Starting phenix.real_space_refine on Wed Sep 25 04:41:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwe_10038/09_2024/6rwe_10038.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwe_10038/09_2024/6rwe_10038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwe_10038/09_2024/6rwe_10038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwe_10038/09_2024/6rwe_10038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwe_10038/09_2024/6rwe_10038.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwe_10038/09_2024/6rwe_10038.cif" } resolution = 3.0 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= 0.001 sd= 0.011 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 94 5.49 5 S 241 5.16 5 C 33829 2.51 5 N 9268 2.21 5 O 10279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 53719 Number of models: 1 Model: "" Number of chains: 26 Chain: "T" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1000 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain breaks: 1 Chain: "U" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 944 Classifications: {'DNA': 45} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "M" Number of atoms: 3100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3100 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 21, 'TRANS': 370} Chain breaks: 1 Chain: "A" Number of atoms: 11558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1464, 11558 Classifications: {'peptide': 1464} Link IDs: {'PTRANS': 59, 'TRANS': 1404} Chain breaks: 7 Chain: "B" Number of atoms: 9371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9371 Classifications: {'peptide': 1180} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 59, 'TRANS': 1120} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 551 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1576 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 942 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4086 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 485} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "Q" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3936 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 457} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4963 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 21, 'TRANS': 588} Chain breaks: 7 Chain: "R" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2771 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5480 SG CYS A 62 90.649 71.327 58.465 1.00 86.36 S ATOM 5499 SG CYS A 65 88.913 67.533 59.204 1.00 74.93 S ATOM 5800 SG CYS A 102 133.400 53.724 81.383 1.00106.46 S ATOM 5825 SG CYS A 105 132.423 50.643 79.363 1.00106.37 S ATOM 6624 SG CYS A 233 133.602 49.473 82.508 1.00111.28 S ATOM 6646 SG CYS A 236 136.439 50.656 80.543 1.00116.24 S ATOM 25261 SG CYS B1104 93.520 52.929 62.398 1.00 64.64 S ATOM 25287 SG CYS B1107 96.088 54.773 64.818 1.00 66.68 S ATOM 25434 SG CYS B1128 95.049 56.587 61.849 1.00 73.77 S ATOM 25462 SG CYS B1131 97.233 52.913 61.324 1.00 75.79 S ATOM 34235 SG CYS I 10 142.893 102.736 130.494 1.00 88.33 S ATOM 34257 SG CYS I 13 141.127 103.758 127.411 1.00 89.40 S ATOM 34377 SG CYS I 30 142.830 101.228 125.524 1.00104.19 S ATOM 34805 SG CYS I 86 73.986 53.941 131.960 1.00202.27 S ATOM 34827 SG CYS I 89 74.211 51.292 135.189 1.00209.68 S ATOM 35025 SG CYS I 114 76.165 55.361 134.566 1.00185.20 S ATOM 35044 SG CYS I 117 77.515 52.315 132.858 1.00196.97 S ATOM 35168 SG CYS J 7 46.492 96.096 111.429 1.00 39.96 S ATOM 35191 SG CYS J 10 42.784 95.566 111.950 1.00 40.75 S ATOM 35471 SG CYS J 45 44.902 94.593 114.738 1.00 39.91 S ATOM 36543 SG CYS L 31 71.469 120.827 84.243 1.00 54.18 S ATOM 36563 SG CYS L 34 69.604 124.444 84.886 1.00 56.73 S ATOM 36667 SG CYS L 48 71.105 123.746 81.554 1.00 59.29 S ATOM 36690 SG CYS L 51 73.593 124.020 84.426 1.00 59.19 S ATOM 42103 SG CYS Q 10 66.776 73.870 58.373 1.00112.27 S ATOM 42256 SG CYS Q 29 63.593 75.667 60.381 1.00 98.85 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P DT T 40 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 40 " occ=0.00 residue: pdb="ZN ZN I 202 " occ=0.75 Time building chain proxies: 21.43, per 1000 atoms: 0.40 Number of scatterers: 53719 At special positions: 0 Unit cell: (163.68, 213.84, 174.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 241 16.00 P 94 15.00 O 10279 8.00 N 9268 7.00 C 33829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.09 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 62 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 236 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 117 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb=" ZN Q 601 " pdb="ZN ZN Q 601 " - pdb=" SG CYS Q 10 " pdb="ZN ZN Q 601 " - pdb=" SG CYS Q 29 " Number of angles added : 24 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12252 Finding SS restraints... Secondary structure from input PDB file: 241 helices and 63 sheets defined 38.4% alpha, 14.6% beta 8 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 14.62 Creating SS restraints... Processing helix chain 'M' and resid 126 through 131 removed outlier: 4.086A pdb=" N ALA M 131 " --> pdb=" O ALA M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 145 Processing helix chain 'M' and resid 154 through 157 removed outlier: 3.597A pdb=" N SER M 157 " --> pdb=" O LEU M 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 154 through 157' Processing helix chain 'M' and resid 158 through 169 removed outlier: 4.241A pdb=" N VAL M 162 " --> pdb=" O ALA M 158 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER M 164 " --> pdb=" O ASP M 160 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL M 165 " --> pdb=" O ILE M 161 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG M 166 " --> pdb=" O VAL M 162 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N THR M 167 " --> pdb=" O ASP M 163 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA M 168 " --> pdb=" O SER M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.691A pdb=" N GLU M 180 " --> pdb=" O ALA M 176 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR M 182 " --> pdb=" O LEU M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 197 through 202 removed outlier: 3.593A pdb=" N TYR M 202 " --> pdb=" O VAL M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 208 removed outlier: 4.377A pdb=" N ILE M 207 " --> pdb=" O PRO M 203 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE M 208 " --> pdb=" O ILE M 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 203 through 208' Processing helix chain 'M' and resid 211 through 216 removed outlier: 3.665A pdb=" N GLN M 214 " --> pdb=" O LYS M 211 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE M 215 " --> pdb=" O GLU M 212 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE M 216 " --> pdb=" O LEU M 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 216' Processing helix chain 'M' and resid 218 through 223 removed outlier: 4.031A pdb=" N LEU M 222 " --> pdb=" O VAL M 218 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS M 223 " --> pdb=" O SER M 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 218 through 223' Processing helix chain 'M' and resid 230 through 234 removed outlier: 3.784A pdb=" N LEU M 233 " --> pdb=" O LYS M 230 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE M 234 " --> pdb=" O LEU M 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 230 through 234' Processing helix chain 'M' and resid 252 through 257 removed outlier: 4.254A pdb=" N THR M 257 " --> pdb=" O SER M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 273 removed outlier: 3.555A pdb=" N LEU M 262 " --> pdb=" O LYS M 258 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU M 267 " --> pdb=" O TYR M 263 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY M 270 " --> pdb=" O SER M 266 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL M 271 " --> pdb=" O LEU M 267 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR M 272 " --> pdb=" O LEU M 268 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU M 273 " --> pdb=" O LEU M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 297 removed outlier: 4.105A pdb=" N ASP M 296 " --> pdb=" O GLU M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 323 No H-bonds generated for 'chain 'M' and resid 321 through 323' Processing helix chain 'M' and resid 324 through 340 removed outlier: 3.704A pdb=" N ILE M 328 " --> pdb=" O ASN M 324 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU M 329 " --> pdb=" O GLU M 325 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR M 331 " --> pdb=" O LYS M 327 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE M 335 " --> pdb=" O TYR M 331 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP M 340 " --> pdb=" O ILE M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 353 Processing helix chain 'M' and resid 356 through 365 removed outlier: 3.553A pdb=" N SER M 362 " --> pdb=" O SER M 358 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU M 363 " --> pdb=" O LYS M 359 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE M 364 " --> pdb=" O VAL M 360 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG M 365 " --> pdb=" O VAL M 361 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 383 removed outlier: 3.757A pdb=" N PHE M 382 " --> pdb=" O ALA M 379 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY M 383 " --> pdb=" O GLU M 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 379 through 383' Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.738A pdb=" N ILE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 20 through 25' Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.515A pdb=" N GLY A 42 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 43 " --> pdb=" O ASN A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 43' Processing helix chain 'A' and resid 91 through 99 removed outlier: 4.796A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.591A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.512A pdb=" N TYR A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.588A pdb=" N LEU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 227 removed outlier: 3.524A pdb=" N LEU A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 removed outlier: 3.636A pdb=" N ILE A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.822A pdb=" N LYS A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.873A pdb=" N LEU A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.025A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 removed outlier: 3.565A pdb=" N GLN A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.620A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.774A pdb=" N VAL A 503 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 3.822A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.695A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 652 through 656 removed outlier: 3.537A pdb=" N SER A 655 " --> pdb=" O ASN A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 681 removed outlier: 3.606A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.861A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 740 removed outlier: 3.863A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.569A pdb=" N TYR A 759 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.501A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 824 removed outlier: 3.545A pdb=" N LEU A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.743A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 849 removed outlier: 3.578A pdb=" N TRP A 842 " --> pdb=" O GLU A 838 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 844 " --> pdb=" O ASN A 840 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 885 removed outlier: 4.096A pdb=" N ARG A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 removed outlier: 3.868A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 removed outlier: 3.616A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 removed outlier: 3.652A pdb=" N VAL A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1011 removed outlier: 3.523A pdb=" N HIS A 998 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1027 removed outlier: 3.746A pdb=" N SER A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1091 through 1107 removed outlier: 4.104A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A1107 " --> pdb=" O LYS A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1116 removed outlier: 3.508A pdb=" N GLN A1116 " --> pdb=" O HIS A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1163 through 1177 Processing helix chain 'A' and resid 1184 through 1192 Processing helix chain 'A' and resid 1217 through 1226 removed outlier: 3.894A pdb=" N ARG A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1257 removed outlier: 3.611A pdb=" N LYS A1256 " --> pdb=" O ASP A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 4.768A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1318 removed outlier: 3.528A pdb=" N LEU A1313 " --> pdb=" O SER A1309 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A1315 " --> pdb=" O GLU A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1335 removed outlier: 3.901A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1454 Processing helix chain 'A' and resid 1484 through 1494 removed outlier: 3.738A pdb=" N GLU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 3.898A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 3.633A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1533 No H-bonds generated for 'chain 'A' and resid 1531 through 1533' Processing helix chain 'A' and resid 1545 through 1553 removed outlier: 3.598A pdb=" N LYS A1551 " --> pdb=" O ALA A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.592A pdb=" N ASN A1567 " --> pdb=" O VAL A1563 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.627A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 3.724A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1627 Processing helix chain 'A' and resid 1636 through 1644 removed outlier: 3.574A pdb=" N ILE A1641 " --> pdb=" O PRO A1637 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL A1642 " --> pdb=" O SER A1638 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A1643 " --> pdb=" O ALA A1639 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 27 removed outlier: 3.532A pdb=" N ILE B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 removed outlier: 4.033A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.808A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 58 through 63 removed outlier: 4.027A pdb=" N ASN B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.602A pdb=" N ILE B 68 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.763A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.536A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.665A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.568A pdb=" N ARG B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 317 Processing helix chain 'B' and resid 322 through 334 removed outlier: 4.400A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.666A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 377 removed outlier: 3.576A pdb=" N LEU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.594A pdb=" N ALA B 386 " --> pdb=" O TYR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 434 removed outlier: 3.640A pdb=" N LEU B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 430 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.667A pdb=" N ARG B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.565A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.807A pdb=" N PHE B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 573 through 577 removed outlier: 4.252A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 577' Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.665A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.516A pdb=" N MET B 672 " --> pdb=" O GLN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.808A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 703 removed outlier: 3.557A pdb=" N LEU B 703 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 removed outlier: 3.673A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 removed outlier: 3.805A pdb=" N HIS B 735 " --> pdb=" O ALA B 732 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 736 " --> pdb=" O LEU B 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 732 through 736' Processing helix chain 'B' and resid 754 through 758 removed outlier: 3.567A pdb=" N ASP B 758 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 812 through 815 removed outlier: 3.951A pdb=" N ARG B 815 " --> pdb=" O ALA B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 812 through 815' Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 960 through 976 Processing helix chain 'B' and resid 991 through 1004 removed outlier: 3.658A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1043 Processing helix chain 'B' and resid 1072 through 1082 removed outlier: 3.512A pdb=" N ARG B1076 " --> pdb=" O GLY B1072 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B1077 " --> pdb=" O GLU B1073 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B1082 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1180 through 1191 removed outlier: 3.563A pdb=" N SER B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.833A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 73 Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.380A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.659A pdb=" N PHE C 219 " --> pdb=" O HIS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.907A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.701A pdb=" N ARG C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR C 282 " --> pdb=" O VAL C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 311 through 330 removed outlier: 3.566A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER C 317 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 removed outlier: 4.149A pdb=" N THR D 8 " --> pdb=" O GLY D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 47 removed outlier: 3.571A pdb=" N SER D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.941A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS D 97 " --> pdb=" O GLN D 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 26 removed outlier: 3.767A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.600A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.983A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.704A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 142' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.924A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 56 through 72 removed outlier: 3.748A pdb=" N HIS F 61 " --> pdb=" O ASP F 57 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 102 removed outlier: 3.827A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 13 through 21 removed outlier: 4.639A pdb=" N LYS G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 66 through 70 removed outlier: 3.655A pdb=" N VAL G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.788A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 133 removed outlier: 4.297A pdb=" N ASN H 131 " --> pdb=" O ASN H 128 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU H 132 " --> pdb=" O TYR H 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 64 removed outlier: 3.533A pdb=" N LYS I 63 " --> pdb=" O SER I 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.569A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 51 removed outlier: 3.623A pdb=" N ARG J 48 " --> pdb=" O TYR J 44 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 51 through 54 removed outlier: 3.536A pdb=" N THR K 54 " --> pdb=" O THR K 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 51 through 54' Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.649A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG K 77 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 138 removed outlier: 3.504A pdb=" N LEU K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL K 130 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 removed outlier: 3.710A pdb=" N ARG N 154 " --> pdb=" O TYR N 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 54 Processing helix chain 'O' and resid 55 through 61 Processing helix chain 'O' and resid 70 through 78 removed outlier: 3.787A pdb=" N ILE O 74 " --> pdb=" O GLN O 70 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN O 77 " --> pdb=" O ILE O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 103 removed outlier: 4.002A pdb=" N ASN O 94 " --> pdb=" O ASP O 90 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE O 95 " --> pdb=" O LYS O 91 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE O 99 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN O 103 " --> pdb=" O ILE O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 121 removed outlier: 3.538A pdb=" N GLN O 117 " --> pdb=" O THR O 113 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER O 118 " --> pdb=" O PHE O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 128 removed outlier: 3.852A pdb=" N LEU O 128 " --> pdb=" O TRP O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 147 removed outlier: 4.518A pdb=" N LYS O 135 " --> pdb=" O HIS O 131 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR O 138 " --> pdb=" O SER O 134 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER O 145 " --> pdb=" O LYS O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 161 removed outlier: 3.983A pdb=" N MET O 156 " --> pdb=" O GLN O 152 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 183 removed outlier: 3.761A pdb=" N HIS O 173 " --> pdb=" O THR O 169 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP O 174 " --> pdb=" O VAL O 170 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TYR O 178 " --> pdb=" O ASP O 174 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG O 181 " --> pdb=" O LYS O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 197 removed outlier: 3.568A pdb=" N ILE O 190 " --> pdb=" O SER O 186 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP O 191 " --> pdb=" O MET O 187 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR O 192 " --> pdb=" O GLY O 188 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR O 193 " --> pdb=" O PHE O 189 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA O 195 " --> pdb=" O ASP O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 221 removed outlier: 3.575A pdb=" N ASN O 210 " --> pdb=" O ARG O 206 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY O 220 " --> pdb=" O LEU O 216 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR O 221 " --> pdb=" O LYS O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 242 removed outlier: 3.840A pdb=" N LEU O 232 " --> pdb=" O GLN O 228 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS O 236 " --> pdb=" O LEU O 232 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER O 239 " --> pdb=" O GLU O 235 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 325 through 346 removed outlier: 4.715A pdb=" N LYS O 331 " --> pdb=" O GLU O 327 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU O 336 " --> pdb=" O LEU O 332 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU O 338 " --> pdb=" O SER O 334 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 369 removed outlier: 3.780A pdb=" N PHE O 361 " --> pdb=" O GLY O 357 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU O 364 " --> pdb=" O VAL O 360 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU O 367 " --> pdb=" O THR O 363 " (cutoff:3.500A) Processing helix chain 'O' and resid 381 through 389 removed outlier: 4.304A pdb=" N MET O 385 " --> pdb=" O ILE O 381 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 397 removed outlier: 3.793A pdb=" N MET O 396 " --> pdb=" O GLN O 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 399 through 409 removed outlier: 3.694A pdb=" N ALA O 409 " --> pdb=" O ASP O 405 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 429 removed outlier: 3.795A pdb=" N LYS O 419 " --> pdb=" O GLU O 415 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER O 420 " --> pdb=" O LYS O 416 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU O 421 " --> pdb=" O LYS O 417 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER O 426 " --> pdb=" O GLN O 422 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA O 429 " --> pdb=" O GLY O 425 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 453 removed outlier: 3.708A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU O 450 " --> pdb=" O LEU O 446 " (cutoff:3.500A) Processing helix chain 'O' and resid 458 through 462 removed outlier: 4.030A pdb=" N VAL O 461 " --> pdb=" O GLU O 458 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP O 462 " --> pdb=" O GLU O 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 458 through 462' Processing helix chain 'O' and resid 470 through 485 removed outlier: 3.597A pdb=" N ALA O 476 " --> pdb=" O HIS O 472 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE O 483 " --> pdb=" O ALA O 479 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE O 484 " --> pdb=" O LEU O 480 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS O 485 " --> pdb=" O CYS O 481 " (cutoff:3.500A) Processing helix chain 'O' and resid 504 through 511 Processing helix chain 'O' and resid 515 through 520 removed outlier: 3.903A pdb=" N PHE O 519 " --> pdb=" O ASN O 515 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N CYS O 520 " --> pdb=" O PRO O 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 515 through 520' Processing helix chain 'O' and resid 521 through 534 removed outlier: 3.556A pdb=" N MET O 527 " --> pdb=" O ASN O 523 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE O 528 " --> pdb=" O VAL O 524 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA O 529 " --> pdb=" O MET O 525 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG O 530 " --> pdb=" O LEU O 526 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 546 removed outlier: 3.525A pdb=" N GLU O 545 " --> pdb=" O PHE O 541 " (cutoff:3.500A) Processing helix chain 'O' and resid 582 through 587 Processing helix chain 'O' and resid 599 through 607 removed outlier: 3.874A pdb=" N ILE O 604 " --> pdb=" O LYS O 600 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU O 605 " --> pdb=" O ASN O 601 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 82 Processing helix chain 'Q' and resid 85 through 90 removed outlier: 3.818A pdb=" N LYS Q 90 " --> pdb=" O ARG Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 123 removed outlier: 3.665A pdb=" N LEU Q 102 " --> pdb=" O HIS Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 147 removed outlier: 4.228A pdb=" N HIS Q 131 " --> pdb=" O LYS Q 127 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE Q 135 " --> pdb=" O HIS Q 131 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE Q 136 " --> pdb=" O VAL Q 132 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN Q 147 " --> pdb=" O THR Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 171 removed outlier: 3.691A pdb=" N LEU Q 165 " --> pdb=" O THR Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 187 removed outlier: 3.607A pdb=" N THR Q 187 " --> pdb=" O LYS Q 183 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 199 removed outlier: 3.994A pdb=" N ILE Q 198 " --> pdb=" O GLN Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 202 through 207 removed outlier: 4.416A pdb=" N GLN Q 206 " --> pdb=" O SER Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 215 Processing helix chain 'Q' and resid 224 through 237 Processing helix chain 'Q' and resid 248 through 260 removed outlier: 3.514A pdb=" N LEU Q 253 " --> pdb=" O CYS Q 249 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU Q 254 " --> pdb=" O GLN Q 250 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS Q 255 " --> pdb=" O GLY Q 251 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS Q 260 " --> pdb=" O LEU Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 277 removed outlier: 4.083A pdb=" N PHE Q 268 " --> pdb=" O PRO Q 264 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS Q 271 " --> pdb=" O TYR Q 267 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN Q 272 " --> pdb=" O PHE Q 268 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL Q 273 " --> pdb=" O TYR Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 320 removed outlier: 3.574A pdb=" N VAL Q 306 " --> pdb=" O ALA Q 302 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU Q 307 " --> pdb=" O GLU Q 303 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER Q 308 " --> pdb=" O LEU Q 304 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU Q 318 " --> pdb=" O ILE Q 314 " (cutoff:3.500A) Processing helix chain 'Q' and resid 327 through 332 removed outlier: 3.701A pdb=" N ILE Q 331 " --> pdb=" O PRO Q 327 " (cutoff:3.500A) Processing helix chain 'Q' and resid 334 through 339 Processing helix chain 'Q' and resid 344 through 357 removed outlier: 3.535A pdb=" N VAL Q 353 " --> pdb=" O GLY Q 349 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR Q 357 " --> pdb=" O VAL Q 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 364 through 369 removed outlier: 3.946A pdb=" N PHE Q 367 " --> pdb=" O SER Q 364 " (cutoff:3.500A) Processing helix chain 'Q' and resid 370 through 381 removed outlier: 3.559A pdb=" N THR Q 374 " --> pdb=" O SER Q 370 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE Q 377 " --> pdb=" O GLU Q 373 " (cutoff:3.500A) Processing helix chain 'Q' and resid 382 through 384 No H-bonds generated for 'chain 'Q' and resid 382 through 384' Processing helix chain 'Q' and resid 406 through 417 removed outlier: 4.314A pdb=" N ARG Q 410 " --> pdb=" O GLN Q 406 " (cutoff:3.500A) Processing helix chain 'Q' and resid 437 through 446 removed outlier: 4.270A pdb=" N LEU Q 442 " --> pdb=" O PHE Q 438 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN Q 443 " --> pdb=" O ILE Q 439 " (cutoff:3.500A) Processing helix chain 'Q' and resid 471 through 492 removed outlier: 3.838A pdb=" N ALA Q 475 " --> pdb=" O ALA Q 471 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY Q 477 " --> pdb=" O LYS Q 473 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG Q 478 " --> pdb=" O GLU Q 474 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR Q 481 " --> pdb=" O GLY Q 477 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS Q 482 " --> pdb=" O ARG Q 478 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL Q 489 " --> pdb=" O SER Q 485 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP Q 490 " --> pdb=" O GLN Q 486 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE Q 491 " --> pdb=" O LEU Q 487 " (cutoff:3.500A) Processing helix chain 'Q' and resid 495 through 510 removed outlier: 3.675A pdb=" N ASP Q 500 " --> pdb=" O GLU Q 496 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N CYS Q 501 " --> pdb=" O GLN Q 497 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE Q 505 " --> pdb=" O CYS Q 501 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA Q 508 " --> pdb=" O ARG Q 504 " (cutoff:3.500A) Processing helix chain 'Q' and resid 511 through 513 No H-bonds generated for 'chain 'Q' and resid 511 through 513' Processing helix chain 'S' and resid 189 through 195 Processing helix chain 'S' and resid 571 through 576 Processing helix chain 'S' and resid 589 through 607 removed outlier: 4.499A pdb=" N ARG S 601 " --> pdb=" O LYS S 597 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER S 605 " --> pdb=" O ARG S 601 " (cutoff:3.500A) Processing helix chain 'S' and resid 607 through 612 removed outlier: 3.604A pdb=" N GLU S 612 " --> pdb=" O GLN S 608 " (cutoff:3.500A) Processing helix chain 'S' and resid 616 through 644 removed outlier: 4.369A pdb=" N SER S 631 " --> pdb=" O GLY S 627 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE S 632 " --> pdb=" O TYR S 628 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA S 633 " --> pdb=" O ARG S 629 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU S 639 " --> pdb=" O ASN S 635 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER S 640 " --> pdb=" O GLU S 636 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN S 642 " --> pdb=" O LEU S 638 " (cutoff:3.500A) Processing helix chain 'S' and resid 671 through 685 removed outlier: 3.581A pdb=" N SER S 677 " --> pdb=" O PRO S 673 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU S 678 " --> pdb=" O GLU S 674 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU S 679 " --> pdb=" O PHE S 675 " (cutoff:3.500A) Processing helix chain 'S' and resid 699 through 703 removed outlier: 3.847A pdb=" N LEU S 702 " --> pdb=" O LEU S 699 " (cutoff:3.500A) Processing helix chain 'S' and resid 713 through 720 Processing helix chain 'S' and resid 732 through 742 removed outlier: 3.820A pdb=" N LYS S 738 " --> pdb=" O LYS S 734 " (cutoff:3.500A) Processing helix chain 'S' and resid 752 through 765 removed outlier: 3.931A pdb=" N ILE S 756 " --> pdb=" O LEU S 752 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN S 757 " --> pdb=" O PHE S 753 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN S 758 " --> pdb=" O GLU S 754 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 38 removed outlier: 3.604A pdb=" N TYR R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG R 33 " --> pdb=" O ARG R 29 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER R 38 " --> pdb=" O ILE R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 129 Processing helix chain 'R' and resid 158 through 166 removed outlier: 4.095A pdb=" N LYS R 164 " --> pdb=" O HIS R 160 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU R 166 " --> pdb=" O PHE R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 174 Processing helix chain 'R' and resid 181 through 192 Processing helix chain 'R' and resid 209 through 226 removed outlier: 3.643A pdb=" N THR R 215 " --> pdb=" O ARG R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 240 removed outlier: 3.973A pdb=" N LYS R 234 " --> pdb=" O SER R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 253 removed outlier: 3.710A pdb=" N LEU R 250 " --> pdb=" O GLN R 246 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP R 251 " --> pdb=" O ILE R 247 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 246 through 253' Processing helix chain 'R' and resid 267 through 278 removed outlier: 3.501A pdb=" N LEU R 271 " --> pdb=" O GLY R 267 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE R 277 " --> pdb=" O TRP R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 299 removed outlier: 4.040A pdb=" N GLN R 298 " --> pdb=" O VAL R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 323 removed outlier: 3.760A pdb=" N CYS R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 355 Processing helix chain 'R' and resid 362 through 380 removed outlier: 3.947A pdb=" N HIS R 372 " --> pdb=" O TYR R 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 421 removed outlier: 4.367A pdb=" N ASN R 402 " --> pdb=" O ASP R 398 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL R 404 " --> pdb=" O LYS R 400 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS R 406 " --> pdb=" O ASN R 402 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS R 407 " --> pdb=" O GLN R 403 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS R 416 " --> pdb=" O ARG R 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 441 removed outlier: 3.945A pdb=" N SER R 437 " --> pdb=" O ASN R 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 70 through 71 removed outlier: 7.270A pdb=" N LEU M 90 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL M 15 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS N 135 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE N 137 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL N 139 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLU N 141 " --> pdb=" O PRO N 59 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP N 92 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 101 through 102 removed outlier: 5.696A pdb=" N PHE M 51 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU M 56 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR M 37 " --> pdb=" O GLU M 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 101 through 102 removed outlier: 6.935A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 304 through 305 removed outlier: 4.877A pdb=" N VAL M 304 " --> pdb=" O PHE M 319 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE M 319 " --> pdb=" O VAL M 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'M' and resid 344 through 345 removed outlier: 3.557A pdb=" N LYS M 372 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR M 396 " --> pdb=" O ILE M 370 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE M 370 " --> pdb=" O THR M 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 3.699A pdb=" N SER A 13 " --> pdb=" O ASN B1199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 80 through 86 removed outlier: 9.989A pdb=" N VAL A 83 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL A 359 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS A 85 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA9, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AB1, first strand: chain 'A' and resid 475 through 476 removed outlier: 3.892A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 3.598A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.256A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB5, first strand: chain 'A' and resid 748 through 752 removed outlier: 6.533A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.625A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N MET B 787 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS B 930 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 789 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.625A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB9, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 6.686A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1504 through 1508 removed outlier: 3.763A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.716A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1460 through 1462 removed outlier: 3.827A pdb=" N CYS A1470 " --> pdb=" O MET A1294 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A1291 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL A1272 " --> pdb=" O VAL A1291 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N HIS A1293 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL A1270 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG A1295 " --> pdb=" O ASP A1268 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.866A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.461A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 29 through 30 removed outlier: 7.120A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 97 through 104 removed outlier: 6.028A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 108 through 109 removed outlier: 3.960A pdb=" N ARG B 119 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AC9, first strand: chain 'B' and resid 400 through 403 Processing sheet with id=AD1, first strand: chain 'B' and resid 229 through 239 removed outlier: 5.338A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AD3, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AD4, first strand: chain 'B' and resid 571 through 572 removed outlier: 6.793A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.523A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.523A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD8, first strand: chain 'B' and resid 857 through 863 removed outlier: 3.873A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 863 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1052 through 1053 removed outlier: 6.652A pdb=" N VAL B1052 " --> pdb=" O ASN Q 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AE2, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AE3, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AE4, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.684A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.684A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.366A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE8, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.750A pdb=" N VAL C 162 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AF1, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.360A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.547A pdb=" N VAL E 88 " --> pdb=" O ASN E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.604A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 132 through 135 removed outlier: 5.297A pdb=" N ASP G 246 " --> pdb=" O ARG G 234 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL G 236 " --> pdb=" O SER G 244 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER G 244 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE G 139 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU G 148 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE G 137 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.714A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 114 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR H 56 " --> pdb=" O ARG H 145 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AF7, first strand: chain 'I' and resid 94 through 99 removed outlier: 3.628A pdb=" N THR I 109 " --> pdb=" O LEU I 99 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 49 through 50 removed outlier: 4.568A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 5 through 6 Processing sheet with id=AG1, first strand: chain 'S' and resid 63 through 66 removed outlier: 7.134A pdb=" N VAL S 547 " --> pdb=" O LEU S 65 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR S 548 " --> pdb=" O VAL S 539 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL S 539 " --> pdb=" O TYR S 548 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ARG S 542 " --> pdb=" O PRO S 505 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 173 through 174 removed outlier: 3.521A pdb=" N TRP S 174 " --> pdb=" O GLU R 196 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 182 through 183 Processing sheet with id=AG4, first strand: chain 'S' and resid 186 through 187 Processing sheet with id=AG5, first strand: chain 'S' and resid 242 through 246 removed outlier: 6.644A pdb=" N ILE S 264 " --> pdb=" O LYS S 243 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE S 245 " --> pdb=" O GLY S 262 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY S 262 " --> pdb=" O ILE S 245 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN S 270 " --> pdb=" O ILE S 263 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG S 273 " --> pdb=" O SER S 287 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 300 through 303 removed outlier: 6.730A pdb=" N ASP S 319 " --> pdb=" O GLN S 301 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE S 326 " --> pdb=" O LEU S 347 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU S 347 " --> pdb=" O ILE S 326 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'S' and resid 362 through 365 removed outlier: 3.732A pdb=" N ARG S 362 " --> pdb=" O PHE S 375 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET S 380 " --> pdb=" O VAL S 393 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TRP S 389 " --> pdb=" O ASP S 384 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 402 through 404 removed outlier: 3.911A pdb=" N ILE S 421 " --> pdb=" O SER S 418 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 449 through 457 removed outlier: 3.566A pdb=" N HIS S 479 " --> pdb=" O ALA S 466 " (cutoff:3.500A) 1732 hydrogen bonds defined for protein. 4824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 25.27 Time building geometry restraints manager: 11.10 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: 9173 1.32 - 1.44: 14485 1.44 - 1.57: 30758 1.57 - 1.69: 185 1.69 - 1.81: 379 Bond restraints: 54980 Sorted by residual: bond pdb=" O3' DA T 49 " pdb=" P DC T 50 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.29e+01 bond pdb=" C GLU Q 292 " pdb=" N ARG Q 293 " ideal model delta sigma weight residual 1.331 1.391 -0.059 1.78e-02 3.16e+03 1.12e+01 bond pdb=" N ILE Q 281 " pdb=" CA ILE Q 281 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.11e+01 bond pdb=" C PRO S 291 " pdb=" O PRO S 291 " ideal model delta sigma weight residual 1.233 1.196 0.037 1.13e-02 7.83e+03 1.08e+01 bond pdb=" N HIS Q 98 " pdb=" CA HIS Q 98 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.29e-02 6.01e+03 9.44e+00 ... (remaining 54975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 71597 2.31 - 4.62: 2632 4.62 - 6.93: 339 6.93 - 9.24: 101 9.24 - 11.54: 17 Bond angle restraints: 74686 Sorted by residual: angle pdb=" O3' DA T 49 " pdb=" P DC T 50 " pdb=" O5' DC T 50 " ideal model delta sigma weight residual 104.00 115.54 -11.54 1.50e+00 4.44e-01 5.92e+01 angle pdb=" N VAL J 14 " pdb=" CA VAL J 14 " pdb=" C VAL J 14 " ideal model delta sigma weight residual 113.53 107.64 5.89 9.80e-01 1.04e+00 3.61e+01 angle pdb=" N PRO R 295 " pdb=" CA PRO R 295 " pdb=" C PRO R 295 " ideal model delta sigma weight residual 110.70 117.74 -7.04 1.22e+00 6.72e-01 3.33e+01 angle pdb=" O GLU Q 292 " pdb=" C GLU Q 292 " pdb=" N ARG Q 293 " ideal model delta sigma weight residual 122.72 116.25 6.47 1.15e+00 7.56e-01 3.17e+01 angle pdb=" C GLU Q 292 " pdb=" N ARG Q 293 " pdb=" CA ARG Q 293 " ideal model delta sigma weight residual 122.31 132.22 -9.91 1.81e+00 3.05e-01 3.00e+01 ... (remaining 74681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 32612 35.75 - 71.51: 545 71.51 - 107.26: 38 107.26 - 143.01: 3 143.01 - 178.76: 9 Dihedral angle restraints: 33207 sinusoidal: 14319 harmonic: 18888 Sorted by residual: dihedral pdb=" CA ASP Q 431 " pdb=" C ASP Q 431 " pdb=" N SER Q 432 " pdb=" CA SER Q 432 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA LEU A 669 " pdb=" C LEU A 669 " pdb=" N ILE A 670 " pdb=" CA ILE A 670 " ideal model delta harmonic sigma weight residual -180.00 -151.76 -28.24 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ILE B 199 " pdb=" C ILE B 199 " pdb=" N GLU B 200 " pdb=" CA GLU B 200 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 33204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 7711 0.104 - 0.209: 592 0.209 - 0.313: 36 0.313 - 0.418: 12 0.418 - 0.522: 1 Chirality restraints: 8352 Sorted by residual: chirality pdb=" CB ILE R 175 " pdb=" CA ILE R 175 " pdb=" CG1 ILE R 175 " pdb=" CG2 ILE R 175 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" CB ILE R 168 " pdb=" CA ILE R 168 " pdb=" CG1 ILE R 168 " pdb=" CG2 ILE R 168 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C3' DC T 12 " pdb=" C4' DC T 12 " pdb=" O3' DC T 12 " pdb=" C2' DC T 12 " both_signs ideal model delta sigma weight residual False -2.66 -2.27 -0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 8349 not shown) Planarity restraints: 9248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 628 " 0.026 2.00e-02 2.50e+03 2.41e-02 1.02e+01 pdb=" CG PHE A 628 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 628 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 628 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 628 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 628 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 628 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 127 " 0.048 5.00e-02 4.00e+02 7.37e-02 8.70e+00 pdb=" N PRO E 128 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO E 128 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 128 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 368 " -0.019 2.00e-02 2.50e+03 2.04e-02 8.31e+00 pdb=" CG TYR R 368 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR R 368 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR R 368 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR R 368 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 368 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR R 368 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR R 368 " 0.003 2.00e-02 2.50e+03 ... (remaining 9245 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 369 2.56 - 3.14: 40203 3.14 - 3.73: 80630 3.73 - 4.31: 116970 4.31 - 4.90: 190520 Nonbonded interactions: 428692 Sorted by model distance: nonbonded pdb=" OD1 ASN S 31 " pdb=" N TYR S 32 " model vdw 1.975 3.120 nonbonded pdb=" ND2 ASN Q 14 " pdb="ZN ZN Q 601 " model vdw 2.089 2.310 nonbonded pdb=" N GLU R 204 " pdb=" OE1 GLU R 204 " model vdw 2.161 3.120 nonbonded pdb=" O GLY R 194 " pdb=" O LEU R 195 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR O 423 " pdb=" OH TYR O 594 " model vdw 2.207 3.040 ... (remaining 428687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.470 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 112.340 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3119 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 : 0.009 0.120 54980 Z= 0.587 Angle : 1.024 11.545 74686 Z= 0.565 Chirality : 0.062 0.522 8352 Planarity : 0.007 0.074 9248 Dihedral : 13.234 178.764 20955 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.45 % Favored : 92.47 % Rotamer: Outliers : 0.73 % Allowed : 3.28 % Favored : 95.99 % Cbeta Deviations : 0.02 % 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: -4.84 (0.08), residues: 6352 helix: -4.18 (0.05), residues: 2214 sheet: -2.54 (0.17), residues: 756 loop : -2.67 (0.09), residues: 3382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP Q 20 HIS 0.024 0.003 HIS B 532 PHE 0.054 0.003 PHE A 628 TYR 0.049 0.003 TYR R 368 ARG 0.021 0.001 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1281 time to evaluate : 4.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 28 LYS cc_start: 0.2158 (mtpp) cc_final: 0.1814 (tttp) REVERT: M 100 VAL cc_start: 0.2328 (t) cc_final: 0.1880 (t) REVERT: M 111 PRO cc_start: 0.6186 (Cg_endo) cc_final: 0.5930 (Cg_exo) REVERT: M 337 MET cc_start: 0.1322 (ttm) cc_final: 0.1047 (pp-130) REVERT: M 397 MET cc_start: 0.2416 (mtt) cc_final: 0.1946 (mtm) REVERT: A 15 ASP cc_start: 0.5425 (m-30) cc_final: 0.4183 (m-30) REVERT: A 325 ASP cc_start: 0.4674 (t0) cc_final: 0.4266 (p0) REVERT: A 697 TYR cc_start: 0.3179 (t80) cc_final: 0.2663 (t80) REVERT: A 1541 ILE cc_start: 0.4150 (pt) cc_final: 0.3308 (pt) REVERT: A 1546 VAL cc_start: 0.4098 (t) cc_final: 0.2257 (m) REVERT: B 152 LEU cc_start: 0.2764 (mp) cc_final: 0.2507 (mt) REVERT: B 345 SER cc_start: 0.5151 (p) cc_final: 0.4859 (t) REVERT: C 301 ASN cc_start: 0.3751 (t0) cc_final: 0.3400 (m-40) REVERT: D 1 MET cc_start: 0.1306 (ptm) cc_final: 0.0575 (ttm) REVERT: E 98 ILE cc_start: 0.7687 (mt) cc_final: 0.7347 (mp) REVERT: G 16 PHE cc_start: 0.6018 (t80) cc_final: 0.5142 (m-80) REVERT: H 78 SER cc_start: 0.6062 (p) cc_final: 0.5717 (m) REVERT: H 102 TYR cc_start: 0.3725 (p90) cc_final: 0.2822 (p90) REVERT: K 81 MET cc_start: 0.2035 (mmm) cc_final: 0.0504 (ppp) REVERT: O 71 ILE cc_start: 0.3695 (mm) cc_final: 0.3210 (pt) REVERT: O 100 LEU cc_start: 0.5938 (mt) cc_final: 0.5340 (mt) REVERT: O 124 LYS cc_start: 0.6629 (mmtp) cc_final: 0.5293 (mtpt) REVERT: O 163 ILE cc_start: 0.5722 (OUTLIER) cc_final: 0.5340 (pt) REVERT: O 221 TYR cc_start: 0.3379 (m-80) cc_final: 0.3058 (m-80) REVERT: O 449 TRP cc_start: 0.5946 (t60) cc_final: 0.5363 (t60) REVERT: O 490 ILE cc_start: 0.3897 (mp) cc_final: 0.3679 (tp) REVERT: O 582 ARG cc_start: 0.4000 (tpt90) cc_final: 0.3548 (mtp-110) REVERT: Q 85 GLN cc_start: 0.1811 (pp30) cc_final: 0.1235 (tm-30) REVERT: Q 240 LYS cc_start: 0.6277 (mmmt) cc_final: 0.5334 (mppt) REVERT: Q 351 ASN cc_start: 0.4610 (m-40) cc_final: 0.4352 (m110) REVERT: Q 421 ARG cc_start: 0.4243 (ttt180) cc_final: 0.3885 (tpm170) REVERT: Q 490 ASP cc_start: 0.2912 (m-30) cc_final: 0.1938 (t0) REVERT: S 16 LEU cc_start: 0.5766 (tm) cc_final: 0.4919 (pp) REVERT: S 32 TYR cc_start: 0.4878 (m-10) cc_final: 0.4618 (t80) REVERT: S 39 LYS cc_start: 0.3759 (mmtp) cc_final: 0.3338 (pttt) REVERT: S 369 PHE cc_start: 0.5253 (t80) cc_final: 0.4877 (t80) REVERT: S 600 GLU cc_start: 0.6737 (tp30) cc_final: 0.5774 (tm-30) REVERT: S 671 SER cc_start: 0.5585 (t) cc_final: 0.5282 (m) REVERT: S 680 ASP cc_start: 0.6023 (m-30) cc_final: 0.5624 (p0) REVERT: S 692 THR cc_start: 0.2368 (p) cc_final: 0.1166 (p) REVERT: S 707 ASP cc_start: 0.3209 (t0) cc_final: 0.2631 (m-30) REVERT: S 736 ILE cc_start: 0.5363 (mt) cc_final: 0.5149 (pt) REVERT: S 749 LYS cc_start: 0.5486 (tttm) cc_final: 0.4997 (ptpt) REVERT: R 23 TYR cc_start: 0.6006 (t80) cc_final: 0.5641 (t80) REVERT: R 122 ASP cc_start: 0.6176 (t0) cc_final: 0.5932 (t70) REVERT: R 157 MET cc_start: 0.3184 (OUTLIER) cc_final: 0.2031 (tpt) REVERT: R 173 MET cc_start: 0.4512 (tpt) cc_final: 0.3580 (pp-130) outliers start: 42 outliers final: 12 residues processed: 1313 average time/residue: 1.1730 time to fit residues: 1996.2931 Evaluate side-chains 661 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 647 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1304 GLU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain N residue 63 ASP Chi-restraints excluded: chain O residue 163 ILE Chi-restraints excluded: chain O residue 201 LYS Chi-restraints excluded: chain O residue 202 ASN Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain Q residue 206 GLN Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 377 ARG Chi-restraints excluded: chain R residue 157 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 546 optimal weight: 10.0000 chunk 490 optimal weight: 0.7980 chunk 272 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 330 optimal weight: 0.1980 chunk 261 optimal weight: 0.8980 chunk 507 optimal weight: 0.0670 chunk 196 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 377 optimal weight: 2.9990 chunk 587 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 54 HIS A 221 HIS A 344 ASN A 489 ASN A 571 HIS ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A1047 GLN A1199 GLN ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1527 GLN B 248 ASN B 423 ASN B 492 ASN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN B 673 ASN ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 ASN C 130 ASN D 88 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN G 64 GLN G 65 HIS G 67 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 134 ASN I 97 HIS L 53 HIS ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN ** O 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 GLN ** O 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 422 GLN O 438 GLN O 584 GLN Q 33 HIS ** Q 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 294 HIS S 388 ASN S 395 GLN S 705 HIS S 720 GLN R 221 HIS R 298 GLN R 402 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3934 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 54980 Z= 0.240 Angle : 0.754 12.899 74686 Z= 0.395 Chirality : 0.046 0.356 8352 Planarity : 0.006 0.072 9248 Dihedral : 14.037 179.225 8060 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.49 % Favored : 94.49 % Rotamer: Outliers : 4.09 % Allowed : 12.32 % Favored : 83.59 % 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: -3.49 (0.09), residues: 6352 helix: -2.55 (0.08), residues: 2278 sheet: -2.04 (0.18), residues: 747 loop : -2.18 (0.10), residues: 3327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Q 118 HIS 0.012 0.001 HIS A 571 PHE 0.038 0.002 PHE A 239 TYR 0.033 0.002 TYR S 548 ARG 0.016 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 856 time to evaluate : 4.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 89 GLN cc_start: 0.3471 (pm20) cc_final: 0.2683 (pp30) REVERT: M 111 PRO cc_start: 0.6292 (Cg_endo) cc_final: 0.6071 (Cg_exo) REVERT: M 337 MET cc_start: 0.1423 (ttm) cc_final: 0.1064 (tmm) REVERT: M 397 MET cc_start: 0.2492 (mtt) cc_final: 0.2175 (mtm) REVERT: A 238 MET cc_start: 0.1437 (OUTLIER) cc_final: 0.0955 (ptt) REVERT: A 325 ASP cc_start: 0.5107 (t0) cc_final: 0.4310 (p0) REVERT: A 555 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.6166 (ttmp) REVERT: A 611 GLU cc_start: 0.3987 (mt-10) cc_final: 0.3192 (mt-10) REVERT: A 1485 MET cc_start: 0.3147 (tpt) cc_final: 0.2601 (tpt) REVERT: A 1588 MET cc_start: 0.6347 (tpt) cc_final: 0.6069 (mmt) REVERT: B 373 MET cc_start: 0.6596 (tmm) cc_final: 0.5999 (tmt) REVERT: B 611 TRP cc_start: 0.5067 (m100) cc_final: 0.4095 (m100) REVERT: B 649 MET cc_start: 0.2877 (OUTLIER) cc_final: 0.2379 (mmm) REVERT: B 672 MET cc_start: 0.0528 (OUTLIER) cc_final: -0.0566 (ptp) REVERT: B 935 ASP cc_start: 0.5829 (p0) cc_final: 0.5236 (m-30) REVERT: B 1155 ASP cc_start: 0.5445 (OUTLIER) cc_final: 0.5161 (p0) REVERT: D 46 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.4999 (pp20) REVERT: D 94 ARG cc_start: 0.4212 (OUTLIER) cc_final: 0.4010 (tpm-80) REVERT: E 52 ARG cc_start: 0.5941 (tmm-80) cc_final: 0.4715 (tpp-160) REVERT: E 93 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7159 (tpp) REVERT: G 16 PHE cc_start: 0.6677 (t80) cc_final: 0.5234 (m-80) REVERT: G 136 TYR cc_start: 0.5598 (OUTLIER) cc_final: 0.5363 (m-80) REVERT: H 6 PHE cc_start: 0.6808 (t80) cc_final: 0.6425 (t80) REVERT: H 78 SER cc_start: 0.6882 (p) cc_final: 0.6540 (m) REVERT: H 102 TYR cc_start: 0.4507 (p90) cc_final: 0.3829 (p90) REVERT: K 74 ASN cc_start: 0.4591 (t0) cc_final: 0.4326 (t0) REVERT: K 81 MET cc_start: 0.2082 (mmm) cc_final: 0.0794 (ptt) REVERT: N 74 PHE cc_start: 0.3001 (t80) cc_final: 0.2365 (t80) REVERT: O 100 LEU cc_start: 0.5491 (mt) cc_final: 0.5256 (mt) REVERT: O 124 LYS cc_start: 0.6563 (mmtp) cc_final: 0.5126 (mtpm) REVERT: O 127 GLU cc_start: 0.5543 (mt-10) cc_final: 0.5102 (mp0) REVERT: O 131 HIS cc_start: 0.5916 (m-70) cc_final: 0.5673 (p-80) REVERT: O 200 ASN cc_start: 0.4200 (t0) cc_final: 0.3833 (t0) REVERT: O 205 ARG cc_start: 0.4932 (OUTLIER) cc_final: 0.4636 (mmm-85) REVERT: O 206 ARG cc_start: 0.6071 (mmm160) cc_final: 0.5503 (mmm160) REVERT: O 382 GLN cc_start: 0.6488 (OUTLIER) cc_final: 0.6150 (pm20) REVERT: O 445 TYR cc_start: 0.5734 (OUTLIER) cc_final: 0.5441 (m-80) REVERT: O 449 TRP cc_start: 0.5509 (t60) cc_final: 0.5255 (t60) REVERT: O 582 ARG cc_start: 0.3992 (tpt90) cc_final: 0.3661 (mtp180) REVERT: Q 74 GLN cc_start: 0.3140 (mt0) cc_final: 0.2832 (tp-100) REVERT: Q 79 GLN cc_start: 0.5721 (tm130) cc_final: 0.5432 (tm-30) REVERT: Q 154 LEU cc_start: 0.2102 (OUTLIER) cc_final: 0.1882 (tp) REVERT: Q 158 MET cc_start: 0.2490 (OUTLIER) cc_final: -0.0994 (pmm) REVERT: Q 200 PRO cc_start: 0.2570 (Cg_exo) cc_final: 0.2227 (Cg_endo) REVERT: Q 212 VAL cc_start: 0.5204 (OUTLIER) cc_final: 0.4979 (t) REVERT: Q 240 LYS cc_start: 0.6381 (mmmt) cc_final: 0.5642 (mppt) REVERT: Q 417 PHE cc_start: 0.6040 (m-80) cc_final: 0.4918 (m-80) REVERT: Q 421 ARG cc_start: 0.4351 (ttt180) cc_final: 0.3806 (tpm170) REVERT: S 16 LEU cc_start: 0.5670 (OUTLIER) cc_final: 0.4917 (pp) REVERT: S 45 PRO cc_start: 0.2024 (Cg_endo) cc_final: 0.1521 (Cg_exo) REVERT: S 238 LEU cc_start: 0.3431 (pt) cc_final: 0.3139 (mm) REVERT: S 386 MET cc_start: 0.3925 (OUTLIER) cc_final: 0.3068 (tmm) REVERT: S 388 ASN cc_start: 0.5147 (t0) cc_final: 0.4101 (p0) REVERT: S 412 ASN cc_start: 0.4601 (t0) cc_final: 0.3924 (p0) REVERT: S 478 MET cc_start: 0.4656 (OUTLIER) cc_final: 0.2954 (tpt) REVERT: S 671 SER cc_start: 0.5477 (t) cc_final: 0.5161 (m) REVERT: S 680 ASP cc_start: 0.5992 (m-30) cc_final: 0.5449 (t0) REVERT: S 692 THR cc_start: 0.2366 (p) cc_final: 0.1225 (p) REVERT: S 736 ILE cc_start: 0.4553 (mt) cc_final: 0.4199 (pt) REVERT: R 122 ASP cc_start: 0.6453 (t0) cc_final: 0.5186 (t0) REVERT: R 173 MET cc_start: 0.5731 (tpt) cc_final: 0.5226 (tpt) outliers start: 237 outliers final: 62 residues processed: 1000 average time/residue: 1.1237 time to fit residues: 1483.8570 Evaluate side-chains 702 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 622 time to evaluate : 4.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1000 MET Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1535 PHE Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1131 CYS Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 201 LYS Chi-restraints excluded: chain O residue 205 ARG Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 382 GLN Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 441 PHE Chi-restraints excluded: chain O residue 445 TYR Chi-restraints excluded: chain O residue 454 VAL Chi-restraints excluded: chain O residue 527 MET Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 154 LEU Chi-restraints excluded: chain Q residue 158 MET Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 242 ILE Chi-restraints excluded: chain S residue 368 HIS Chi-restraints excluded: chain S residue 386 MET Chi-restraints excluded: chain S residue 478 MET Chi-restraints excluded: chain S residue 510 THR Chi-restraints excluded: chain S residue 765 SER Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 410 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 326 optimal weight: 0.0970 chunk 182 optimal weight: 4.9990 chunk 489 optimal weight: 4.9990 chunk 400 optimal weight: 0.4980 chunk 162 optimal weight: 1.9990 chunk 588 optimal weight: 6.9990 chunk 635 optimal weight: 1.9990 chunk 524 optimal weight: 2.9990 chunk 583 optimal weight: 8.9990 chunk 200 optimal weight: 0.0570 chunk 472 optimal weight: 4.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 HIS A 378 HIS A 489 ASN A 535 GLN A 571 HIS ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN A 620 ASN A 636 HIS A 656 GLN A1047 GLN A1072 ASN ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 492 ASN B 499 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 702 ASN B 896 GLN ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1045 GLN B1199 ASN C 58 ASN D 88 GLN F 100 GLN G 67 ASN G 74 ASN H 52 GLN K 64 GLN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 GLN O 342 HIS ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 488 HIS Q 30 GLN Q 65 ASN Q 85 GLN Q 325 GLN S 232 ASN ** S 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 289 ASN R 298 GLN ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5364 moved from start: 0.6022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.195 54980 Z= 0.359 Angle : 0.826 16.257 74686 Z= 0.432 Chirality : 0.049 0.294 8352 Planarity : 0.007 0.105 9248 Dihedral : 13.960 177.734 8037 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.31 % Favored : 93.67 % Rotamer: Outliers : 4.89 % Allowed : 14.63 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.36 % 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: -2.80 (0.10), residues: 6352 helix: -1.62 (0.10), residues: 2265 sheet: -1.75 (0.17), residues: 792 loop : -2.03 (0.10), residues: 3295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP F 146 HIS 0.022 0.002 HIS B 361 PHE 0.089 0.003 PHE A1570 TYR 0.046 0.003 TYR E 168 ARG 0.019 0.001 ARG S 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1020 time to evaluate : 4.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 159 ILE cc_start: 0.4098 (OUTLIER) cc_final: 0.3880 (pp) REVERT: M 337 MET cc_start: 0.1514 (ttm) cc_final: 0.0967 (tmm) REVERT: M 397 MET cc_start: 0.2221 (mtt) cc_final: 0.1896 (OUTLIER) REVERT: A 57 PHE cc_start: 0.6020 (t80) cc_final: 0.5489 (t80) REVERT: A 63 SER cc_start: 0.4194 (p) cc_final: 0.3601 (m) REVERT: A 323 ILE cc_start: 0.6546 (OUTLIER) cc_final: 0.6244 (pp) REVERT: A 331 GLU cc_start: 0.3782 (OUTLIER) cc_final: 0.3554 (mp0) REVERT: A 351 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6239 (mttt) REVERT: A 505 LEU cc_start: 0.6973 (mt) cc_final: 0.6758 (mm) REVERT: A 572 THR cc_start: 0.6778 (m) cc_final: 0.6194 (p) REVERT: A 611 GLU cc_start: 0.5124 (mt-10) cc_final: 0.4494 (mt-10) REVERT: A 662 SER cc_start: 0.6419 (p) cc_final: 0.6139 (m) REVERT: A 926 GLN cc_start: 0.6003 (mt0) cc_final: 0.5470 (tp40) REVERT: A 960 MET cc_start: 0.5206 (mmp) cc_final: 0.4919 (mmp) REVERT: A 1089 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6347 (pp) REVERT: A 1099 LYS cc_start: 0.4941 (OUTLIER) cc_final: 0.4689 (mttp) REVERT: A 1178 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.5001 (pt) REVERT: A 1620 GLN cc_start: 0.7588 (tp40) cc_final: 0.7214 (tm-30) REVERT: A 1634 LEU cc_start: 0.6984 (mt) cc_final: 0.6596 (mt) REVERT: B 205 MET cc_start: 0.6026 (ptp) cc_final: 0.5781 (ptp) REVERT: B 248 ASN cc_start: 0.5900 (m110) cc_final: 0.5597 (m-40) REVERT: B 257 GLN cc_start: 0.3965 (tp40) cc_final: 0.3757 (tp40) REVERT: B 443 LYS cc_start: 0.6459 (tptp) cc_final: 0.6088 (tppt) REVERT: B 451 MET cc_start: 0.5421 (OUTLIER) cc_final: 0.5134 (tpt) REVERT: B 502 MET cc_start: 0.6203 (ttm) cc_final: 0.5942 (ttp) REVERT: B 512 LEU cc_start: 0.6249 (mt) cc_final: 0.5842 (tp) REVERT: B 533 THR cc_start: 0.6306 (OUTLIER) cc_final: 0.6094 (t) REVERT: B 716 MET cc_start: 0.6206 (ppp) cc_final: 0.5949 (ptp) REVERT: B 787 MET cc_start: 0.6197 (ppp) cc_final: 0.5706 (pp-130) REVERT: B 1155 ASP cc_start: 0.5661 (OUTLIER) cc_final: 0.5214 (p0) REVERT: B 1198 TYR cc_start: 0.7242 (m-80) cc_final: 0.6993 (m-80) REVERT: C 58 ASN cc_start: 0.6676 (OUTLIER) cc_final: 0.6456 (m-40) REVERT: C 71 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.6253 (mmt) REVERT: D 15 THR cc_start: 0.8154 (t) cc_final: 0.7858 (t) REVERT: E 50 MET cc_start: 0.5398 (pmt) cc_final: 0.4787 (ppp) REVERT: E 57 MET cc_start: 0.5655 (tmm) cc_final: 0.5385 (tmm) REVERT: E 121 MET cc_start: 0.5454 (tpp) cc_final: 0.5043 (tpp) REVERT: E 137 GLU cc_start: 0.3864 (pt0) cc_final: 0.3644 (pt0) REVERT: F 116 ASP cc_start: 0.7595 (t0) cc_final: 0.7298 (t70) REVERT: G 95 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5650 (pp) REVERT: G 134 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.5642 (tp30) REVERT: G 136 TYR cc_start: 0.5612 (OUTLIER) cc_final: 0.5389 (m-80) REVERT: G 234 ARG cc_start: 0.6880 (mtt-85) cc_final: 0.6441 (mmm160) REVERT: H 56 THR cc_start: 0.5593 (m) cc_final: 0.5314 (m) REVERT: H 130 ARG cc_start: 0.4760 (ptp90) cc_final: 0.4376 (ptp90) REVERT: J 1 MET cc_start: 0.5635 (ttm) cc_final: 0.5294 (mtm) REVERT: K 55 SER cc_start: 0.7180 (t) cc_final: 0.6800 (p) REVERT: L 42 ARG cc_start: 0.5940 (ptp-110) cc_final: 0.5205 (mtt-85) REVERT: N 90 MET cc_start: 0.4589 (OUTLIER) cc_final: 0.3406 (tmt) REVERT: O 126 TRP cc_start: 0.5233 (p90) cc_final: 0.4543 (p90) REVERT: O 127 GLU cc_start: 0.5664 (mt-10) cc_final: 0.5195 (mp0) REVERT: O 182 MET cc_start: 0.3198 (OUTLIER) cc_final: 0.2783 (mtp) REVERT: O 205 ARG cc_start: 0.5000 (OUTLIER) cc_final: 0.4697 (mmm-85) REVERT: O 206 ARG cc_start: 0.6111 (mmm160) cc_final: 0.5443 (mmm160) REVERT: O 238 ILE cc_start: 0.4773 (mm) cc_final: 0.4322 (mm) REVERT: O 382 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.6602 (pm20) REVERT: O 385 MET cc_start: 0.7371 (tpp) cc_final: 0.7083 (tpp) REVERT: O 412 GLU cc_start: 0.5480 (mt-10) cc_final: 0.4853 (mp0) REVERT: O 582 ARG cc_start: 0.3784 (tpt90) cc_final: 0.3222 (mtp180) REVERT: O 584 GLN cc_start: 0.5651 (tp40) cc_final: 0.3962 (mp10) REVERT: Q 74 GLN cc_start: 0.3212 (mt0) cc_final: 0.2474 (tp40) REVERT: Q 79 GLN cc_start: 0.5867 (tm130) cc_final: 0.5542 (tm-30) REVERT: Q 139 LYS cc_start: 0.5418 (tttt) cc_final: 0.4344 (tptt) REVERT: Q 155 GLN cc_start: 0.4173 (OUTLIER) cc_final: 0.3561 (mp-120) REVERT: Q 158 MET cc_start: 0.3132 (tpp) cc_final: 0.0268 (ptm) REVERT: Q 199 LEU cc_start: 0.5296 (OUTLIER) cc_final: 0.5017 (tt) REVERT: Q 240 LYS cc_start: 0.6393 (mmmt) cc_final: 0.5634 (mppt) REVERT: Q 311 MET cc_start: 0.5578 (mmp) cc_final: 0.5343 (ttt) REVERT: Q 421 ARG cc_start: 0.4607 (ttt180) cc_final: 0.4052 (tpm170) REVERT: Q 480 LEU cc_start: 0.5297 (OUTLIER) cc_final: 0.4944 (pp) REVERT: Q 513 MET cc_start: 0.0697 (mpt) cc_final: 0.0318 (mtt) REVERT: S 45 PRO cc_start: 0.2192 (Cg_endo) cc_final: 0.1602 (Cg_exo) REVERT: S 304 ASP cc_start: 0.6249 (t0) cc_final: 0.5620 (m-30) REVERT: S 347 LEU cc_start: 0.4277 (tm) cc_final: 0.4028 (mm) REVERT: S 678 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.6074 (tt) REVERT: S 692 THR cc_start: 0.1438 (p) cc_final: 0.1086 (p) REVERT: S 698 LYS cc_start: 0.1535 (pptt) cc_final: 0.1136 (pttt) REVERT: S 749 LYS cc_start: 0.4662 (ptpt) cc_final: 0.4316 (ptmm) REVERT: R 205 VAL cc_start: 0.5390 (p) cc_final: 0.5148 (m) REVERT: R 281 LYS cc_start: 0.4125 (mptp) cc_final: 0.3740 (mmmt) outliers start: 283 outliers final: 77 residues processed: 1205 average time/residue: 1.1051 time to fit residues: 1758.4996 Evaluate side-chains 835 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 736 time to evaluate : 4.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1099 LYS Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1503 HIS Chi-restraints excluded: chain A residue 1570 PHE Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1057 MET Chi-restraints excluded: chain B residue 1066 HIS Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 36 CYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain J residue 46 CYS Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 182 MET Chi-restraints excluded: chain O residue 201 LYS Chi-restraints excluded: chain O residue 205 ARG Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 378 THR Chi-restraints excluded: chain O residue 382 GLN Chi-restraints excluded: chain O residue 488 HIS Chi-restraints excluded: chain Q residue 20 TRP Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 199 LEU Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 366 TYR Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 317 ILE Chi-restraints excluded: chain S residue 320 ILE Chi-restraints excluded: chain S residue 400 SER Chi-restraints excluded: chain S residue 495 SER Chi-restraints excluded: chain S residue 496 THR Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 538 LEU Chi-restraints excluded: chain S residue 678 LEU Chi-restraints excluded: chain S residue 714 PHE Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 410 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 581 optimal weight: 7.9990 chunk 442 optimal weight: 2.9990 chunk 305 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 395 optimal weight: 6.9990 chunk 590 optimal weight: 10.0000 chunk 625 optimal weight: 6.9990 chunk 308 optimal weight: 0.8980 chunk 559 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 351 HIS A 521 GLN A 553 GLN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 HIS A 620 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1113 HIS ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS B 295 ASN B 492 ASN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 GLN B 886 ASN B 896 GLN B 899 GLN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 ASN B1038 HIS B1066 HIS C 93 GLN E 146 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN L 53 HIS ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 131 HIS O 168 GLN O 172 HIS O 390 GLN O 391 GLN ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 85 GLN Q 145 ASN Q 434 HIS ** S 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 223 ASN R 228 ASN ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.8867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 54980 Z= 0.376 Angle : 0.875 18.028 74686 Z= 0.451 Chirality : 0.051 0.520 8352 Planarity : 0.007 0.179 9248 Dihedral : 14.141 179.814 8034 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.30 % Favored : 93.67 % Rotamer: Outliers : 5.34 % Allowed : 17.79 % Favored : 76.87 % 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: -2.56 (0.10), residues: 6352 helix: -1.30 (0.10), residues: 2256 sheet: -1.54 (0.18), residues: 753 loop : -2.01 (0.10), residues: 3343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP S 438 HIS 0.067 0.002 HIS O 488 PHE 0.028 0.003 PHE R 438 TYR 0.036 0.003 TYR A1080 ARG 0.023 0.001 ARG O 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 1105 time to evaluate : 4.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 57 ASN cc_start: 0.4632 (p0) cc_final: 0.4323 (p0) REVERT: M 159 ILE cc_start: 0.4365 (OUTLIER) cc_final: 0.4125 (pp) REVERT: M 337 MET cc_start: 0.1152 (ttm) cc_final: 0.0792 (tmm) REVERT: M 346 ILE cc_start: 0.2067 (OUTLIER) cc_final: 0.1540 (pp) REVERT: M 397 MET cc_start: 0.2586 (mtt) cc_final: 0.2158 (mtt) REVERT: A 26 ASN cc_start: 0.7825 (t0) cc_final: 0.7414 (t0) REVERT: A 59 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6259 (mtp85) REVERT: A 103 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5676 (mt) REVERT: A 205 ARG cc_start: 0.6839 (mtm110) cc_final: 0.6550 (ttt-90) REVERT: A 209 THR cc_start: 0.7885 (m) cc_final: 0.7351 (p) REVERT: A 238 MET cc_start: 0.3047 (OUTLIER) cc_final: 0.2551 (mpp) REVERT: A 329 ARG cc_start: 0.6433 (mmm160) cc_final: 0.6011 (tpt170) REVERT: A 627 ASP cc_start: 0.5534 (p0) cc_final: 0.5298 (p0) REVERT: A 750 ILE cc_start: 0.8108 (mm) cc_final: 0.7821 (mp) REVERT: A 827 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8242 (m) REVERT: A 934 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7988 (mmtt) REVERT: A 1089 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6285 (pp) REVERT: A 1199 GLN cc_start: 0.5742 (OUTLIER) cc_final: 0.5464 (mp10) REVERT: A 1262 LEU cc_start: 0.6771 (mt) cc_final: 0.6264 (mt) REVERT: A 1269 LYS cc_start: 0.6271 (mtmt) cc_final: 0.5790 (mtpp) REVERT: A 1323 HIS cc_start: 0.5834 (m170) cc_final: 0.5615 (m170) REVERT: A 1513 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6982 (tm-30) REVERT: A 1589 MET cc_start: 0.8181 (mmm) cc_final: 0.7959 (mmm) REVERT: A 1620 GLN cc_start: 0.7884 (tp40) cc_final: 0.7486 (tm-30) REVERT: A 1621 PHE cc_start: 0.7080 (m-80) cc_final: 0.6643 (m-80) REVERT: A 1643 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8369 (p) REVERT: A 1655 ASP cc_start: 0.7914 (t70) cc_final: 0.7606 (t0) REVERT: B 134 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7852 (mtm180) REVERT: B 252 TYR cc_start: 0.7433 (t80) cc_final: 0.7231 (t80) REVERT: B 401 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6683 (pp20) REVERT: B 443 LYS cc_start: 0.7309 (tptp) cc_final: 0.6667 (tppt) REVERT: B 446 MET cc_start: 0.7943 (tmt) cc_final: 0.7534 (tmm) REVERT: B 460 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7569 (mppt) REVERT: B 552 SER cc_start: 0.6407 (OUTLIER) cc_final: 0.5955 (p) REVERT: B 641 TYR cc_start: 0.6712 (m-10) cc_final: 0.6313 (m-80) REVERT: B 724 GLN cc_start: 0.7922 (tt0) cc_final: 0.7675 (tt0) REVERT: B 845 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8419 (mt) REVERT: B 883 GLU cc_start: 0.6408 (mm-30) cc_final: 0.6074 (mp0) REVERT: B 977 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7176 (pp) REVERT: B 1103 VAL cc_start: 0.7966 (m) cc_final: 0.7685 (p) REVERT: B 1133 MET cc_start: 0.6556 (ptm) cc_final: 0.6154 (ptp) REVERT: B 1151 ILE cc_start: 0.2066 (OUTLIER) cc_final: 0.1034 (tt) REVERT: B 1155 ASP cc_start: 0.6062 (OUTLIER) cc_final: 0.5509 (p0) REVERT: B 1166 LYS cc_start: 0.6573 (OUTLIER) cc_final: 0.6109 (ttpp) REVERT: C 93 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: C 107 LYS cc_start: 0.7864 (ttmt) cc_final: 0.7546 (ttmm) REVERT: C 128 ASP cc_start: 0.7415 (p0) cc_final: 0.7140 (p0) REVERT: D 16 LEU cc_start: 0.7767 (tp) cc_final: 0.7050 (pp) REVERT: E 23 VAL cc_start: 0.8299 (t) cc_final: 0.7975 (t) REVERT: E 93 MET cc_start: 0.7127 (tpp) cc_final: 0.6377 (tpp) REVERT: E 121 MET cc_start: 0.5778 (tpp) cc_final: 0.5577 (tpp) REVERT: E 164 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8689 (tm) REVERT: E 200 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.6272 (pmt170) REVERT: F 103 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7802 (tpt) REVERT: G 63 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7866 (mtpt) REVERT: G 95 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6330 (pp) REVERT: G 234 ARG cc_start: 0.7205 (mtt-85) cc_final: 0.6637 (mmm160) REVERT: H 41 ASP cc_start: 0.7527 (m-30) cc_final: 0.7123 (m-30) REVERT: H 123 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8166 (ttt) REVERT: I 94 MET cc_start: 0.0727 (ttt) cc_final: 0.0513 (ppp) REVERT: K 55 SER cc_start: 0.8169 (t) cc_final: 0.7830 (p) REVERT: K 79 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8805 (t) REVERT: K 111 THR cc_start: 0.7511 (OUTLIER) cc_final: 0.7298 (m) REVERT: K 122 LYS cc_start: 0.7890 (tttt) cc_final: 0.7474 (tptp) REVERT: K 134 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7737 (mmtp) REVERT: L 42 ARG cc_start: 0.6303 (ptp-110) cc_final: 0.5925 (mtt-85) REVERT: L 68 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7052 (mt-10) REVERT: N 90 MET cc_start: 0.4863 (OUTLIER) cc_final: 0.4184 (tmt) REVERT: N 171 PHE cc_start: 0.7670 (m-80) cc_final: 0.7466 (m-80) REVERT: O 124 LYS cc_start: 0.7231 (mmtp) cc_final: 0.5794 (mtpm) REVERT: O 156 MET cc_start: 0.5480 (tpp) cc_final: 0.5141 (ttt) REVERT: O 173 HIS cc_start: 0.3707 (t-90) cc_final: 0.3271 (t-90) REVERT: O 182 MET cc_start: 0.1813 (OUTLIER) cc_final: 0.0910 (mtp) REVERT: O 205 ARG cc_start: 0.5585 (OUTLIER) cc_final: 0.5289 (mmm-85) REVERT: O 206 ARG cc_start: 0.6438 (mmm160) cc_final: 0.5159 (mpp-170) REVERT: O 385 MET cc_start: 0.7268 (tpp) cc_final: 0.6292 (tmm) REVERT: O 396 MET cc_start: 0.4527 (mpt) cc_final: 0.4254 (mpt) REVERT: O 416 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6503 (tppt) REVERT: O 453 TYR cc_start: 0.6611 (t80) cc_final: 0.6086 (t80) REVERT: O 582 ARG cc_start: 0.3902 (tpt90) cc_final: 0.2977 (mtp180) REVERT: O 584 GLN cc_start: 0.5789 (tp40) cc_final: 0.4142 (mp10) REVERT: Q 82 GLN cc_start: 0.4415 (tp-100) cc_final: 0.4153 (tp-100) REVERT: Q 123 MET cc_start: 0.5434 (ptm) cc_final: 0.5137 (ptt) REVERT: Q 139 LYS cc_start: 0.5649 (tttt) cc_final: 0.4859 (tptt) REVERT: Q 155 GLN cc_start: 0.4069 (mm110) cc_final: 0.3451 (mp-120) REVERT: Q 158 MET cc_start: 0.4539 (tpp) cc_final: 0.4076 (tpt) REVERT: Q 183 LYS cc_start: 0.5766 (ttpp) cc_final: 0.5306 (tptp) REVERT: Q 226 LEU cc_start: 0.4451 (OUTLIER) cc_final: 0.4229 (tp) REVERT: Q 240 LYS cc_start: 0.6561 (mmmt) cc_final: 0.5362 (mttp) REVERT: Q 241 GLU cc_start: 0.4809 (OUTLIER) cc_final: 0.4473 (pm20) REVERT: Q 258 MET cc_start: 0.5409 (ptt) cc_final: 0.5176 (ptm) REVERT: Q 303 GLU cc_start: 0.4646 (mp0) cc_final: 0.4094 (mp0) REVERT: Q 311 MET cc_start: 0.5590 (mmp) cc_final: 0.5370 (ttt) REVERT: Q 421 ARG cc_start: 0.5067 (ttt180) cc_final: 0.4239 (tpm170) REVERT: Q 513 MET cc_start: 0.0225 (mpt) cc_final: -0.0269 (mtt) REVERT: S 45 PRO cc_start: 0.1992 (Cg_endo) cc_final: 0.1473 (Cg_exo) REVERT: S 238 LEU cc_start: 0.4257 (pt) cc_final: 0.3806 (mm) REVERT: S 347 LEU cc_start: 0.4447 (OUTLIER) cc_final: 0.4192 (tm) REVERT: S 412 ASN cc_start: 0.3941 (t0) cc_final: 0.3367 (p0) REVERT: S 421 ILE cc_start: 0.5646 (tt) cc_final: 0.5268 (tt) REVERT: S 456 VAL cc_start: 0.2139 (OUTLIER) cc_final: 0.1704 (m) REVERT: S 464 LEU cc_start: 0.4436 (OUTLIER) cc_final: 0.3996 (OUTLIER) REVERT: S 738 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.4646 (tppt) REVERT: S 749 LYS cc_start: 0.4613 (OUTLIER) cc_final: 0.4233 (ptmm) REVERT: R 139 GLU cc_start: 0.6234 (mt-10) cc_final: 0.5774 (mt-10) REVERT: R 170 LEU cc_start: 0.4173 (OUTLIER) cc_final: 0.3970 (mm) REVERT: R 196 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6172 (tp30) REVERT: R 205 VAL cc_start: 0.6035 (p) cc_final: 0.5768 (m) REVERT: R 207 ASN cc_start: 0.5310 (t0) cc_final: 0.4572 (t0) REVERT: R 268 LEU cc_start: 0.6911 (tm) cc_final: 0.6667 (tp) REVERT: R 274 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.5366 (tpt) REVERT: R 281 LYS cc_start: 0.5705 (mptp) cc_final: 0.5433 (mmmt) REVERT: R 409 HIS cc_start: 0.6283 (OUTLIER) cc_final: 0.6079 (p-80) outliers start: 309 outliers final: 100 residues processed: 1302 average time/residue: 1.1799 time to fit residues: 2004.1750 Evaluate side-chains 925 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 783 time to evaluate : 4.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 346 ILE Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1199 GLN Chi-restraints excluded: chain A residue 1513 GLU Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 939 SER Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1166 LYS Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 24 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 182 MET Chi-restraints excluded: chain O residue 205 ARG Chi-restraints excluded: chain O residue 416 LYS Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain Q residue 130 GLU Chi-restraints excluded: chain Q residue 181 TYR Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 241 GLU Chi-restraints excluded: chain Q residue 265 GLU Chi-restraints excluded: chain Q residue 304 LEU Chi-restraints excluded: chain Q residue 366 TYR Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 363 ILE Chi-restraints excluded: chain S residue 369 PHE Chi-restraints excluded: chain S residue 443 ASP Chi-restraints excluded: chain S residue 451 ILE Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain S residue 464 LEU Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 600 GLU Chi-restraints excluded: chain S residue 736 ILE Chi-restraints excluded: chain S residue 738 LYS Chi-restraints excluded: chain S residue 749 LYS Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 410 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 520 optimal weight: 0.3980 chunk 355 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 465 optimal weight: 0.0000 chunk 258 optimal weight: 0.8980 chunk 533 optimal weight: 0.8980 chunk 432 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 319 optimal weight: 0.4980 chunk 561 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 571 HIS ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN A 840 ASN A1026 GLN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1447 GLN A1567 ASN B 183 HIS B 295 ASN B 325 GLN B 399 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 688 HIS ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN B1053 ASN B1066 HIS ** B1089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 88 ASN D 30 HIS E 106 GLN E 136 ASN G 154 ASN I 125 ASN ** N 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 131 HIS ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 422 GLN O 438 GLN Q 74 GLN Q 85 GLN Q 157 HIS Q 206 GLN ** S 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 624 GLN R 228 ASN ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.9497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 54980 Z= 0.204 Angle : 0.687 15.093 74686 Z= 0.352 Chirality : 0.045 0.308 8352 Planarity : 0.005 0.063 9248 Dihedral : 13.884 179.731 8029 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.16 % Favored : 94.82 % Rotamer: Outliers : 4.46 % Allowed : 22.80 % Favored : 72.74 % 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: -2.09 (0.10), residues: 6352 helix: -0.80 (0.11), residues: 2261 sheet: -1.33 (0.18), residues: 731 loop : -1.82 (0.10), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP S 438 HIS 0.022 0.001 HIS B 282 PHE 0.030 0.002 PHE S 714 TYR 0.034 0.002 TYR O 193 ARG 0.013 0.001 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 873 time to evaluate : 4.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 57 ASN cc_start: 0.4233 (p0) cc_final: 0.3961 (p0) REVERT: M 65 TYR cc_start: 0.4890 (p90) cc_final: 0.4620 (p90) REVERT: M 159 ILE cc_start: 0.4355 (OUTLIER) cc_final: 0.4004 (pp) REVERT: M 166 ARG cc_start: 0.2254 (mtt180) cc_final: 0.1149 (mtt90) REVERT: M 337 MET cc_start: 0.1605 (ttm) cc_final: 0.1093 (tmm) REVERT: M 397 MET cc_start: 0.2513 (mtt) cc_final: 0.2002 (mtt) REVERT: A 5 LYS cc_start: 0.7430 (mppt) cc_final: 0.6842 (mppt) REVERT: A 26 ASN cc_start: 0.8100 (t0) cc_final: 0.7551 (t0) REVERT: A 59 ARG cc_start: 0.6832 (tpm170) cc_final: 0.5965 (mtp85) REVERT: A 103 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.6028 (mt) REVERT: A 205 ARG cc_start: 0.6773 (mtm110) cc_final: 0.6563 (ttt-90) REVERT: A 209 THR cc_start: 0.7953 (m) cc_final: 0.7431 (p) REVERT: A 238 MET cc_start: 0.2712 (OUTLIER) cc_final: 0.2168 (mpp) REVERT: A 321 LYS cc_start: 0.7156 (tmmt) cc_final: 0.6652 (tppp) REVERT: A 322 ASN cc_start: 0.5205 (m-40) cc_final: 0.4862 (m-40) REVERT: A 329 ARG cc_start: 0.6676 (mmm160) cc_final: 0.6464 (tpt170) REVERT: A 355 PHE cc_start: 0.7918 (m-80) cc_final: 0.7673 (m-80) REVERT: A 536 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7873 (mt) REVERT: A 627 ASP cc_start: 0.5613 (p0) cc_final: 0.5331 (p0) REVERT: A 892 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7739 (tp) REVERT: A 934 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8041 (mmmt) REVERT: A 1012 LYS cc_start: 0.5802 (ttpt) cc_final: 0.5451 (tppt) REVERT: A 1049 MET cc_start: 0.8056 (mmt) cc_final: 0.7800 (mmt) REVERT: A 1089 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6466 (pp) REVERT: A 1199 GLN cc_start: 0.5495 (OUTLIER) cc_final: 0.5026 (mp10) REVERT: A 1242 ILE cc_start: 0.6366 (pp) cc_final: 0.6021 (pp) REVERT: A 1326 GLU cc_start: 0.5024 (pt0) cc_final: 0.4821 (mm-30) REVERT: A 1620 GLN cc_start: 0.7844 (tp40) cc_final: 0.7399 (tm-30) REVERT: A 1655 ASP cc_start: 0.7903 (t70) cc_final: 0.7653 (t0) REVERT: B 134 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7875 (mtm180) REVERT: B 443 LYS cc_start: 0.7218 (tptp) cc_final: 0.6506 (mttm) REVERT: B 446 MET cc_start: 0.7850 (tmt) cc_final: 0.7364 (tmm) REVERT: B 460 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7627 (mppt) REVERT: B 512 LEU cc_start: 0.6932 (mt) cc_final: 0.6253 (tp) REVERT: B 600 GLN cc_start: 0.7362 (tp40) cc_final: 0.7079 (tp40) REVERT: B 634 ARG cc_start: 0.7114 (ttm110) cc_final: 0.6837 (ttp80) REVERT: B 641 TYR cc_start: 0.7179 (m-10) cc_final: 0.6968 (m-80) REVERT: B 898 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5019 (tp) REVERT: B 1037 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7663 (ppt-90) REVERT: B 1103 VAL cc_start: 0.7977 (m) cc_final: 0.7670 (p) REVERT: B 1151 ILE cc_start: 0.1839 (OUTLIER) cc_final: 0.0917 (tt) REVERT: B 1155 ASP cc_start: 0.5946 (OUTLIER) cc_final: 0.5404 (p0) REVERT: B 1198 TYR cc_start: 0.8094 (m-80) cc_final: 0.7322 (m-80) REVERT: C 107 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7696 (ttmm) REVERT: C 128 ASP cc_start: 0.7737 (p0) cc_final: 0.7319 (p0) REVERT: D 16 LEU cc_start: 0.7699 (tp) cc_final: 0.7152 (pp) REVERT: E 22 MET cc_start: 0.8094 (ttp) cc_final: 0.7817 (ttm) REVERT: E 23 VAL cc_start: 0.8275 (t) cc_final: 0.7973 (t) REVERT: E 50 MET cc_start: 0.5154 (pmm) cc_final: 0.4828 (pmm) REVERT: E 93 MET cc_start: 0.7127 (tpp) cc_final: 0.6362 (tpp) REVERT: E 94 LYS cc_start: 0.7165 (mmmm) cc_final: 0.6890 (tmtt) REVERT: G 63 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7856 (mtpt) REVERT: G 84 TYR cc_start: 0.7701 (p90) cc_final: 0.7297 (p90) REVERT: G 95 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6295 (pp) REVERT: G 234 ARG cc_start: 0.6955 (mtt-85) cc_final: 0.6580 (mtm180) REVERT: G 245 VAL cc_start: 0.4352 (OUTLIER) cc_final: 0.3948 (p) REVERT: H 41 ASP cc_start: 0.7521 (m-30) cc_final: 0.7214 (m-30) REVERT: H 77 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.6013 (ptt90) REVERT: H 136 LYS cc_start: 0.6402 (ptpp) cc_final: 0.6104 (ttmm) REVERT: J 12 LYS cc_start: 0.8413 (tttp) cc_final: 0.7964 (tttp) REVERT: K 55 SER cc_start: 0.8394 (t) cc_final: 0.8179 (p) REVERT: K 79 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8881 (t) REVERT: K 103 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7870 (mt) REVERT: K 110 GLU cc_start: 0.7391 (pp20) cc_final: 0.7003 (pp20) REVERT: K 111 THR cc_start: 0.7794 (OUTLIER) cc_final: 0.7481 (m) REVERT: K 122 LYS cc_start: 0.7964 (tttt) cc_final: 0.7476 (tptp) REVERT: K 126 ASP cc_start: 0.7543 (m-30) cc_final: 0.7301 (m-30) REVERT: K 134 LYS cc_start: 0.8290 (mmmt) cc_final: 0.7724 (mmtp) REVERT: L 42 ARG cc_start: 0.6251 (ptp-110) cc_final: 0.5807 (mtt-85) REVERT: L 68 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7326 (mt-10) REVERT: N 90 MET cc_start: 0.5155 (OUTLIER) cc_final: 0.4610 (tmm) REVERT: N 169 GLU cc_start: 0.5947 (pt0) cc_final: 0.5574 (mt-10) REVERT: N 171 PHE cc_start: 0.7766 (m-80) cc_final: 0.7480 (m-80) REVERT: O 95 ILE cc_start: 0.5170 (OUTLIER) cc_final: 0.4945 (pp) REVERT: O 124 LYS cc_start: 0.6935 (mmtp) cc_final: 0.5724 (mtpm) REVERT: O 173 HIS cc_start: 0.3721 (t-90) cc_final: 0.3421 (t-90) REVERT: O 182 MET cc_start: 0.2568 (OUTLIER) cc_final: 0.2068 (mtp) REVERT: O 187 MET cc_start: 0.6122 (mtp) cc_final: 0.5659 (mtm) REVERT: O 201 LYS cc_start: 0.6180 (OUTLIER) cc_final: 0.5729 (tttt) REVERT: O 205 ARG cc_start: 0.5705 (OUTLIER) cc_final: 0.5440 (mmm-85) REVERT: O 206 ARG cc_start: 0.6403 (mmm160) cc_final: 0.5141 (mpp-170) REVERT: O 228 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7151 (pm20) REVERT: O 243 GLU cc_start: 0.6575 (mt-10) cc_final: 0.5818 (tp30) REVERT: O 356 GLU cc_start: 0.6272 (mt-10) cc_final: 0.5628 (tm-30) REVERT: O 453 TYR cc_start: 0.6085 (t80) cc_final: 0.5765 (t80) REVERT: O 527 MET cc_start: 0.5087 (tmt) cc_final: 0.4749 (tmm) REVERT: O 582 ARG cc_start: 0.3964 (tpt90) cc_final: 0.3003 (mtp180) REVERT: O 584 GLN cc_start: 0.5666 (tp40) cc_final: 0.4031 (mp10) REVERT: Q 21 ARG cc_start: 0.5308 (mpt-90) cc_final: 0.4573 (mmt90) REVERT: Q 82 GLN cc_start: 0.4426 (tp-100) cc_final: 0.4196 (tp-100) REVERT: Q 123 MET cc_start: 0.5856 (ptm) cc_final: 0.5643 (ptt) REVERT: Q 139 LYS cc_start: 0.5638 (tttt) cc_final: 0.4913 (tptt) REVERT: Q 154 LEU cc_start: 0.2311 (OUTLIER) cc_final: 0.1866 (tt) REVERT: Q 155 GLN cc_start: 0.4054 (OUTLIER) cc_final: 0.3823 (mm110) REVERT: Q 183 LYS cc_start: 0.6067 (ttpp) cc_final: 0.5580 (tptp) REVERT: Q 226 LEU cc_start: 0.4366 (OUTLIER) cc_final: 0.4106 (tp) REVERT: Q 227 TYR cc_start: 0.5139 (m-10) cc_final: 0.4555 (m-10) REVERT: Q 240 LYS cc_start: 0.6727 (mmmt) cc_final: 0.5683 (mttp) REVERT: Q 241 GLU cc_start: 0.5288 (OUTLIER) cc_final: 0.4957 (pm20) REVERT: Q 360 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6267 (pptt) REVERT: Q 421 ARG cc_start: 0.5210 (ttt180) cc_final: 0.4223 (tpm170) REVERT: Q 513 MET cc_start: 0.0448 (mpt) cc_final: 0.0081 (mpt) REVERT: S 45 PRO cc_start: 0.1945 (Cg_endo) cc_final: 0.1407 (Cg_exo) REVERT: S 285 MET cc_start: 0.4941 (ppp) cc_final: 0.4074 (tpp) REVERT: S 347 LEU cc_start: 0.4488 (OUTLIER) cc_final: 0.3961 (mm) REVERT: S 386 MET cc_start: 0.4133 (ttp) cc_final: 0.3244 (tmm) REVERT: S 421 ILE cc_start: 0.5664 (tt) cc_final: 0.5269 (tt) REVERT: S 456 VAL cc_start: 0.1730 (OUTLIER) cc_final: 0.1237 (p) REVERT: S 464 LEU cc_start: 0.4504 (OUTLIER) cc_final: 0.4179 (pt) REVERT: S 467 PHE cc_start: 0.6168 (m-10) cc_final: 0.5914 (m-10) REVERT: S 538 LEU cc_start: 0.5772 (pp) cc_final: 0.5377 (pp) REVERT: S 698 LYS cc_start: 0.1358 (pptt) cc_final: 0.0485 (pttp) REVERT: S 749 LYS cc_start: 0.4660 (OUTLIER) cc_final: 0.4340 (ptmm) REVERT: R 205 VAL cc_start: 0.6217 (p) cc_final: 0.5912 (m) REVERT: R 207 ASN cc_start: 0.5023 (t0) cc_final: 0.4476 (t0) REVERT: R 247 ILE cc_start: 0.5428 (OUTLIER) cc_final: 0.4483 (mp) REVERT: R 268 LEU cc_start: 0.6942 (tm) cc_final: 0.6586 (tp) REVERT: R 274 MET cc_start: 0.6340 (mmp) cc_final: 0.5705 (tpt) REVERT: R 281 LYS cc_start: 0.5879 (mptp) cc_final: 0.5610 (mmmt) REVERT: R 359 MET cc_start: 0.3208 (pmm) cc_final: 0.2854 (ptp) outliers start: 258 outliers final: 86 residues processed: 1046 average time/residue: 1.1631 time to fit residues: 1599.0501 Evaluate side-chains 860 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 737 time to evaluate : 4.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1199 GLN Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 141 GLU Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 164 LEU Chi-restraints excluded: chain O residue 182 MET Chi-restraints excluded: chain O residue 201 LYS Chi-restraints excluded: chain O residue 205 ARG Chi-restraints excluded: chain O residue 228 GLN Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain Q residue 154 LEU Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain Q residue 241 GLU Chi-restraints excluded: chain Q residue 265 GLU Chi-restraints excluded: chain Q residue 360 LYS Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain S residue 464 LEU Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 749 LYS Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 410 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 210 optimal weight: 3.9990 chunk 563 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 367 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 625 optimal weight: 0.6980 chunk 519 optimal weight: 5.9990 chunk 289 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 207 optimal weight: 0.0770 chunk 328 optimal weight: 0.0570 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN A 571 HIS ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1567 ASN B 166 GLN B 183 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS B 480 GLN B 669 GLN B 824 HIS ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN C 93 GLN D 30 HIS E 106 GLN E 136 ASN G 20 HIS G 216 HIS O 117 GLN O 131 HIS O 422 GLN O 488 HIS Q 85 GLN S 473 HIS ** S 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 228 ASN R 263 ASN ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.9941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 54980 Z= 0.201 Angle : 0.679 22.727 74686 Z= 0.344 Chirality : 0.045 0.304 8352 Planarity : 0.004 0.064 9248 Dihedral : 13.826 179.657 8029 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.40 % Favored : 94.58 % Rotamer: Outliers : 4.37 % Allowed : 23.63 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.10), residues: 6352 helix: -0.53 (0.11), residues: 2267 sheet: -1.21 (0.19), residues: 743 loop : -1.71 (0.10), residues: 3342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP S 438 HIS 0.011 0.001 HIS A 571 PHE 0.025 0.001 PHE B 301 TYR 0.026 0.002 TYR S 469 ARG 0.013 0.001 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 863 time to evaluate : 4.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 65 TYR cc_start: 0.5181 (p90) cc_final: 0.4914 (p90) REVERT: M 159 ILE cc_start: 0.4346 (OUTLIER) cc_final: 0.4071 (pp) REVERT: M 166 ARG cc_start: 0.2258 (ttt180) cc_final: 0.1305 (ttt90) REVERT: M 337 MET cc_start: 0.1892 (ttm) cc_final: 0.1196 (tmm) REVERT: M 359 LYS cc_start: 0.4421 (tptt) cc_final: 0.3807 (tptt) REVERT: M 397 MET cc_start: 0.2605 (mtt) cc_final: 0.2017 (mtt) REVERT: A 5 LYS cc_start: 0.7639 (mppt) cc_final: 0.7245 (mppt) REVERT: A 26 ASN cc_start: 0.8090 (t0) cc_final: 0.7508 (t0) REVERT: A 59 ARG cc_start: 0.6791 (tpm170) cc_final: 0.5823 (mtp85) REVERT: A 103 LEU cc_start: 0.6465 (OUTLIER) cc_final: 0.6257 (mt) REVERT: A 114 GLU cc_start: 0.7716 (tp30) cc_final: 0.7489 (mm-30) REVERT: A 209 THR cc_start: 0.8019 (m) cc_final: 0.7535 (p) REVERT: A 214 ASP cc_start: 0.6476 (t0) cc_final: 0.6264 (t0) REVERT: A 238 MET cc_start: 0.2799 (OUTLIER) cc_final: 0.2290 (mpp) REVERT: A 321 LYS cc_start: 0.7247 (tmmt) cc_final: 0.6821 (tppp) REVERT: A 322 ASN cc_start: 0.5382 (m-40) cc_final: 0.4974 (m-40) REVERT: A 329 ARG cc_start: 0.6801 (mmm160) cc_final: 0.6592 (tpt170) REVERT: A 355 PHE cc_start: 0.8088 (m-80) cc_final: 0.7853 (m-80) REVERT: A 756 LYS cc_start: 0.7274 (mmpt) cc_final: 0.7065 (mtpm) REVERT: A 892 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8187 (tt) REVERT: A 914 ASP cc_start: 0.7162 (m-30) cc_final: 0.6850 (m-30) REVERT: A 934 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8128 (OUTLIER) REVERT: A 937 ASN cc_start: 0.7215 (m-40) cc_final: 0.6508 (t0) REVERT: A 1012 LYS cc_start: 0.5872 (ttpt) cc_final: 0.5573 (tppt) REVERT: A 1170 MET cc_start: 0.8402 (mmp) cc_final: 0.8026 (mmm) REVERT: A 1269 LYS cc_start: 0.6082 (mtmt) cc_final: 0.5657 (mtpp) REVERT: A 1513 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6506 (tm-30) REVERT: A 1583 ASP cc_start: 0.7318 (t0) cc_final: 0.6954 (t0) REVERT: A 1620 GLN cc_start: 0.8024 (tp40) cc_final: 0.7575 (tm-30) REVERT: B 16 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.5059 (p90) REVERT: B 134 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8012 (mtm180) REVERT: B 236 ILE cc_start: 0.8760 (tp) cc_final: 0.8559 (tt) REVERT: B 443 LYS cc_start: 0.6980 (tptp) cc_final: 0.6395 (mttm) REVERT: B 446 MET cc_start: 0.7870 (tmt) cc_final: 0.7340 (tmm) REVERT: B 460 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7802 (mppt) REVERT: B 512 LEU cc_start: 0.6839 (mt) cc_final: 0.6135 (tp) REVERT: B 634 ARG cc_start: 0.7321 (ttm110) cc_final: 0.7112 (mtp-110) REVERT: B 724 GLN cc_start: 0.7860 (tt0) cc_final: 0.7552 (mt0) REVERT: B 898 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5123 (tp) REVERT: B 1037 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7556 (ppt170) REVERT: B 1151 ILE cc_start: 0.2077 (OUTLIER) cc_final: 0.1162 (tt) REVERT: B 1155 ASP cc_start: 0.5605 (OUTLIER) cc_final: 0.5209 (p0) REVERT: C 106 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6581 (pp) REVERT: C 315 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8065 (t80) REVERT: D 16 LEU cc_start: 0.8021 (tp) cc_final: 0.7612 (pp) REVERT: D 89 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7012 (mp) REVERT: E 23 VAL cc_start: 0.8279 (t) cc_final: 0.7981 (t) REVERT: E 50 MET cc_start: 0.5193 (pmm) cc_final: 0.4852 (pmm) REVERT: E 93 MET cc_start: 0.7293 (tpp) cc_final: 0.6477 (tpp) REVERT: E 94 LYS cc_start: 0.7260 (mmmm) cc_final: 0.6961 (tmtt) REVERT: E 121 MET cc_start: 0.5921 (tpp) cc_final: 0.5682 (tpp) REVERT: E 182 ASP cc_start: 0.7785 (t0) cc_final: 0.7437 (t0) REVERT: F 76 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7715 (tttt) REVERT: F 119 ARG cc_start: 0.7315 (ttm-80) cc_final: 0.6865 (mmt180) REVERT: G 63 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7911 (mtpt) REVERT: G 84 TYR cc_start: 0.7775 (p90) cc_final: 0.7343 (p90) REVERT: G 95 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6523 (pp) REVERT: G 128 GLN cc_start: 0.5858 (mp10) cc_final: 0.5567 (mp10) REVERT: G 138 PHE cc_start: 0.4608 (OUTLIER) cc_final: 0.3708 (m-10) REVERT: G 234 ARG cc_start: 0.6895 (mtt-85) cc_final: 0.6560 (mtm180) REVERT: H 35 GLN cc_start: 0.6075 (pm20) cc_final: 0.4971 (pt0) REVERT: H 41 ASP cc_start: 0.7643 (m-30) cc_final: 0.7287 (m-30) REVERT: H 77 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.6090 (ptt90) REVERT: H 105 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6795 (tt0) REVERT: H 136 LYS cc_start: 0.6756 (ptpp) cc_final: 0.6473 (ttmm) REVERT: I 68 LYS cc_start: 0.4778 (ttpp) cc_final: 0.4000 (ptmt) REVERT: J 12 LYS cc_start: 0.8565 (tttp) cc_final: 0.8286 (tttp) REVERT: J 19 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: J 67 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5929 (pp20) REVERT: K 55 SER cc_start: 0.8313 (t) cc_final: 0.8110 (p) REVERT: K 79 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8934 (t) REVERT: K 103 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7943 (mt) REVERT: K 110 GLU cc_start: 0.7746 (pp20) cc_final: 0.7119 (pp20) REVERT: K 111 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7380 (m) REVERT: K 122 LYS cc_start: 0.8006 (tttt) cc_final: 0.7555 (tptp) REVERT: K 126 ASP cc_start: 0.7637 (m-30) cc_final: 0.7386 (m-30) REVERT: K 134 LYS cc_start: 0.8455 (mmmt) cc_final: 0.7838 (mmtp) REVERT: L 42 ARG cc_start: 0.6313 (ptp-110) cc_final: 0.5956 (mtt-85) REVERT: N 30 LYS cc_start: 0.6533 (pttt) cc_final: 0.6257 (tppt) REVERT: N 90 MET cc_start: 0.5576 (OUTLIER) cc_final: 0.4658 (tmm) REVERT: N 141 GLU cc_start: 0.5147 (OUTLIER) cc_final: 0.4736 (tt0) REVERT: N 169 GLU cc_start: 0.5376 (OUTLIER) cc_final: 0.5134 (mt-10) REVERT: N 171 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: O 124 LYS cc_start: 0.7006 (mmtp) cc_final: 0.5801 (mtpm) REVERT: O 163 ILE cc_start: 0.6697 (mm) cc_final: 0.6484 (mm) REVERT: O 173 HIS cc_start: 0.3787 (t-90) cc_final: 0.3534 (t-90) REVERT: O 182 MET cc_start: 0.1603 (OUTLIER) cc_final: 0.0928 (mtp) REVERT: O 201 LYS cc_start: 0.6264 (OUTLIER) cc_final: 0.6041 (tttp) REVERT: O 205 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.5622 (mmm-85) REVERT: O 206 ARG cc_start: 0.6456 (mmm160) cc_final: 0.5875 (tpp-160) REVERT: O 243 GLU cc_start: 0.6717 (mt-10) cc_final: 0.5972 (tp30) REVERT: O 356 GLU cc_start: 0.6248 (mt-10) cc_final: 0.5627 (tm-30) REVERT: O 426 SER cc_start: 0.6503 (t) cc_final: 0.5629 (m) REVERT: O 582 ARG cc_start: 0.4173 (tpt90) cc_final: 0.3069 (mtp180) REVERT: O 584 GLN cc_start: 0.5497 (tp40) cc_final: 0.3867 (mp10) REVERT: Q 82 GLN cc_start: 0.4256 (tp-100) cc_final: 0.4008 (tp-100) REVERT: Q 153 LYS cc_start: 0.2158 (mmmt) cc_final: 0.1877 (tppt) REVERT: Q 154 LEU cc_start: 0.2518 (OUTLIER) cc_final: 0.2018 (tt) REVERT: Q 155 GLN cc_start: 0.4116 (OUTLIER) cc_final: 0.3916 (mm110) REVERT: Q 157 HIS cc_start: 0.5166 (t-90) cc_final: 0.4859 (t70) REVERT: Q 158 MET cc_start: 0.3525 (OUTLIER) cc_final: 0.1254 (ppp) REVERT: Q 183 LYS cc_start: 0.6112 (ttpp) cc_final: 0.5575 (tptp) REVERT: Q 190 MET cc_start: 0.3284 (tpp) cc_final: 0.1817 (tpt) REVERT: Q 240 LYS cc_start: 0.6818 (mmmt) cc_final: 0.5762 (mttp) REVERT: Q 241 GLU cc_start: 0.5206 (OUTLIER) cc_final: 0.4884 (pm20) REVERT: Q 479 LEU cc_start: 0.3960 (OUTLIER) cc_final: 0.3715 (tm) REVERT: Q 513 MET cc_start: 0.0469 (mpt) cc_final: 0.0070 (mtt) REVERT: S 45 PRO cc_start: 0.1903 (Cg_endo) cc_final: 0.1355 (Cg_exo) REVERT: S 285 MET cc_start: 0.4768 (ppp) cc_final: 0.3860 (tpp) REVERT: S 347 LEU cc_start: 0.4060 (OUTLIER) cc_final: 0.3755 (tm) REVERT: S 383 ILE cc_start: 0.2882 (OUTLIER) cc_final: 0.2612 (pt) REVERT: S 386 MET cc_start: 0.4474 (ttp) cc_final: 0.3535 (tmm) REVERT: S 421 ILE cc_start: 0.5607 (tt) cc_final: 0.5176 (tt) REVERT: S 456 VAL cc_start: 0.2148 (OUTLIER) cc_final: 0.1769 (p) REVERT: S 464 LEU cc_start: 0.4786 (OUTLIER) cc_final: 0.4480 (pt) REVERT: S 467 PHE cc_start: 0.6032 (m-10) cc_final: 0.5642 (m-10) REVERT: S 471 MET cc_start: 0.3200 (pmt) cc_final: 0.2908 (ppp) REVERT: S 538 LEU cc_start: 0.5695 (pp) cc_final: 0.5343 (pp) REVERT: S 749 LYS cc_start: 0.4646 (OUTLIER) cc_final: 0.4308 (ptmm) REVERT: R 29 ARG cc_start: 0.5716 (mmm-85) cc_final: 0.5359 (tpt90) REVERT: R 207 ASN cc_start: 0.5412 (t0) cc_final: 0.4558 (t0) REVERT: R 247 ILE cc_start: 0.5782 (OUTLIER) cc_final: 0.5198 (mp) REVERT: R 268 LEU cc_start: 0.7287 (tm) cc_final: 0.6898 (tp) REVERT: R 271 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6499 (mt) REVERT: R 274 MET cc_start: 0.6736 (mmp) cc_final: 0.6262 (tpt) REVERT: R 281 LYS cc_start: 0.6275 (mptp) cc_final: 0.5934 (mmtt) REVERT: R 359 MET cc_start: 0.3257 (pmm) cc_final: 0.2799 (ptp) outliers start: 253 outliers final: 93 residues processed: 1034 average time/residue: 1.1373 time to fit residues: 1554.2691 Evaluate side-chains 900 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 763 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 256 MET Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1302 TYR Chi-restraints excluded: chain A residue 1513 GLU Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 848 ILE Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1192 MET Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 141 GLU Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain N residue 171 PHE Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 182 MET Chi-restraints excluded: chain O residue 201 LYS Chi-restraints excluded: chain O residue 205 ARG Chi-restraints excluded: chain O residue 488 HIS Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain Q residue 130 GLU Chi-restraints excluded: chain Q residue 154 LEU Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 158 MET Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain Q residue 241 GLU Chi-restraints excluded: chain Q residue 479 LEU Chi-restraints excluded: chain Q residue 498 LEU Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 383 ILE Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain S residue 464 LEU Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 510 THR Chi-restraints excluded: chain S residue 668 SER Chi-restraints excluded: chain S residue 738 LYS Chi-restraints excluded: chain S residue 749 LYS Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 410 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 603 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 356 optimal weight: 5.9990 chunk 457 optimal weight: 0.0870 chunk 354 optimal weight: 0.3980 chunk 526 optimal weight: 2.9990 chunk 349 optimal weight: 2.9990 chunk 623 optimal weight: 5.9990 chunk 390 optimal weight: 3.9990 chunk 380 optimal weight: 0.7980 chunk 287 optimal weight: 0.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 344 ASN A 380 ASN A 571 HIS ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1568 ASN B 166 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 824 HIS ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN B 912 GLN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN D 30 HIS E 106 GLN E 136 ASN O 117 GLN O 131 HIS ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 422 GLN O 438 GLN Q 85 GLN Q 486 GLN ** S 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 571 HIS R 228 ASN R 263 ASN ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 1.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.213 54980 Z= 0.274 Angle : 0.757 18.931 74686 Z= 0.385 Chirality : 0.048 0.760 8352 Planarity : 0.005 0.084 9248 Dihedral : 13.894 179.767 8029 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.22 % Favored : 93.75 % Rotamer: Outliers : 4.82 % Allowed : 24.01 % Favored : 71.17 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.10), residues: 6352 helix: -0.43 (0.11), residues: 2260 sheet: -1.06 (0.18), residues: 748 loop : -1.70 (0.10), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP O 125 HIS 0.106 0.002 HIS O 488 PHE 0.063 0.002 PHE Q 438 TYR 0.021 0.002 TYR R 159 ARG 0.019 0.001 ARG B 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 961 time to evaluate : 4.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 65 TYR cc_start: 0.5793 (p90) cc_final: 0.5442 (p90) REVERT: M 166 ARG cc_start: 0.2479 (ttt180) cc_final: 0.1512 (ttt90) REVERT: M 337 MET cc_start: 0.2324 (ttm) cc_final: 0.1907 (tmm) REVERT: M 359 LYS cc_start: 0.5176 (tptt) cc_final: 0.4798 (tttm) REVERT: M 397 MET cc_start: 0.2314 (mtt) cc_final: 0.1979 (mtt) REVERT: A 5 LYS cc_start: 0.7697 (mppt) cc_final: 0.7323 (mmtp) REVERT: A 59 ARG cc_start: 0.6919 (tpm170) cc_final: 0.6280 (mtp85) REVERT: A 104 PHE cc_start: 0.6686 (m-80) cc_final: 0.6369 (m-80) REVERT: A 118 TYR cc_start: 0.7405 (m-80) cc_final: 0.7102 (m-80) REVERT: A 120 CYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7755 (t) REVERT: A 130 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8152 (mm) REVERT: A 179 ASN cc_start: 0.7205 (t0) cc_final: 0.6982 (t0) REVERT: A 209 THR cc_start: 0.8455 (m) cc_final: 0.8248 (p) REVERT: A 238 MET cc_start: 0.3555 (OUTLIER) cc_final: 0.2915 (mpp) REVERT: A 321 LYS cc_start: 0.7721 (tmmt) cc_final: 0.7300 (tppt) REVERT: A 322 ASN cc_start: 0.5563 (m-40) cc_final: 0.5166 (m-40) REVERT: A 348 LYS cc_start: 0.7608 (mtmm) cc_final: 0.7077 (mptt) REVERT: A 355 PHE cc_start: 0.8451 (m-80) cc_final: 0.8173 (m-80) REVERT: A 615 ARG cc_start: 0.7644 (mmm160) cc_final: 0.7073 (mtm180) REVERT: A 852 ASP cc_start: 0.6231 (t0) cc_final: 0.5683 (t70) REVERT: A 892 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8246 (tt) REVERT: A 934 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8334 (mmmt) REVERT: A 937 ASN cc_start: 0.7450 (m-40) cc_final: 0.6774 (t160) REVERT: A 960 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8194 (mpp) REVERT: A 961 VAL cc_start: 0.9029 (m) cc_final: 0.8755 (m) REVERT: A 1242 ILE cc_start: 0.7461 (pp) cc_final: 0.7256 (pp) REVERT: A 1269 LYS cc_start: 0.7329 (mtmt) cc_final: 0.6938 (mtpp) REVERT: A 1314 GLN cc_start: 0.7445 (tm130) cc_final: 0.7105 (tm-30) REVERT: A 1495 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.7059 (tppt) REVERT: A 1513 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6254 (tm-30) REVERT: A 1583 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7297 (t0) REVERT: A 1620 GLN cc_start: 0.8145 (tp40) cc_final: 0.7817 (tm-30) REVERT: B 16 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6507 (p90) REVERT: B 134 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8567 (mtm180) REVERT: B 173 ASN cc_start: 0.6498 (t0) cc_final: 0.6274 (t160) REVERT: B 265 ARG cc_start: 0.7213 (tpp80) cc_final: 0.6950 (tpm170) REVERT: B 280 LEU cc_start: 0.6718 (mt) cc_final: 0.6480 (mt) REVERT: B 355 ASP cc_start: 0.6069 (m-30) cc_final: 0.5813 (m-30) REVERT: B 443 LYS cc_start: 0.7286 (tptp) cc_final: 0.7046 (mttm) REVERT: B 446 MET cc_start: 0.8198 (tmt) cc_final: 0.7568 (tmm) REVERT: B 460 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8172 (mppt) REVERT: B 462 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7780 (tt0) REVERT: B 512 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6013 (tp) REVERT: B 604 ILE cc_start: 0.8053 (mt) cc_final: 0.7814 (mt) REVERT: B 724 GLN cc_start: 0.7850 (tt0) cc_final: 0.7620 (mt0) REVERT: B 808 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7263 (tptt) REVERT: B 866 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7933 (mp) REVERT: B 898 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.5966 (tp) REVERT: B 1037 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7870 (ppt-90) REVERT: B 1065 ARG cc_start: 0.7539 (ptp90) cc_final: 0.7307 (ptp-110) REVERT: B 1126 VAL cc_start: 0.7699 (OUTLIER) cc_final: 0.7482 (t) REVERT: B 1133 MET cc_start: 0.6422 (ptm) cc_final: 0.6159 (ptm) REVERT: B 1166 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6492 (ttpp) REVERT: C 34 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: C 112 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7929 (mtt) REVERT: C 128 ASP cc_start: 0.8210 (p0) cc_final: 0.7886 (p0) REVERT: C 129 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: C 174 ARG cc_start: 0.7726 (ptp-170) cc_final: 0.7500 (ptp-170) REVERT: C 315 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: D 16 LEU cc_start: 0.8190 (tp) cc_final: 0.7930 (pp) REVERT: D 37 LEU cc_start: 0.7687 (tt) cc_final: 0.7337 (mt) REVERT: E 7 ARG cc_start: 0.7567 (tpt170) cc_final: 0.6821 (tmm-80) REVERT: E 50 MET cc_start: 0.5652 (pmm) cc_final: 0.5250 (pmm) REVERT: E 93 MET cc_start: 0.7422 (tpp) cc_final: 0.6602 (tpp) REVERT: F 76 LYS cc_start: 0.8378 (ttmm) cc_final: 0.8134 (tttt) REVERT: F 110 ASP cc_start: 0.7192 (m-30) cc_final: 0.6975 (m-30) REVERT: F 119 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7277 (mmt180) REVERT: G 59 GLN cc_start: 0.7713 (mp10) cc_final: 0.7437 (mm-40) REVERT: G 63 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8274 (mtpt) REVERT: G 95 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6633 (pp) REVERT: G 138 PHE cc_start: 0.4856 (OUTLIER) cc_final: 0.3707 (m-10) REVERT: G 234 ARG cc_start: 0.7031 (mtt-85) cc_final: 0.6642 (mmm160) REVERT: H 77 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6506 (ptt90) REVERT: H 100 THR cc_start: 0.8771 (p) cc_final: 0.8516 (t) REVERT: H 126 GLU cc_start: 0.6671 (tp30) cc_final: 0.6449 (tp30) REVERT: I 32 GLN cc_start: 0.6652 (mp10) cc_final: 0.6314 (mp10) REVERT: I 68 LYS cc_start: 0.5010 (ttpp) cc_final: 0.4761 (ptmt) REVERT: J 67 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6587 (pp20) REVERT: K 54 THR cc_start: 0.8579 (t) cc_final: 0.8110 (m) REVERT: K 55 SER cc_start: 0.8404 (t) cc_final: 0.8044 (p) REVERT: K 79 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.9081 (t) REVERT: K 111 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.7918 (m) REVERT: K 122 LYS cc_start: 0.7876 (tttt) cc_final: 0.7646 (tptp) REVERT: K 134 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8390 (tppp) REVERT: N 90 MET cc_start: 0.5838 (OUTLIER) cc_final: 0.4947 (tmm) REVERT: N 141 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5978 (tt0) REVERT: O 124 LYS cc_start: 0.7268 (mmtp) cc_final: 0.6192 (mtpm) REVERT: O 156 MET cc_start: 0.5383 (tpp) cc_final: 0.4834 (ttt) REVERT: O 163 ILE cc_start: 0.6782 (mm) cc_final: 0.6528 (mm) REVERT: O 173 HIS cc_start: 0.3792 (t-90) cc_final: 0.3532 (t-90) REVERT: O 182 MET cc_start: 0.2196 (OUTLIER) cc_final: 0.1441 (mtp) REVERT: O 187 MET cc_start: 0.6605 (mtp) cc_final: 0.6226 (mtm) REVERT: O 196 LYS cc_start: 0.5481 (ttmm) cc_final: 0.4258 (tptt) REVERT: O 201 LYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6360 (tttt) REVERT: O 205 ARG cc_start: 0.6164 (OUTLIER) cc_final: 0.5859 (mmm-85) REVERT: O 206 ARG cc_start: 0.6453 (mmm160) cc_final: 0.6046 (tpp-160) REVERT: O 228 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7550 (pm20) REVERT: O 243 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6068 (tp30) REVERT: O 422 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6290 (tm-30) REVERT: O 522 GLU cc_start: 0.4714 (tt0) cc_final: 0.4391 (mm-30) REVERT: O 582 ARG cc_start: 0.4758 (tpt90) cc_final: 0.3417 (mtp180) REVERT: O 584 GLN cc_start: 0.5643 (tp40) cc_final: 0.3952 (mp10) REVERT: Q 125 PHE cc_start: 0.4535 (OUTLIER) cc_final: 0.4241 (m-10) REVERT: Q 139 LYS cc_start: 0.5592 (tttt) cc_final: 0.5371 (tmtm) REVERT: Q 183 LYS cc_start: 0.6511 (ttpp) cc_final: 0.6156 (tptp) REVERT: Q 190 MET cc_start: 0.3482 (tpp) cc_final: 0.2370 (tpt) REVERT: Q 240 LYS cc_start: 0.6909 (mmmt) cc_final: 0.5911 (mttp) REVERT: Q 334 LEU cc_start: 0.5213 (pp) cc_final: 0.4943 (tm) REVERT: Q 415 LYS cc_start: 0.8134 (tptt) cc_final: 0.7803 (ttmt) REVERT: S 45 PRO cc_start: 0.1953 (Cg_endo) cc_final: 0.1390 (Cg_exo) REVERT: S 258 SER cc_start: 0.3748 (OUTLIER) cc_final: 0.3492 (t) REVERT: S 347 LEU cc_start: 0.4008 (OUTLIER) cc_final: 0.3670 (tm) REVERT: S 386 MET cc_start: 0.3713 (ttp) cc_final: 0.3280 (tmm) REVERT: S 412 ASN cc_start: 0.4010 (t0) cc_final: 0.3646 (p0) REVERT: S 456 VAL cc_start: 0.3340 (OUTLIER) cc_final: 0.2997 (m) REVERT: S 464 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.5326 (pt) REVERT: S 467 PHE cc_start: 0.6167 (m-10) cc_final: 0.5565 (m-10) REVERT: S 471 MET cc_start: 0.3622 (OUTLIER) cc_final: 0.3372 (ppp) REVERT: S 478 MET cc_start: 0.6243 (mtm) cc_final: 0.6016 (mtm) REVERT: S 538 LEU cc_start: 0.6110 (pp) cc_final: 0.5779 (pp) REVERT: R 28 SER cc_start: 0.6250 (OUTLIER) cc_final: 0.5784 (t) REVERT: R 29 ARG cc_start: 0.5796 (mmm-85) cc_final: 0.5449 (tpt90) REVERT: R 173 MET cc_start: 0.5387 (tpt) cc_final: 0.4669 (tpt) REVERT: R 207 ASN cc_start: 0.6112 (t0) cc_final: 0.5276 (t0) REVERT: R 231 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7120 (tm) REVERT: R 271 LEU cc_start: 0.7423 (mm) cc_final: 0.7185 (mt) REVERT: R 276 GLN cc_start: 0.7568 (tt0) cc_final: 0.7338 (tt0) REVERT: R 359 MET cc_start: 0.4485 (pmm) cc_final: 0.4033 (ptp) outliers start: 279 outliers final: 91 residues processed: 1140 average time/residue: 1.2162 time to fit residues: 1806.5195 Evaluate side-chains 887 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 751 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1453 HIS Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1495 LYS Chi-restraints excluded: chain A residue 1513 GLU Chi-restraints excluded: chain A residue 1583 ASP Chi-restraints excluded: chain A residue 1655 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 808 LYS Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 896 GLN Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1166 LYS Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain N residue 90 MET Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 141 GLU Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 182 MET Chi-restraints excluded: chain O residue 201 LYS Chi-restraints excluded: chain O residue 205 ARG Chi-restraints excluded: chain O residue 228 GLN Chi-restraints excluded: chain O residue 235 GLU Chi-restraints excluded: chain O residue 422 GLN Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain O residue 526 LEU Chi-restraints excluded: chain Q residue 85 GLN Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 258 SER Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain S residue 464 LEU Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 471 MET Chi-restraints excluded: chain S residue 495 SER Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 510 THR Chi-restraints excluded: chain S residue 765 SER Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 410 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 385 optimal weight: 1.9990 chunk 249 optimal weight: 0.0070 chunk 372 optimal weight: 0.6980 chunk 187 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 396 optimal weight: 0.0970 chunk 424 optimal weight: 1.9990 chunk 308 optimal weight: 0.0060 chunk 58 optimal weight: 0.2980 chunk 490 optimal weight: 3.9990 overall best weight: 0.2212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 ASN A1047 GLN A1072 ASN A1323 HIS B 166 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 688 HIS B 739 ASN B 824 HIS ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN D 23 HIS E 106 GLN G 20 HIS O 117 GLN O 131 HIS ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 422 GLN ** O 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 472 HIS Q 85 GLN Q 87 GLN Q 131 HIS S 473 HIS S 479 HIS R 263 ASN R 272 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 1.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 54980 Z= 0.184 Angle : 0.695 17.575 74686 Z= 0.348 Chirality : 0.045 0.296 8352 Planarity : 0.004 0.077 9248 Dihedral : 13.777 179.813 8029 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.91 % Favored : 95.07 % Rotamer: Outliers : 3.28 % Allowed : 27.41 % Favored : 69.30 % 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: -1.49 (0.10), residues: 6352 helix: -0.17 (0.11), residues: 2241 sheet: -0.88 (0.19), residues: 721 loop : -1.60 (0.10), residues: 3390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP O 125 HIS 0.009 0.001 HIS S 473 PHE 0.028 0.001 PHE Q 41 TYR 0.030 0.002 TYR O 136 ARG 0.023 0.001 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 809 time to evaluate : 4.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 65 TYR cc_start: 0.5807 (p90) cc_final: 0.5443 (p90) REVERT: M 166 ARG cc_start: 0.2404 (ttt180) cc_final: 0.1497 (ttt90) REVERT: M 337 MET cc_start: 0.2322 (ttm) cc_final: 0.1894 (tmm) REVERT: M 359 LYS cc_start: 0.5263 (tptt) cc_final: 0.4964 (tttm) REVERT: M 397 MET cc_start: 0.2381 (mtt) cc_final: 0.2106 (mtp) REVERT: A 5 LYS cc_start: 0.7857 (mppt) cc_final: 0.7548 (mmtm) REVERT: A 59 ARG cc_start: 0.6785 (tpm170) cc_final: 0.6328 (mtp85) REVERT: A 104 PHE cc_start: 0.6549 (m-80) cc_final: 0.6116 (m-80) REVERT: A 120 CYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7738 (t) REVERT: A 130 ILE cc_start: 0.8426 (mm) cc_final: 0.8094 (mm) REVERT: A 209 THR cc_start: 0.8355 (m) cc_final: 0.8148 (p) REVERT: A 238 MET cc_start: 0.3261 (OUTLIER) cc_final: 0.2651 (mpp) REVERT: A 321 LYS cc_start: 0.7636 (tmmt) cc_final: 0.7177 (tppt) REVERT: A 322 ASN cc_start: 0.5536 (m-40) cc_final: 0.5210 (m-40) REVERT: A 348 LYS cc_start: 0.7727 (mtmm) cc_final: 0.7006 (mptt) REVERT: A 783 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7637 (tttm) REVERT: A 852 ASP cc_start: 0.6092 (t0) cc_final: 0.5735 (t70) REVERT: A 892 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8190 (tt) REVERT: A 900 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7750 (m) REVERT: A 934 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8253 (mmmt) REVERT: A 960 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.5551 (mpt) REVERT: A 961 VAL cc_start: 0.8975 (m) cc_final: 0.8732 (m) REVERT: A 1000 MET cc_start: 0.8998 (mtt) cc_final: 0.8505 (mtt) REVERT: A 1049 MET cc_start: 0.8380 (mmp) cc_final: 0.8139 (mmt) REVERT: A 1104 TYR cc_start: 0.7658 (t80) cc_final: 0.7447 (t80) REVERT: A 1176 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7617 (mmp-170) REVERT: A 1199 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5479 (mt0) REVERT: A 1227 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7092 (mpp) REVERT: A 1269 LYS cc_start: 0.7197 (mtmt) cc_final: 0.6746 (mtpp) REVERT: A 1485 MET cc_start: 0.7980 (tpt) cc_final: 0.7728 (tpt) REVERT: A 1513 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6304 (tm-30) REVERT: A 1583 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7251 (t0) REVERT: A 1620 GLN cc_start: 0.7972 (tp40) cc_final: 0.7612 (tm-30) REVERT: A 1655 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: B 16 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6600 (p90) REVERT: B 71 LYS cc_start: 0.4570 (mmtt) cc_final: 0.4358 (ttmm) REVERT: B 134 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8556 (mtm180) REVERT: B 355 ASP cc_start: 0.5889 (m-30) cc_final: 0.5626 (m-30) REVERT: B 443 LYS cc_start: 0.7260 (tptp) cc_final: 0.6877 (mttm) REVERT: B 462 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7762 (tt0) REVERT: B 512 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.5922 (tp) REVERT: B 604 ILE cc_start: 0.8051 (mt) cc_final: 0.7707 (mt) REVERT: B 700 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8654 (tp) REVERT: B 808 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7043 (tptt) REVERT: B 866 LEU cc_start: 0.8434 (tt) cc_final: 0.7918 (mp) REVERT: B 898 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.5984 (tp) REVERT: B 958 MET cc_start: 0.8356 (mtm) cc_final: 0.8048 (mtt) REVERT: B 977 ILE cc_start: 0.8480 (pp) cc_final: 0.8109 (pt) REVERT: B 1037 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7855 (ppt-90) REVERT: B 1065 ARG cc_start: 0.7546 (ptp90) cc_final: 0.7330 (ptp-110) REVERT: B 1126 VAL cc_start: 0.7650 (OUTLIER) cc_final: 0.7394 (t) REVERT: B 1133 MET cc_start: 0.6136 (ptm) cc_final: 0.5898 (ptm) REVERT: B 1198 TYR cc_start: 0.8430 (m-80) cc_final: 0.7554 (m-80) REVERT: C 112 MET cc_start: 0.8152 (ttm) cc_final: 0.7912 (mtm) REVERT: C 129 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: C 174 ARG cc_start: 0.7723 (ptp90) cc_final: 0.7363 (ptp90) REVERT: C 283 GLU cc_start: 0.7021 (tp30) cc_final: 0.6701 (tm-30) REVERT: D 1 MET cc_start: 0.1443 (ptm) cc_final: 0.1109 (OUTLIER) REVERT: D 16 LEU cc_start: 0.7991 (tp) cc_final: 0.7790 (pp) REVERT: D 37 LEU cc_start: 0.7701 (tt) cc_final: 0.7397 (mp) REVERT: D 48 GLU cc_start: 0.6345 (mt-10) cc_final: 0.5898 (mt-10) REVERT: D 85 SER cc_start: 0.8449 (t) cc_final: 0.8124 (p) REVERT: D 89 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7068 (mp) REVERT: E 7 ARG cc_start: 0.7448 (tpt170) cc_final: 0.6726 (tmm-80) REVERT: E 50 MET cc_start: 0.5656 (pmm) cc_final: 0.5277 (pmm) REVERT: E 93 MET cc_start: 0.7414 (tpp) cc_final: 0.6587 (tpp) REVERT: E 106 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7616 (mm110) REVERT: F 76 LYS cc_start: 0.8323 (ttmm) cc_final: 0.7989 (tttt) REVERT: F 119 ARG cc_start: 0.7673 (ttm-80) cc_final: 0.7208 (mmt180) REVERT: G 59 GLN cc_start: 0.7665 (mp10) cc_final: 0.7426 (mm-40) REVERT: G 63 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8190 (mtpt) REVERT: G 85 GLU cc_start: 0.7984 (tt0) cc_final: 0.7582 (pt0) REVERT: G 95 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6583 (pp) REVERT: G 138 PHE cc_start: 0.5210 (OUTLIER) cc_final: 0.4378 (m-10) REVERT: G 234 ARG cc_start: 0.6944 (mtt-85) cc_final: 0.6593 (mmm160) REVERT: H 22 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7752 (mtmt) REVERT: H 35 GLN cc_start: 0.6330 (pm20) cc_final: 0.5426 (pt0) REVERT: H 37 LYS cc_start: 0.8280 (ptmt) cc_final: 0.7902 (pttp) REVERT: H 77 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6546 (ptt90) REVERT: H 100 THR cc_start: 0.8730 (p) cc_final: 0.8490 (t) REVERT: H 105 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6858 (tt0) REVERT: I 49 THR cc_start: 0.7099 (OUTLIER) cc_final: 0.6861 (t) REVERT: K 54 THR cc_start: 0.8690 (t) cc_final: 0.8283 (m) REVERT: K 55 SER cc_start: 0.8338 (t) cc_final: 0.7993 (p) REVERT: K 67 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6943 (mt-10) REVERT: K 99 ASN cc_start: 0.7903 (p0) cc_final: 0.7461 (p0) REVERT: K 134 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8426 (tppp) REVERT: K 137 GLU cc_start: 0.7703 (tp30) cc_final: 0.7459 (tp30) REVERT: N 90 MET cc_start: 0.5759 (ttp) cc_final: 0.4900 (tmm) REVERT: N 141 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5839 (tt0) REVERT: O 124 LYS cc_start: 0.7316 (mmtp) cc_final: 0.6177 (mtpm) REVERT: O 163 ILE cc_start: 0.6994 (mm) cc_final: 0.6728 (mm) REVERT: O 173 HIS cc_start: 0.3765 (t-90) cc_final: 0.3140 (t70) REVERT: O 182 MET cc_start: 0.2054 (OUTLIER) cc_final: 0.1419 (mtp) REVERT: O 187 MET cc_start: 0.6472 (mtp) cc_final: 0.5889 (mmt) REVERT: O 196 LYS cc_start: 0.5345 (ttmm) cc_final: 0.4106 (tptt) REVERT: O 201 LYS cc_start: 0.6436 (tmtp) cc_final: 0.6123 (tttt) REVERT: O 206 ARG cc_start: 0.6413 (mmm160) cc_final: 0.6024 (tpp-160) REVERT: O 228 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: O 243 GLU cc_start: 0.6569 (mt-10) cc_final: 0.6123 (tp30) REVERT: O 423 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.5126 (t80) REVERT: O 426 SER cc_start: 0.7227 (t) cc_final: 0.6358 (m) REVERT: O 522 GLU cc_start: 0.4694 (tt0) cc_final: 0.4398 (mm-30) REVERT: O 582 ARG cc_start: 0.4697 (tpt90) cc_final: 0.3403 (mtp180) REVERT: O 584 GLN cc_start: 0.5659 (tp40) cc_final: 0.3950 (mp10) REVERT: Q 21 ARG cc_start: 0.5676 (mtt90) cc_final: 0.5385 (mmt90) REVERT: Q 181 TYR cc_start: 0.5029 (t80) cc_final: 0.4801 (t80) REVERT: Q 183 LYS cc_start: 0.6209 (ttpp) cc_final: 0.5931 (tptp) REVERT: Q 190 MET cc_start: 0.3835 (tpp) cc_final: 0.2597 (tpt) REVERT: Q 240 LYS cc_start: 0.6320 (mmmt) cc_final: 0.5686 (mttp) REVERT: Q 241 GLU cc_start: 0.5342 (OUTLIER) cc_final: 0.4979 (pm20) REVERT: Q 334 LEU cc_start: 0.5081 (pp) cc_final: 0.4814 (tm) REVERT: Q 415 LYS cc_start: 0.8124 (tptt) cc_final: 0.7817 (ttmt) REVERT: S 45 PRO cc_start: 0.2022 (Cg_endo) cc_final: 0.1472 (Cg_exo) REVERT: S 285 MET cc_start: 0.3999 (ppp) cc_final: 0.3460 (tpp) REVERT: S 347 LEU cc_start: 0.3929 (OUTLIER) cc_final: 0.3624 (tm) REVERT: S 386 MET cc_start: 0.3647 (ttp) cc_final: 0.2848 (tmm) REVERT: S 456 VAL cc_start: 0.3117 (OUTLIER) cc_final: 0.2749 (m) REVERT: S 464 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.5138 (OUTLIER) REVERT: S 467 PHE cc_start: 0.6242 (m-10) cc_final: 0.5435 (m-10) REVERT: S 538 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5835 (pp) REVERT: S 600 GLU cc_start: 0.5931 (tp30) cc_final: 0.4868 (pt0) REVERT: S 711 LEU cc_start: 0.2936 (OUTLIER) cc_final: 0.2608 (tt) REVERT: S 769 GLN cc_start: 0.5591 (tp-100) cc_final: 0.4807 (pt0) REVERT: R 28 SER cc_start: 0.6258 (OUTLIER) cc_final: 0.5810 (t) REVERT: R 29 ARG cc_start: 0.5806 (mmm-85) cc_final: 0.5425 (tpt90) REVERT: R 207 ASN cc_start: 0.6141 (t0) cc_final: 0.5285 (t0) REVERT: R 231 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7063 (tm) REVERT: R 271 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7147 (mt) REVERT: R 274 MET cc_start: 0.7633 (mmp) cc_final: 0.7370 (tpt) REVERT: R 359 MET cc_start: 0.4441 (pmm) cc_final: 0.3945 (ptp) outliers start: 190 outliers final: 69 residues processed: 949 average time/residue: 1.2341 time to fit residues: 1535.7459 Evaluate side-chains 837 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 728 time to evaluate : 4.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1199 GLN Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1273 THR Chi-restraints excluded: chain A residue 1453 HIS Chi-restraints excluded: chain A residue 1457 ILE Chi-restraints excluded: chain A residue 1492 ILE Chi-restraints excluded: chain A residue 1513 GLU Chi-restraints excluded: chain A residue 1583 ASP Chi-restraints excluded: chain A residue 1655 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 611 TRP Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 808 LYS Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 75 ASN Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 141 GLU Chi-restraints excluded: chain O residue 182 MET Chi-restraints excluded: chain O residue 228 GLN Chi-restraints excluded: chain O residue 423 TYR Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain Q residue 92 PHE Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 130 GLU Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain Q residue 241 GLU Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 498 LEU Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain S residue 464 LEU Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 510 THR Chi-restraints excluded: chain S residue 538 LEU Chi-restraints excluded: chain S residue 711 LEU Chi-restraints excluded: chain R residue 28 SER Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 409 HIS Chi-restraints excluded: chain R residue 410 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 567 optimal weight: 7.9990 chunk 597 optimal weight: 1.9990 chunk 545 optimal weight: 0.7980 chunk 581 optimal weight: 0.2980 chunk 349 optimal weight: 6.9990 chunk 253 optimal weight: 0.6980 chunk 456 optimal weight: 0.0770 chunk 178 optimal weight: 0.9980 chunk 525 optimal weight: 0.0060 chunk 549 optimal weight: 8.9990 chunk 579 optimal weight: 0.5980 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN ** A1323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 600 GLN B 669 GLN B 824 HIS ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS G 20 HIS G 26 ASN L 66 GLN O 117 GLN O 131 HIS ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 478 GLN Q 85 GLN R 263 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 1.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 54980 Z= 0.185 Angle : 0.693 17.088 74686 Z= 0.346 Chirality : 0.045 0.277 8352 Planarity : 0.004 0.067 9248 Dihedral : 13.710 179.833 8029 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.24 % Favored : 94.74 % Rotamer: Outliers : 2.80 % Allowed : 28.33 % Favored : 68.87 % 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: -1.37 (0.10), residues: 6352 helix: -0.03 (0.11), residues: 2237 sheet: -0.83 (0.19), residues: 728 loop : -1.54 (0.10), residues: 3387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP O 125 HIS 0.009 0.001 HIS A 571 PHE 0.025 0.001 PHE B 301 TYR 0.024 0.001 TYR G 73 ARG 0.016 0.001 ARG S 762 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 776 time to evaluate : 4.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 65 TYR cc_start: 0.5932 (p90) cc_final: 0.5562 (p90) REVERT: M 166 ARG cc_start: 0.2296 (ttt180) cc_final: 0.1401 (ttt90) REVERT: M 337 MET cc_start: 0.2324 (ttm) cc_final: 0.1900 (tmm) REVERT: M 359 LYS cc_start: 0.5308 (tptt) cc_final: 0.5064 (tttm) REVERT: M 397 MET cc_start: 0.2539 (mtt) cc_final: 0.2273 (mtp) REVERT: A 5 LYS cc_start: 0.7814 (mppt) cc_final: 0.7555 (mttm) REVERT: A 59 ARG cc_start: 0.6775 (tpm170) cc_final: 0.6333 (mtp85) REVERT: A 104 PHE cc_start: 0.6806 (m-80) cc_final: 0.6370 (m-80) REVERT: A 120 CYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7745 (t) REVERT: A 130 ILE cc_start: 0.8404 (mm) cc_final: 0.8003 (mm) REVERT: A 179 ASN cc_start: 0.6621 (t0) cc_final: 0.6197 (t0) REVERT: A 209 THR cc_start: 0.8514 (m) cc_final: 0.8313 (p) REVERT: A 238 MET cc_start: 0.3635 (OUTLIER) cc_final: 0.3049 (mpp) REVERT: A 321 LYS cc_start: 0.7787 (tmmt) cc_final: 0.7306 (tppt) REVERT: A 322 ASN cc_start: 0.5662 (m-40) cc_final: 0.5326 (m-40) REVERT: A 329 ARG cc_start: 0.7269 (ttt90) cc_final: 0.6916 (mtp85) REVERT: A 347 ARG cc_start: 0.6937 (pmm-80) cc_final: 0.4380 (ppp-140) REVERT: A 348 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7032 (mptt) REVERT: A 852 ASP cc_start: 0.6286 (t0) cc_final: 0.5853 (t70) REVERT: A 892 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8192 (tt) REVERT: A 934 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8254 (mmmt) REVERT: A 961 VAL cc_start: 0.8872 (m) cc_final: 0.8602 (m) REVERT: A 1026 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7927 (mm110) REVERT: A 1049 MET cc_start: 0.8213 (mmp) cc_final: 0.7978 (mmt) REVERT: A 1170 MET cc_start: 0.8529 (mmp) cc_final: 0.8149 (mmm) REVERT: A 1176 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.7663 (mmp-170) REVERT: A 1199 GLN cc_start: 0.6030 (OUTLIER) cc_final: 0.5626 (mt0) REVERT: A 1227 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.7019 (mpp) REVERT: A 1269 LYS cc_start: 0.7175 (mtmt) cc_final: 0.6722 (mtpp) REVERT: A 1295 ARG cc_start: 0.6460 (tpt170) cc_final: 0.6187 (tpp80) REVERT: A 1485 MET cc_start: 0.8163 (tpt) cc_final: 0.7922 (tpt) REVERT: A 1513 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6303 (tm-30) REVERT: A 1583 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7218 (t0) REVERT: B 16 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6556 (p90) REVERT: B 71 LYS cc_start: 0.4688 (mmtt) cc_final: 0.4478 (ttmm) REVERT: B 134 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8556 (mtm180) REVERT: B 154 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5807 (tt0) REVERT: B 265 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6986 (tpm170) REVERT: B 280 LEU cc_start: 0.6155 (mt) cc_final: 0.5913 (mt) REVERT: B 355 ASP cc_start: 0.5990 (m-30) cc_final: 0.5723 (m-30) REVERT: B 443 LYS cc_start: 0.7299 (tptp) cc_final: 0.6898 (mttm) REVERT: B 512 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.5941 (tp) REVERT: B 600 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7756 (tp-100) REVERT: B 604 ILE cc_start: 0.8250 (mt) cc_final: 0.7912 (mt) REVERT: B 720 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7435 (tm-30) REVERT: B 755 ASN cc_start: 0.7347 (m-40) cc_final: 0.7098 (t0) REVERT: B 808 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7233 (tptt) REVERT: B 866 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7914 (mp) REVERT: B 958 MET cc_start: 0.8388 (mtm) cc_final: 0.8074 (mtt) REVERT: B 977 ILE cc_start: 0.8471 (pp) cc_final: 0.8099 (pt) REVERT: B 1020 GLU cc_start: 0.7843 (mp0) cc_final: 0.7521 (pm20) REVERT: B 1037 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7738 (ppt170) REVERT: B 1065 ARG cc_start: 0.7615 (ptp90) cc_final: 0.7387 (ptp-110) REVERT: B 1126 VAL cc_start: 0.7750 (OUTLIER) cc_final: 0.7436 (t) REVERT: B 1198 TYR cc_start: 0.8444 (m-80) cc_final: 0.7600 (m-80) REVERT: C 112 MET cc_start: 0.8347 (ttm) cc_final: 0.7986 (mtt) REVERT: C 129 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: C 174 ARG cc_start: 0.7753 (ptp90) cc_final: 0.7520 (ptp-170) REVERT: D 1 MET cc_start: 0.1213 (ptm) cc_final: 0.0957 (ptm) REVERT: D 16 LEU cc_start: 0.8029 (tp) cc_final: 0.7768 (pp) REVERT: D 37 LEU cc_start: 0.7676 (tt) cc_final: 0.7474 (mp) REVERT: D 85 SER cc_start: 0.8393 (t) cc_final: 0.8148 (p) REVERT: E 7 ARG cc_start: 0.7361 (tpt170) cc_final: 0.6654 (tmm-80) REVERT: E 93 MET cc_start: 0.7423 (tpp) cc_final: 0.6597 (tpp) REVERT: E 106 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7625 (mm110) REVERT: F 76 LYS cc_start: 0.8349 (ttmm) cc_final: 0.8012 (tttt) REVERT: F 87 LYS cc_start: 0.7148 (tttt) cc_final: 0.6879 (tttp) REVERT: F 119 ARG cc_start: 0.7829 (ttm-80) cc_final: 0.7380 (mmt180) REVERT: G 59 GLN cc_start: 0.7696 (mp10) cc_final: 0.7434 (mm-40) REVERT: G 63 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8187 (mtpt) REVERT: G 85 GLU cc_start: 0.7986 (tt0) cc_final: 0.7615 (pt0) REVERT: G 95 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6496 (pp) REVERT: G 138 PHE cc_start: 0.5195 (OUTLIER) cc_final: 0.4358 (m-10) REVERT: G 234 ARG cc_start: 0.6931 (mtt-85) cc_final: 0.6565 (mmm160) REVERT: H 22 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7816 (mtmt) REVERT: H 35 GLN cc_start: 0.6371 (pm20) cc_final: 0.5446 (pt0) REVERT: H 37 LYS cc_start: 0.8157 (ptmt) cc_final: 0.7739 (pttp) REVERT: H 41 ASP cc_start: 0.8073 (m-30) cc_final: 0.7741 (m-30) REVERT: H 77 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6642 (ptt90) REVERT: H 100 THR cc_start: 0.8738 (p) cc_final: 0.8494 (t) REVERT: I 49 THR cc_start: 0.7084 (OUTLIER) cc_final: 0.6852 (t) REVERT: I 94 MET cc_start: 0.1678 (tmt) cc_final: 0.1366 (tmm) REVERT: K 54 THR cc_start: 0.8674 (t) cc_final: 0.8316 (m) REVERT: K 55 SER cc_start: 0.8317 (t) cc_final: 0.7952 (p) REVERT: K 99 ASN cc_start: 0.8012 (p0) cc_final: 0.7485 (p0) REVERT: K 134 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8415 (tppp) REVERT: L 30 ILE cc_start: 0.8842 (mm) cc_final: 0.8264 (mm) REVERT: N 90 MET cc_start: 0.5786 (ttp) cc_final: 0.4927 (tmm) REVERT: N 141 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.6019 (tt0) REVERT: O 124 LYS cc_start: 0.7279 (mmtp) cc_final: 0.6294 (mtpm) REVERT: O 147 ILE cc_start: 0.7154 (mp) cc_final: 0.6686 (pp) REVERT: O 163 ILE cc_start: 0.6690 (mm) cc_final: 0.6430 (mm) REVERT: O 173 HIS cc_start: 0.3824 (t-90) cc_final: 0.3619 (t-90) REVERT: O 182 MET cc_start: 0.2114 (OUTLIER) cc_final: 0.1507 (mtp) REVERT: O 187 MET cc_start: 0.6586 (mtp) cc_final: 0.5943 (mmt) REVERT: O 196 LYS cc_start: 0.5350 (ttmm) cc_final: 0.4078 (tptt) REVERT: O 201 LYS cc_start: 0.6449 (tmtp) cc_final: 0.6142 (tttt) REVERT: O 206 ARG cc_start: 0.6549 (mmm160) cc_final: 0.5306 (mpp80) REVERT: O 228 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: O 243 GLU cc_start: 0.6569 (mt-10) cc_final: 0.6192 (tp30) REVERT: O 385 MET cc_start: 0.6999 (tpt) cc_final: 0.5908 (tmm) REVERT: O 478 GLN cc_start: 0.6443 (OUTLIER) cc_final: 0.6216 (tm-30) REVERT: O 490 ILE cc_start: 0.6790 (tp) cc_final: 0.6357 (tp) REVERT: O 522 GLU cc_start: 0.4707 (tt0) cc_final: 0.4428 (mm-30) REVERT: O 582 ARG cc_start: 0.4686 (tpt90) cc_final: 0.3410 (mtp180) REVERT: O 584 GLN cc_start: 0.5665 (tp40) cc_final: 0.3863 (mp10) REVERT: Q 21 ARG cc_start: 0.5832 (mtt90) cc_final: 0.5470 (mmt90) REVERT: Q 139 LYS cc_start: 0.5290 (tttt) cc_final: 0.4725 (ptpt) REVERT: Q 183 LYS cc_start: 0.6099 (ttpp) cc_final: 0.5834 (tptp) REVERT: Q 190 MET cc_start: 0.3947 (tpp) cc_final: 0.2744 (tpt) REVERT: Q 240 LYS cc_start: 0.6303 (mmmt) cc_final: 0.5687 (mttp) REVERT: Q 311 MET cc_start: 0.4830 (ppp) cc_final: 0.4572 (tmm) REVERT: Q 334 LEU cc_start: 0.5139 (pp) cc_final: 0.4817 (tm) REVERT: Q 415 LYS cc_start: 0.8146 (tptt) cc_final: 0.7827 (ttmt) REVERT: S 45 PRO cc_start: 0.1972 (Cg_endo) cc_final: 0.1453 (Cg_exo) REVERT: S 285 MET cc_start: 0.3980 (ppp) cc_final: 0.3415 (tpp) REVERT: S 347 LEU cc_start: 0.3464 (OUTLIER) cc_final: 0.3096 (tm) REVERT: S 386 MET cc_start: 0.3278 (ttp) cc_final: 0.2514 (tmm) REVERT: S 456 VAL cc_start: 0.3086 (OUTLIER) cc_final: 0.2747 (m) REVERT: S 464 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.5086 (OUTLIER) REVERT: S 471 MET cc_start: 0.4712 (ppp) cc_final: 0.4381 (ptt) REVERT: S 478 MET cc_start: 0.6690 (mtm) cc_final: 0.5767 (mmm) REVERT: S 538 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.5642 (pp) REVERT: S 600 GLU cc_start: 0.6122 (tp30) cc_final: 0.5024 (pt0) REVERT: S 711 LEU cc_start: 0.2959 (OUTLIER) cc_final: 0.2674 (tt) REVERT: S 769 GLN cc_start: 0.5538 (tp-100) cc_final: 0.4844 (pt0) REVERT: R 29 ARG cc_start: 0.5802 (mmm-85) cc_final: 0.5537 (tpt90) REVERT: R 207 ASN cc_start: 0.6081 (t0) cc_final: 0.5293 (t0) REVERT: R 231 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7366 (tm) REVERT: R 268 LEU cc_start: 0.7762 (tm) cc_final: 0.7489 (tp) REVERT: R 271 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7251 (mt) REVERT: R 274 MET cc_start: 0.7694 (mmp) cc_final: 0.7313 (tpt) REVERT: R 348 LYS cc_start: 0.7828 (mmmm) cc_final: 0.7271 (mptt) REVERT: R 359 MET cc_start: 0.4303 (pmm) cc_final: 0.3900 (ptp) outliers start: 162 outliers final: 71 residues processed: 896 average time/residue: 1.1591 time to fit residues: 1370.6222 Evaluate side-chains 829 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 722 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1026 GLN Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1199 GLN Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1492 ILE Chi-restraints excluded: chain A residue 1513 GLU Chi-restraints excluded: chain A residue 1583 ASP Chi-restraints excluded: chain A residue 1588 MET Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 265 ARG Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 808 LYS Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 141 GLU Chi-restraints excluded: chain O residue 182 MET Chi-restraints excluded: chain O residue 228 GLN Chi-restraints excluded: chain O residue 478 GLN Chi-restraints excluded: chain Q residue 85 GLN Chi-restraints excluded: chain Q residue 125 PHE Chi-restraints excluded: chain Q residue 130 GLU Chi-restraints excluded: chain Q residue 158 MET Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain Q residue 308 SER Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 498 LEU Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 247 ILE Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain S residue 464 LEU Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 510 THR Chi-restraints excluded: chain S residue 538 LEU Chi-restraints excluded: chain S residue 711 LEU Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 409 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 381 optimal weight: 4.9990 chunk 614 optimal weight: 0.8980 chunk 375 optimal weight: 5.9990 chunk 291 optimal weight: 0.8980 chunk 427 optimal weight: 0.2980 chunk 644 optimal weight: 0.7980 chunk 593 optimal weight: 3.9990 chunk 513 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 396 optimal weight: 8.9990 chunk 314 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1323 HIS B 166 GLN B 243 GLN B 295 ASN B 473 GLN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 824 HIS ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN B1038 HIS G 20 HIS H 43 ASN O 131 HIS ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 488 HIS Q 85 GLN ** R 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 1.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 54980 Z= 0.216 Angle : 0.721 16.812 74686 Z= 0.358 Chirality : 0.046 0.350 8352 Planarity : 0.004 0.073 9248 Dihedral : 13.704 179.645 8029 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 2.40 % Allowed : 29.02 % Favored : 68.58 % 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: -1.36 (0.10), residues: 6352 helix: -0.02 (0.11), residues: 2236 sheet: -0.81 (0.19), residues: 738 loop : -1.54 (0.10), residues: 3378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP O 125 HIS 0.009 0.001 HIS A 571 PHE 0.045 0.001 PHE B 301 TYR 0.031 0.002 TYR Q 269 ARG 0.015 0.001 ARG S 762 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12704 Ramachandran restraints generated. 6352 Oldfield, 0 Emsley, 6352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 746 time to evaluate : 4.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 65 TYR cc_start: 0.6031 (p90) cc_final: 0.5662 (p90) REVERT: M 166 ARG cc_start: 0.2338 (ttt180) cc_final: 0.1466 (ttt90) REVERT: M 337 MET cc_start: 0.2327 (ttm) cc_final: 0.1899 (tmm) REVERT: M 359 LYS cc_start: 0.5287 (tptt) cc_final: 0.5063 (tttm) REVERT: M 397 MET cc_start: 0.2214 (mtt) cc_final: 0.1818 (mtp) REVERT: A 5 LYS cc_start: 0.7920 (mppt) cc_final: 0.7631 (mttm) REVERT: A 59 ARG cc_start: 0.6896 (tpm170) cc_final: 0.6471 (mtp85) REVERT: A 104 PHE cc_start: 0.6848 (m-80) cc_final: 0.6414 (m-80) REVERT: A 120 CYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7875 (t) REVERT: A 130 ILE cc_start: 0.8445 (mm) cc_final: 0.8000 (mt) REVERT: A 179 ASN cc_start: 0.6650 (t0) cc_final: 0.6180 (t0) REVERT: A 209 THR cc_start: 0.8683 (m) cc_final: 0.8309 (p) REVERT: A 238 MET cc_start: 0.3895 (OUTLIER) cc_final: 0.3223 (mpp) REVERT: A 321 LYS cc_start: 0.7847 (tmmt) cc_final: 0.7385 (tppt) REVERT: A 322 ASN cc_start: 0.5797 (m-40) cc_final: 0.5367 (m110) REVERT: A 329 ARG cc_start: 0.7351 (ttt90) cc_final: 0.7003 (mtp85) REVERT: A 347 ARG cc_start: 0.6976 (pmm-80) cc_final: 0.4435 (ppp-140) REVERT: A 348 LYS cc_start: 0.7795 (mtmm) cc_final: 0.7072 (mptt) REVERT: A 435 ASN cc_start: 0.5977 (t0) cc_final: 0.5754 (t0) REVERT: A 852 ASP cc_start: 0.6638 (t0) cc_final: 0.6175 (t70) REVERT: A 892 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8237 (tt) REVERT: A 934 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8356 (mmmt) REVERT: A 960 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.5394 (mpt) REVERT: A 961 VAL cc_start: 0.8938 (m) cc_final: 0.8685 (m) REVERT: A 1026 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7993 (mm110) REVERT: A 1176 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7672 (mmp-170) REVERT: A 1199 GLN cc_start: 0.6251 (OUTLIER) cc_final: 0.5930 (mt0) REVERT: A 1219 ILE cc_start: 0.7329 (mm) cc_final: 0.6904 (OUTLIER) REVERT: A 1269 LYS cc_start: 0.7441 (mtmt) cc_final: 0.6963 (mtpp) REVERT: A 1295 ARG cc_start: 0.6573 (tpt170) cc_final: 0.6345 (tpp80) REVERT: A 1306 TYR cc_start: 0.7012 (m-80) cc_final: 0.5733 (m-80) REVERT: A 1513 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6205 (tm-30) REVERT: A 1583 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7097 (t0) REVERT: A 1588 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8232 (tpt) REVERT: B 16 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6636 (p90) REVERT: B 355 ASP cc_start: 0.6185 (m-30) cc_final: 0.5901 (m-30) REVERT: B 443 LYS cc_start: 0.7263 (tptp) cc_final: 0.6877 (mttm) REVERT: B 512 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.5982 (tp) REVERT: B 720 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7466 (tm-30) REVERT: B 808 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7349 (tptt) REVERT: B 866 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7908 (mp) REVERT: B 898 LEU cc_start: 0.6696 (pt) cc_final: 0.6122 (tp) REVERT: B 958 MET cc_start: 0.8437 (mtm) cc_final: 0.8095 (mtt) REVERT: B 977 ILE cc_start: 0.8495 (pp) cc_final: 0.8128 (pt) REVERT: B 1020 GLU cc_start: 0.7848 (mp0) cc_final: 0.7530 (pm20) REVERT: B 1037 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7663 (ppt170) REVERT: B 1126 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7561 (t) REVERT: B 1160 GLU cc_start: 0.6617 (mp0) cc_final: 0.6000 (mm-30) REVERT: C 112 MET cc_start: 0.8368 (ttm) cc_final: 0.8167 (mtm) REVERT: C 129 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: C 174 ARG cc_start: 0.7822 (ptp90) cc_final: 0.7561 (ptp-170) REVERT: D 1 MET cc_start: 0.1298 (ptm) cc_final: 0.1023 (ptm) REVERT: D 37 LEU cc_start: 0.7704 (tt) cc_final: 0.7497 (mt) REVERT: D 45 ASP cc_start: 0.7376 (t0) cc_final: 0.7087 (t0) REVERT: D 85 SER cc_start: 0.8406 (t) cc_final: 0.8174 (p) REVERT: E 7 ARG cc_start: 0.7414 (tpt170) cc_final: 0.6791 (tmm-80) REVERT: E 93 MET cc_start: 0.7474 (tpp) cc_final: 0.6732 (tpp) REVERT: E 122 LYS cc_start: 0.7011 (mmmt) cc_final: 0.6590 (mmtt) REVERT: F 76 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8049 (tttt) REVERT: F 119 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7420 (mmt180) REVERT: G 59 GLN cc_start: 0.7717 (mp10) cc_final: 0.7460 (mm-40) REVERT: G 63 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8194 (mtpt) REVERT: G 85 GLU cc_start: 0.8053 (tt0) cc_final: 0.7668 (pt0) REVERT: G 95 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6508 (pp) REVERT: G 138 PHE cc_start: 0.5134 (OUTLIER) cc_final: 0.4300 (m-10) REVERT: G 234 ARG cc_start: 0.6955 (mtt-85) cc_final: 0.6579 (mmm160) REVERT: H 22 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7895 (mtmt) REVERT: H 35 GLN cc_start: 0.6496 (pm20) cc_final: 0.5603 (pt0) REVERT: H 100 THR cc_start: 0.8746 (p) cc_final: 0.8499 (t) REVERT: K 54 THR cc_start: 0.8712 (t) cc_final: 0.8389 (m) REVERT: K 55 SER cc_start: 0.8209 (t) cc_final: 0.7896 (p) REVERT: K 98 GLU cc_start: 0.8356 (pt0) cc_final: 0.8140 (pt0) REVERT: K 99 ASN cc_start: 0.8174 (p0) cc_final: 0.7603 (p0) REVERT: K 101 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8458 (tp) REVERT: K 134 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8437 (tppp) REVERT: L 30 ILE cc_start: 0.8934 (mm) cc_final: 0.8341 (mm) REVERT: N 90 MET cc_start: 0.5912 (ttp) cc_final: 0.5055 (tmm) REVERT: N 141 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6555 (tt0) REVERT: O 124 LYS cc_start: 0.7261 (mmtp) cc_final: 0.6282 (mtpm) REVERT: O 147 ILE cc_start: 0.7258 (mp) cc_final: 0.6713 (pp) REVERT: O 163 ILE cc_start: 0.6905 (mm) cc_final: 0.6612 (mm) REVERT: O 182 MET cc_start: 0.2173 (OUTLIER) cc_final: 0.1575 (mtp) REVERT: O 187 MET cc_start: 0.6752 (mtp) cc_final: 0.6098 (mmt) REVERT: O 196 LYS cc_start: 0.5416 (ttmm) cc_final: 0.4236 (tptt) REVERT: O 201 LYS cc_start: 0.6560 (tmtp) cc_final: 0.6231 (tttt) REVERT: O 206 ARG cc_start: 0.6377 (mmm160) cc_final: 0.5521 (mpp80) REVERT: O 228 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7756 (pm20) REVERT: O 243 GLU cc_start: 0.6374 (mt-10) cc_final: 0.5927 (tp30) REVERT: O 385 MET cc_start: 0.6990 (tpt) cc_final: 0.5877 (tmm) REVERT: O 423 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.5949 (t80) REVERT: O 582 ARG cc_start: 0.4740 (tpt90) cc_final: 0.3431 (mtp180) REVERT: O 584 GLN cc_start: 0.5642 (tp40) cc_final: 0.3835 (mp10) REVERT: Q 21 ARG cc_start: 0.5890 (mtt90) cc_final: 0.5513 (mmt90) REVERT: Q 139 LYS cc_start: 0.5305 (tttt) cc_final: 0.5077 (tmtm) REVERT: Q 183 LYS cc_start: 0.6156 (ttpp) cc_final: 0.5881 (tptp) REVERT: Q 190 MET cc_start: 0.4128 (tpp) cc_final: 0.3245 (tpt) REVERT: Q 240 LYS cc_start: 0.6321 (mmmt) cc_final: 0.5857 (mttp) REVERT: Q 311 MET cc_start: 0.4633 (ppp) cc_final: 0.4393 (tmm) REVERT: Q 334 LEU cc_start: 0.5364 (pp) cc_final: 0.4887 (tm) REVERT: Q 385 PHE cc_start: 0.7179 (m-10) cc_final: 0.6918 (m-80) REVERT: Q 415 LYS cc_start: 0.8190 (tptt) cc_final: 0.7847 (ttmt) REVERT: S 45 PRO cc_start: 0.2056 (Cg_endo) cc_final: 0.1505 (Cg_exo) REVERT: S 347 LEU cc_start: 0.3498 (OUTLIER) cc_final: 0.3121 (tm) REVERT: S 357 LEU cc_start: 0.5606 (pp) cc_final: 0.5187 (mp) REVERT: S 380 MET cc_start: 0.5191 (ptp) cc_final: 0.4841 (ptm) REVERT: S 386 MET cc_start: 0.3301 (ttp) cc_final: 0.2533 (tmm) REVERT: S 412 ASN cc_start: 0.3890 (t0) cc_final: 0.3512 (p0) REVERT: S 456 VAL cc_start: 0.3304 (OUTLIER) cc_final: 0.2951 (m) REVERT: S 464 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5630 (OUTLIER) REVERT: S 471 MET cc_start: 0.4607 (ppp) cc_final: 0.4132 (ptt) REVERT: S 538 LEU cc_start: 0.5662 (OUTLIER) cc_final: 0.5378 (pp) REVERT: S 600 GLU cc_start: 0.6463 (tp30) cc_final: 0.5247 (pt0) REVERT: S 711 LEU cc_start: 0.3060 (OUTLIER) cc_final: 0.2725 (tt) REVERT: S 769 GLN cc_start: 0.5553 (tp-100) cc_final: 0.5087 (mp10) REVERT: S 777 MET cc_start: 0.3559 (pp-130) cc_final: 0.3353 (pp-130) REVERT: R 29 ARG cc_start: 0.5813 (mmm-85) cc_final: 0.5546 (tpt90) REVERT: R 207 ASN cc_start: 0.6084 (t0) cc_final: 0.5302 (t0) REVERT: R 231 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7463 (tm) REVERT: R 271 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7365 (mt) REVERT: R 348 LYS cc_start: 0.7907 (mmmm) cc_final: 0.7330 (mptt) REVERT: R 359 MET cc_start: 0.4283 (pmm) cc_final: 0.3863 (ptp) outliers start: 139 outliers final: 68 residues processed: 845 average time/residue: 1.1896 time to fit residues: 1318.2901 Evaluate side-chains 796 residues out of total 5810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 697 time to evaluate : 4.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 130 GLU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1022 CYS Chi-restraints excluded: chain A residue 1026 GLN Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1199 GLN Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1513 GLU Chi-restraints excluded: chain A residue 1583 ASP Chi-restraints excluded: chain A residue 1588 MET Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 808 LYS Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 141 GLU Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 182 MET Chi-restraints excluded: chain O residue 228 GLN Chi-restraints excluded: chain O residue 423 TYR Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain Q residue 130 GLU Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 498 LEU Chi-restraints excluded: chain Q residue 511 HIS Chi-restraints excluded: chain S residue 189 THR Chi-restraints excluded: chain S residue 247 ILE Chi-restraints excluded: chain S residue 260 LEU Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain S residue 456 VAL Chi-restraints excluded: chain S residue 464 LEU Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain S residue 506 THR Chi-restraints excluded: chain S residue 510 THR Chi-restraints excluded: chain S residue 538 LEU Chi-restraints excluded: chain S residue 711 LEU Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 409 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 647 random chunks: chunk 407 optimal weight: 0.7980 chunk 546 optimal weight: 9.9990 chunk 157 optimal weight: 0.5980 chunk 473 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 514 optimal weight: 0.4980 chunk 215 optimal weight: 4.9990 chunk 527 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1323 HIS B 166 GLN B 473 GLN B 600 GLN B 669 GLN B 824 HIS ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 HIS G 20 HIS ** G 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 131 HIS ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 478 GLN O 488 HIS Q 85 GLN S 58 HIS R 263 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.206243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.164796 restraints weight = 73224.819| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.46 r_work: 0.3670 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 666 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 667 | |-----------------------------------------------------------------------------| r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 1.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 54980 Z= 0.210 Angle : 0.716 16.494 74686 Z= 0.356 Chirality : 0.047 1.028 8352 Planarity : 0.004 0.067 9248 Dihedral : 13.662 179.636 8029 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.23 % Favored : 94.76 % Rotamer: Outliers : 2.56 % Allowed : 28.99 % Favored : 68.46 % 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: -1.27 (0.10), residues: 6352 helix: 0.06 (0.11), residues: 2236 sheet: -0.77 (0.19), residues: 741 loop : -1.50 (0.10), residues: 3375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP O 125 HIS 0.008 0.001 HIS A 571 PHE 0.074 0.002 PHE S 369 TYR 0.023 0.002 TYR O 193 ARG 0.013 0.001 ARG S 762 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22628.26 seconds wall clock time: 396 minutes 46.37 seconds (23806.37 seconds total)