 630 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP 4 632 " --> pdb=" O VAL 4 589 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR 4 591 " --> pdb=" O ASP 4 632 " (cutoff:3.500A) Processing sheet with id= R, 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= S, first strand: chain '4' and resid 654 through 658 Processing sheet with id= T, first strand: chain '4' and resid 339 through 344 removed outlier: 6.771A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '5' and resid 60 through 64 removed outlier: 6.481A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL 5 63 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE 5 138 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain '5' and resid 290 through 297 removed outlier: 3.771A pdb=" N THR 5 290 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) 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) Processing sheet with id= W, 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: 4.258A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '5' and resid 552 through 556 removed outlier: 3.767A pdb=" N GLY 5 416 " --> pdb=" O ALA 5 523 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL 5 437 " --> pdb=" O VAL 5 476 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '5' and resid 453 through 455 Processing sheet with id= Z, first strand: chain '5' and resid 501 through 504 Processing sheet with id= AA, first strand: chain '5' and resid 173 through 178 removed outlier: 6.658A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '6' and resid 150 through 154 removed outlier: 6.528A pdb=" N GLN 6 264 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE 6 153 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER 6 266 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain '6' and resid 394 through 400 removed outlier: 6.771A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N THR 6 297 " --> pdb=" O LYS 6 358 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS 6 358 " --> pdb=" O THR 6 297 " (cutoff:3.500A) removed outlier: 14.523A pdb=" N TYR 6 450 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 12.158A pdb=" N ASP 6 378 " --> pdb=" O TYR 6 450 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE 6 452 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ILE 6 380 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE 6 454 " --> pdb=" O ILE 6 380 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ARG 6 382 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ALA 6 456 " --> pdb=" O ARG 6 382 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR 6 398 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL 6 459 " --> pdb=" O LYS 6 396 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS 6 396 " --> pdb=" O VAL 6 459 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain '6' and resid 571 through 574 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) Processing sheet with id= AE, first strand: chain '6' and resid 611 through 614 Processing sheet with id= AF, first strand: chain '6' and resid 660 through 662 Processing sheet with id= AG, first strand: chain '6' and resid 301 through 306 removed outlier: 6.955A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain '7' and resid 77 through 81 removed outlier: 6.241A pdb=" N PHE 7 201 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE 7 80 " --> pdb=" O PHE 7 201 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR 7 203 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain '7' and resid 330 through 336 removed outlier: 3.768A pdb=" N ARG 7 247 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN 7 316 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE 7 245 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG 7 382 " --> pdb=" O ASP 7 350 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA 7 358 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR 7 374 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain '7' and resid 252 through 255 Processing sheet with id= AK, first strand: chain '7' and resid 267 through 272 Processing sheet with id= AL, first strand: chain '7' and resid 456 through 459 removed outlier: 3.960A pdb=" N ALA 7 567 " --> pdb=" O LEU 7 458 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '7' and resid 545 through 547 Processing sheet with id= AN, first strand: chain '8' and resid 106 through 112 removed outlier: 6.688A pdb=" N VAL 8 119 " --> pdb=" O CYS 8 107 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ALA 8 109 " --> pdb=" O ILE 8 117 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE 8 117 " --> pdb=" O ALA 8 109 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG 8 111 " --> pdb=" O GLN 8 115 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN 8 115 " --> pdb=" O ARG 8 111 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL 8 116 " --> pdb=" O ILE 8 78 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE 8 78 " --> pdb=" O VAL 8 116 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LYS 8 51 " --> pdb=" O LEU 8 35 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU 8 35 " --> pdb=" O LYS 8 51 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '8' and resid 169 through 172 Processing sheet with id= AP, first strand: chain '9' and resid 265 through 268 removed outlier: 3.935A pdb=" N ILE 9 279 " --> pdb=" O LEU 9 268 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '9' and resid 659 through 661 Processing sheet with id= AR, first strand: chain 'B' and resid 241 through 245 removed outlier: 6.692A pdb=" N HIS B 294 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL B 244 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG B 296 " --> pdb=" O VAL B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'B' and resid 455 through 458 removed outlier: 3.503A pdb=" N GLY B 322 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR B 389 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG B 327 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG B 387 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR B 449 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU B 407 " --> pdb=" O THR B 449 " (cutoff:3.500A) Processing sheet with id= AT, 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= AU, first strand: chain 'B' and resid 679 through 683 Processing sheet with id= AV, first strand: chain 'B' and resid 579 through 582 Processing sheet with id= AW, first strand: chain 'B' and resid 630 through 633 Processing sheet with id= AX, first strand: chain 'B' and resid 331 through 336 removed outlier: 6.350A pdb=" N VAL B 381 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'C' and resid 95 through 99 removed outlier: 7.166A pdb=" N LYS C 154 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE C 98 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER C 156 " --> pdb=" O ILE C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= AY Processing sheet with id= AZ, first strand: chain 'C' and resid 165 through 167 removed outlier: 7.887A pdb=" N LEU C 166 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N SER C 181 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG C 291 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'C' and resid 209 through 213 Processing sheet with id= BB, first strand: chain 'C' and resid 273 through 279 removed outlier: 3.908A pdb=" N LYS C 188 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN C 259 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL C 186 " --> pdb=" O GLN C 259 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'C' and resid 298 through 301 Processing sheet with id= BD, first strand: chain 'C' and resid 545 through 549 Processing sheet with id= BE, first strand: chain 'C' and resid 444 through 446 Processing sheet with id= BF, first strand: chain 'C' and resid 494 through 496 Processing sheet with id= BG, first strand: chain 'C' and resid 193 through 198 removed outlier: 6.786A pdb=" N THR C 249 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'D' and resid 240 through 244 removed outlier: 6.326A pdb=" N LYS D 302 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU D 243 " --> pdb=" O LYS D 302 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ARG D 304 " --> pdb=" O LEU D 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'D' and resid 414 through 420 removed outlier: 3.611A pdb=" N ARG D 334 " --> pdb=" O LYS D 398 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN D 400 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL D 332 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR D 438 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL D 463 " --> pdb=" O THR D 438 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG D 440 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL D 461 " --> pdb=" O ARG D 440 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE D 442 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR D 459 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id= BJ, 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= BK, first strand: chain 'D' and resid 704 through 708 removed outlier: 3.516A pdb=" N GLY D 568 " --> pdb=" O ALA D 675 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'D' and resid 603 through 608 Processing sheet with id= BM, first strand: chain 'D' and resid 653 through 656 Processing sheet with id= BN, first strand: chain 'D' and resid 341 through 344 removed outlier: 6.836A pdb=" N SER D 390 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'E' and resid 60 through 64 removed outlier: 6.309A pdb=" N GLN E 136 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL E 63 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE E 138 " --> pdb=" O VAL E 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= BO Processing sheet with id= BP, first strand: chain 'E' and resid 291 through 297 removed outlier: 6.836A pdb=" N LYS E 257 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR E 169 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE E 255 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR E 275 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASP E 279 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N GLY E 332 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL E 295 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE E 333 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR E 293 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'E' and resid 189 through 193 removed outlier: 4.406A pdb=" N SER E 180 " --> pdb=" O ILE E 244 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'E' and resid 552 through 556 removed outlier: 3.504A pdb=" N GLY E 416 " --> pdb=" O ALA E 523 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'E' and resid 501 through 504 Processing sheet with id= BT, first strand: chain 'E' and resid 173 through 178 removed outlier: 6.802A pdb=" N LYS E 249 " --> pdb=" O THR E 177 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'E' and resid 452 through 455 removed outlier: 4.120A pdb=" N GLY E 466 " --> pdb=" O SER E 452 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN E 454 " --> pdb=" O LEU E 464 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU E 464 " --> pdb=" O GLN E 454 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'F' and resid 150 through 154 removed outlier: 6.659A pdb=" N GLN F 264 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE F 153 " --> pdb=" O GLN F 264 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N SER F 266 " --> pdb=" O ILE F 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'F' and resid 394 through 400 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) removed outlier: 14.708A pdb=" N TYR F 450 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 12.244A pdb=" N ASP F 378 " --> pdb=" O TYR F 450 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE F 452 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N ILE F 380 " --> pdb=" O ILE F 452 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE F 454 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ARG F 382 " --> pdb=" O PHE F 454 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA F 456 " --> pdb=" O ARG F 382 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR F 398 " --> pdb=" O CYS F 457 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL F 459 " --> pdb=" O LYS F 396 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS F 396 " --> pdb=" O VAL F 459 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'F' and resid 301 through 304 removed outlier: 3.691A pdb=" N GLU F 303 " --> pdb=" O LEU F 354 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'F' and resid 711 through 715 removed outlier: 3.708A pdb=" N GLY F 575 " --> pdb=" O ALA F 682 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY F 634 " --> pdb=" O SER F 677 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU F 679 " --> pdb=" O GLY F 634 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS F 636 " --> pdb=" O LEU F 679 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ALA F 681 " --> pdb=" O CYS F 636 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE F 638 " --> pdb=" O ALA F 681 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 596 " --> pdb=" O ILE F 635 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'F' and resid 611 through 614 Processing sheet with id= CA, first strand: chain 'F' and resid 660 through 662 Processing sheet with id= CB, first strand: chain 'G' and resid 77 through 81 removed outlier: 6.231A pdb=" N PHE G 201 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE G 80 " --> pdb=" O PHE G 201 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TYR G 203 " --> pdb=" O ILE G 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= CB Processing sheet with id= CC, first strand: chain 'G' and resid 238 through 245 removed outlier: 3.898A pdb=" N ASP G 347 " --> pdb=" O ILE G 245 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG G 382 " --> pdb=" O ASP G 350 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE G 354 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ALA G 378 " --> pdb=" O ILE G 354 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'G' and resid 267 through 272 removed outlier: 3.542A pdb=" N TYR G 267 " --> pdb=" O CYS G 262 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'G' and resid 334 through 336 removed outlier: 6.228A pdb=" N SER G 308 " --> pdb=" O VAL G 255 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL G 255 " --> pdb=" O SER G 308 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE G 310 " --> pdb=" O PRO G 253 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'G' and resid 357 through 359 Processing sheet with id= CG, first strand: chain 'G' and resid 596 through 598 Processing sheet with id= CH, first strand: chain 'G' and resid 496 through 499 Processing sheet with id= CI, first strand: chain 'G' and resid 545 through 548 2436 hydrogen bonds defined for protein. 6939 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: 26.93 Time building geometry restraints manager: 24.86 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=" BE BEF G1103 " pdb=" F1 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=" BE BEF 31004 " pdb=" F1 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=" BE BEF 41103 " pdb=" F1 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=" BE BEF D1103 " pdb=" F1 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=" BE BEF 31002 " pdb=" F2 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: 96.33 - 104.21: 997 104.21 - 112.09: 35114 112.09 - 119.97: 26311 119.97 - 127.85: 29812 127.85 - 135.73: 454 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: 435 2.47 - 3.08: 48522 3.08 - 3.69: 104638 3.69 - 4.29: 151863 4.29 - 4.90: 247882 Nonbonded interactions: 553340 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 553335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 12.430 Check model and map are aligned: 0.880 Set scattering table: 0.610 Process input model: 157.960 Find NCS groups from input model: 5.330 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: 0.020 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.310 ------------------------------------------------------------------------------- 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= 0.475 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 *********************** 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 : 6.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 14 residues processed: 430 average time/residue: 0.6479 time to fit residues: 483.3128 Evaluate side-chains 311 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 297 time to evaluate : 6.105 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.6139 time to fit residues: 23.3412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 707 optimal weight: 4.9990 chunk 635 optimal weight: 5.9990 chunk 352 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 428 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 656 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 399 optimal weight: 3.9990 chunk 488 optimal weight: 7.9990 chunk 760 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 507 ASN 4 543 GLN ** 5 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 814 ASN 7 293 GLN ** 7 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 85 GLN 8 89 ASN 8 168 ASN ** 8 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 369 HIS ** 9 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 699 ASN B 353 GLN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 GLN F 366 ASN F 501 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 68520 Z= 0.272 Angle : 0.567 9.402 92688 Z= 0.286 Chirality : 0.042 0.186 10680 Planarity : 0.004 0.054 11887 Dihedral : 7.451 143.501 9371 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.56 % Allowed : 7.40 % Favored : 92.04 % 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: 1.61 (0.09), residues: 3236 sheet: -0.51 (0.13), residues: 1511 loop : -0.26 (0.10), residues: 3578 *********************** 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 355 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 313 time to evaluate : 6.757 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 26 residues processed: 338 average time/residue: 0.6356 time to fit residues: 380.0224 Evaluate side-chains 317 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 291 time to evaluate : 6.155 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.5608 time to fit residues: 34.9257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 422 optimal weight: 4.9990 chunk 236 optimal weight: 8.9990 chunk 633 optimal weight: 7.9990 chunk 518 optimal weight: 6.9990 chunk 209 optimal weight: 0.9990 chunk 762 optimal weight: 8.9990 chunk 823 optimal weight: 0.5980 chunk 678 optimal weight: 0.9990 chunk 756 optimal weight: 8.9990 chunk 259 optimal weight: 20.0000 chunk 611 optimal weight: 20.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 543 GLN 7 334 HIS ** 8 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 68520 Z= 0.210 Angle : 0.524 10.059 92688 Z= 0.262 Chirality : 0.041 0.204 10680 Planarity : 0.004 0.058 11887 Dihedral : 7.091 148.642 9371 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.60 % Allowed : 9.68 % Favored : 89.72 % 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: 0.65 (0.09), residues: 8325 helix: 1.69 (0.09), residues: 3232 sheet: -0.48 (0.14), residues: 1417 loop : -0.25 (0.10), residues: 3676 *********************** 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 369 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 324 time to evaluate : 6.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 19 residues processed: 361 average time/residue: 0.6609 time to fit residues: 423.8673 Evaluate side-chains 310 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 291 time to evaluate : 6.135 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5447 time to fit residues: 27.7426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 753 optimal weight: 3.9990 chunk 573 optimal weight: 5.9990 chunk 395 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 363 optimal weight: 0.0270 chunk 511 optimal weight: 8.9990 chunk 765 optimal weight: 3.9990 chunk 810 optimal weight: 2.9990 chunk 399 optimal weight: 0.0070 chunk 725 optimal weight: 20.0000 chunk 218 optimal weight: 0.8980 overall best weight: 1.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 349 ASN 4 543 GLN 7 165 ASN 7 293 GLN ** 8 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 286 GLN ** 9 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 68520 Z= 0.151 Angle : 0.505 10.419 92688 Z= 0.251 Chirality : 0.041 0.214 10680 Planarity : 0.003 0.059 11887 Dihedral : 6.844 154.929 9371 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.80 % Allowed : 10.83 % Favored : 88.37 % 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: 1.79 (0.09), residues: 3236 sheet: -0.48 (0.14), residues: 1430 loop : -0.18 (0.10), residues: 3659 *********************** 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 377 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 317 time to evaluate : 6.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 23 residues processed: 363 average time/residue: 0.6354 time to fit residues: 409.5744 Evaluate side-chains 317 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 294 time to evaluate : 6.172 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5119 time to fit residues: 30.7007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 674 optimal weight: 20.0000 chunk 459 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 603 optimal weight: 2.9990 chunk 334 optimal weight: 7.9990 chunk 691 optimal weight: 5.9990 chunk 559 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 413 optimal weight: 0.7980 chunk 727 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 543 GLN 7 112 HIS ** 8 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 699 ASN B 710 ASN ** 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: 0.8051 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 68520 Z= 0.307 Angle : 0.560 11.391 92688 Z= 0.280 Chirality : 0.042 0.201 10680 Planarity : 0.004 0.059 11887 Dihedral : 6.921 162.425 9371 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.95 % Allowed : 12.19 % Favored : 86.86 % 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: 1.70 (0.09), residues: 3238 sheet: -0.49 (0.14), residues: 1459 loop : -0.27 (0.10), residues: 3628 *********************** 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 376 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 305 time to evaluate : 6.527 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 36 residues processed: 362 average time/residue: 0.6457 time to fit residues: 417.3686 Evaluate side-chains 326 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 290 time to evaluate : 6.287 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.5232 time to fit residues: 44.4376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 272 optimal weight: 7.9990 chunk 729 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 475 optimal weight: 20.0000 chunk 199 optimal weight: 8.9990 chunk 810 optimal weight: 8.9990 chunk 673 optimal weight: 3.9990 chunk 375 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 425 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 349 ASN ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 543 GLN ** 8 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 699 ASN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 68520 Z= 0.182 Angle : 0.518 11.401 92688 Z= 0.256 Chirality : 0.041 0.218 10680 Planarity : 0.003 0.060 11887 Dihedral : 6.770 164.216 9371 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.76 % Allowed : 13.00 % Favored : 86.24 % 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: 0.70 (0.09), residues: 8325 helix: 1.74 (0.09), residues: 3244 sheet: -0.47 (0.14), residues: 1447 loop : -0.22 (0.10), residues: 3634 *********************** 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 369 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 312 time to evaluate : 6.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 24 residues processed: 357 average time/residue: 0.6574 time to fit residues: 418.3934 Evaluate side-chains 318 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 294 time to evaluate : 6.243 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.5336 time to fit residues: 32.9363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 781 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 461 optimal weight: 4.9990 chunk 592 optimal weight: 7.9990 chunk 458 optimal weight: 8.9990 chunk 682 optimal weight: 10.0000 chunk 452 optimal weight: 10.0000 chunk 807 optimal weight: 5.9990 chunk 505 optimal weight: 6.9990 chunk 492 optimal weight: 5.9990 chunk 372 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 313 ASN 3 349 ASN ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 543 GLN 5 284 ASN 6 157 HIS ** 8 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 699 ASN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 68520 Z= 0.353 Angle : 0.598 12.232 92688 Z= 0.299 Chirality : 0.042 0.204 10680 Planarity : 0.004 0.060 11887 Dihedral : 6.954 165.278 9371 Min Nonbonded Distance : 1.461 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.68 % Allowed : 13.88 % Favored : 85.44 % 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: 1.58 (0.09), residues: 3236 sheet: -0.46 (0.14), residues: 1442 loop : -0.35 (0.10), residues: 3647 *********************** 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 354 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 303 time to evaluate : 6.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 26 residues processed: 341 average time/residue: 0.6555 time to fit residues: 397.9180 Evaluate side-chains 314 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 288 time to evaluate : 6.100 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.5173 time to fit residues: 33.7709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 499 optimal weight: 6.9990 chunk 322 optimal weight: 0.9990 chunk 482 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 513 optimal weight: 6.9990 chunk 550 optimal weight: 2.9990 chunk 399 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 634 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 349 ASN ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 543 GLN 7 297 GLN 8 85 GLN 8 89 ASN ** 8 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 68520 Z= 0.274 Angle : 0.562 12.542 92688 Z= 0.279 Chirality : 0.042 0.213 10680 Planarity : 0.004 0.064 11887 Dihedral : 6.878 165.734 9371 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.64 % Allowed : 14.32 % Favored : 85.04 % 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: 0.52 (0.09), residues: 8325 helix: 1.61 (0.09), residues: 3226 sheet: -0.48 (0.14), residues: 1470 loop : -0.36 (0.10), residues: 3629 *********************** 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 349 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 301 time to evaluate : 6.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 20 residues processed: 341 average time/residue: 0.6446 time to fit residues: 393.2697 Evaluate side-chains 306 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 286 time to evaluate : 6.099 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5105 time to fit residues: 27.9496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 734 optimal weight: 7.9990 chunk 773 optimal weight: 3.9990 chunk 705 optimal weight: 3.9990 chunk 752 optimal weight: 0.5980 chunk 453 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 591 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 680 optimal weight: 4.9990 chunk 711 optimal weight: 40.0000 chunk 750 optimal weight: 6.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 349 ASN ** 4 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 543 GLN 7 293 GLN 8 85 GLN 8 89 ASN ** 8 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 68520 Z= 0.274 Angle : 0.565 12.929 92688 Z= 0.281 Chirality : 0.042 0.212 10680 Planarity : 0.004 0.060 11887 Dihedral : 6.861 165.043 9371 Min Nonbonded Distance : 1.485 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.45 % Allowed : 14.66 % Favored : 84.89 % 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: 0.52 (0.09), residues: 8325 helix: 1.61 (0.09), residues: 3221 sheet: -0.47 (0.14), residues: 1467 loop : -0.38 (0.10), residues: 3637 *********************** 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 326 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 292 time to evaluate : 6.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 13 residues processed: 317 average time/residue: 0.6477 time to fit residues: 365.9748 Evaluate side-chains 299 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 286 time to evaluate : 6.168 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5311 time to fit residues: 21.3269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 494 optimal weight: 0.7980 chunk 795 optimal weight: 7.9990 chunk 485 optimal weight: 0.6980 chunk 377 optimal weight: 10.0000 chunk 553 optimal weight: 8.9990 chunk 834 optimal weight: 2.9990 chunk 768 optimal weight: 2.9990 chunk 664 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 513 optimal weight: 5.9990 chunk 407 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 340 GLN 3 349 ASN 4 543 GLN 5 284 ASN 8 85 GLN 8 89 ASN ** 8 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 699 ASN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN F 340 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 68520 Z= 0.143 Angle : 0.525 11.738 92688 Z= 0.258 Chirality : 0.041 0.216 10680 Planarity : 0.003 0.061 11887 Dihedral : 6.583 163.147 9371 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.23 % Allowed : 15.00 % Favored : 84.77 % 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: 0.73 (0.09), residues: 8325 helix: 1.78 (0.09), residues: 3219 sheet: -0.41 (0.14), residues: 1477 loop : -0.23 (0.10), residues: 3629 ********************** 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 326 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 309 time to evaluate : 6.346 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 321 average time/residue: 0.6707 time to fit residues: 380.2929 Evaluate side-chains 299 residues out of total 7499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 294 time to evaluate : 6.159 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5593 time to fit residues: 13.3473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 838 random chunks: chunk 528 optimal weight: 0.8980 chunk 708 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 612 optimal weight: 8.9990 chunk 98 optimal weight: 0.0970 chunk 184 optimal weight: 5.9990 chunk 665 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 683 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 543 GLN 7 293 GLN ** 8 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 85 GLN 8 89 ASN ** 8 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.058720 restraints weight = 242085.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.058281 restraints weight = 150573.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058750 restraints weight = 133540.853| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 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 = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 68520 Z= 0.209 Angle : 0.540 13.410 92688 Z= 0.266 Chirality : 0.041 0.217 10680 Planarity : 0.004 0.061 11887 Dihedral : 6.579 161.524 9371 Min Nonbonded Distance : 1.497 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.21 % Allowed : 15.12 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.09), residues: 8325 helix: 1.80 (0.09), residues: 3215 sheet: -0.40 (0.14), residues: 1484 loop : -0.24 (0.10), residues: 3626 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9297.33 seconds wall clock time: 169 minutes 0.00 seconds (10140.00 seconds total)