Starting phenix.real_space_refine on Wed Apr 8 22:08:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cu2_45926/04_2026/9cu2_45926.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cu2_45926/04_2026/9cu2_45926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cu2_45926/04_2026/9cu2_45926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cu2_45926/04_2026/9cu2_45926.map" model { file = "/net/cci-nas-00/data/ceres_data/9cu2_45926/04_2026/9cu2_45926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cu2_45926/04_2026/9cu2_45926.cif" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Mo 4 10.26 5 Fe 76 7.16 5 P 8 5.49 5 Mg 4 5.21 5 S 384 5.16 5 C 26775 2.51 5 N 7174 2.21 5 O 11851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 131 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46276 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3790 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3871 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3874 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "E" Number of atoms: 2077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2077 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 8, 'TRANS': 265} Chain: "F" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2145 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "G" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "H" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "J" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3874 Chain: "K" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "L" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2060 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 8, 'TRANS': 263} Chain: "M" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2121 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 8, 'TRANS': 271} Chain: "N" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {' FE': 2, 'CLF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'CLF': 1, 'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 270 Classifications: {'water': 270} Link IDs: {None: 269} Chain: "B" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 346 Classifications: {'water': 346} Link IDs: {None: 345} Chain: "C" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 271 Classifications: {'water': 271} Link IDs: {None: 270} Chain: "D" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 320 Classifications: {'water': 320} Link IDs: {None: 319} Chain: "E" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 290 Classifications: {'water': 290} Link IDs: {None: 289} Chain: "F" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 280 Classifications: {'water': 280} Link IDs: {None: 279} Chain: "G" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "H" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 256 Classifications: {'water': 256} Link IDs: {None: 255} Chain: "I" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 349 Classifications: {'water': 349} Link IDs: {None: 348} Chain: "J" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 287 Classifications: {'water': 287} Link IDs: {None: 286} Chain: "K" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 368 Classifications: {'water': 368} Link IDs: {None: 367} Chain: "L" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 311 Classifications: {'water': 311} Link IDs: {None: 310} Chain: "M" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 294 Classifications: {'water': 294} Link IDs: {None: 293} Chain: "N" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 72.954 86.157 74.273 1.00 26.86 S ATOM 4549 SG CYS B 95 49.507 85.627 80.417 1.00 25.78 S ATOM 1167 SG CYS A 154 50.797 91.279 79.631 1.00 27.27 S ATOM 462 SG CYS A 62 56.227 87.569 79.391 1.00 19.07 S ATOM 649 SG CYS A 88 52.383 88.660 85.477 1.00 31.36 S ATOM 649 SG CYS A 88 52.383 88.660 85.477 1.00 31.36 S ATOM 5002 SG CYS B 153 47.561 90.084 83.163 1.00 28.97 S ATOM 4369 SG CYS B 70 48.077 83.831 86.706 1.00 24.21 S ATOM 4549 SG CYS B 95 49.507 85.627 80.417 1.00 25.78 S ATOM 10056 SG CYS C 275 66.281 45.802 141.212 1.00 47.72 S ATOM 12516 SG CYS D 95 65.222 30.148 123.707 1.00 54.79 S ATOM 9134 SG CYS C 154 69.371 28.133 126.703 1.00 39.55 S ATOM 8429 SG CYS C 62 67.059 34.080 128.330 1.00 23.14 S ATOM 8616 SG CYS C 88 70.837 34.587 124.111 1.00 39.26 S ATOM 12969 SG CYS D 153 69.966 27.616 121.477 1.00 55.16 S ATOM 12336 SG CYS D 70 67.444 32.397 117.281 1.00 43.85 S ATOM 12516 SG CYS D 95 65.222 30.148 123.707 1.00 54.79 S ATOM 18693 SG CYS F 98 44.734 115.913 49.123 1.00 6.26 S ATOM 18964 SG CYS F 133 40.296 111.104 47.283 1.00 10.87 S ATOM 16615 SG CYS E 98 45.610 109.206 48.199 1.00 2.64 S ATOM 16886 SG CYS E 133 45.199 114.059 43.873 1.00 7.88 S ATOM 20463 SG CYS G 42 41.752 103.408 60.155 1.00 39.52 S ATOM 20498 SG CYS G 47 42.778 105.837 57.804 1.00 36.84 S ATOM 20514 SG CYS G 50 47.082 106.926 61.727 1.00 36.11 S ATOM 20925 SG CYS G 102 45.738 104.162 63.508 1.00 35.06 S ATOM 23157 SG CYS H 275 52.259 151.882 74.709 1.00 26.76 S ATOM 25617 SG CYS I 95 75.465 152.676 80.453 1.00 22.71 S ATOM 22238 SG CYS H 154 74.136 147.007 79.532 1.00 27.30 S ATOM 21533 SG CYS H 62 68.693 150.583 79.395 1.00 18.87 S ATOM 21720 SG CYS H 88 72.528 149.453 85.425 1.00 28.87 S ATOM 21720 SG CYS H 88 72.528 149.453 85.425 1.00 28.87 S ATOM 26070 SG CYS I 153 77.452 148.075 83.107 1.00 31.12 S ATOM 25437 SG CYS I 70 76.975 154.261 86.679 1.00 22.79 S ATOM 25617 SG CYS I 95 75.465 152.676 80.453 1.00 22.71 S ATOM 31124 SG CYS J 275 58.559 192.288 141.112 1.00 39.58 S ATOM 33584 SG CYS K 95 60.605 207.930 123.430 1.00 53.42 S ATOM 30202 SG CYS J 154 55.721 209.886 126.605 1.00 35.92 S ATOM 29497 SG CYS J 62 57.658 204.063 128.410 1.00 20.51 S ATOM 29684 SG CYS J 88 53.792 205.322 122.465 1.00 29.42 S ATOM 29684 SG CYS J 88 53.792 205.322 122.465 1.00 29.42 S ATOM 34037 SG CYS K 153 54.962 210.724 121.816 1.00 45.76 S ATOM 33404 SG CYS K 70 57.482 205.746 117.163 1.00 33.44 S ATOM 39748 SG CYS M 98 80.299 122.224 49.209 1.00 8.96 S ATOM 40019 SG CYS M 133 84.384 127.153 47.802 1.00 14.24 S ATOM 37683 SG CYS L 98 79.258 128.918 48.244 1.00 3.81 S ATOM 37954 SG CYS L 133 79.736 124.153 43.789 1.00 3.67 S ATOM 41492 SG CYS N 42 83.185 134.751 60.267 1.00 38.75 S ATOM 41527 SG CYS N 47 82.096 132.533 57.871 1.00 38.15 S ATOM 41543 SG CYS N 50 77.805 131.268 61.669 1.00 34.53 S ATOM 41954 SG CYS N 102 79.331 133.986 63.615 1.00 32.90 S Time building chain proxies: 12.62, per 1000 atoms: 0.27 Number of scatterers: 46276 At special positions: 0 Unit cell: (126.42, 238.875, 173.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Mo 4 41.97 Fe 76 26.01 S 384 16.00 P 8 15.00 Mg 4 11.99 O 11851 8.00 N 7174 7.00 C 26775 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=32, symmetry=0 Number of additional bonds: simple=32, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES G 201 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 50 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 47 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 42 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 102 " pdb=" FES N 201 " pdb="FE2 FES N 201 " - pdb=" SG CYS N 50 " pdb="FE2 FES N 201 " - pdb=" SG CYS N 102 " pdb="FE1 FES N 201 " - pdb=" SG CYS N 47 " pdb="FE1 FES N 201 " - pdb=" SG CYS N 42 " pdb=" SF4 F 301 " pdb="FE3 SF4 F 301 " - pdb=" SG CYS E 98 " pdb="FE4 SF4 F 301 " - pdb=" SG CYS E 133 " pdb="FE2 SF4 F 301 " - pdb=" SG CYS F 133 " pdb="FE1 SF4 F 301 " - pdb=" SG CYS F 98 " pdb=" SF4 M 301 " pdb="FE3 SF4 M 301 " - pdb=" SG CYS L 98 " pdb="FE2 SF4 M 301 " - pdb=" SG CYS M 133 " pdb="FE4 SF4 M 301 " - pdb=" SG CYS L 133 " pdb="FE1 SF4 M 301 " - pdb=" SG CYS M 98 " Number of angles added : 36 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9776 Finding SS restraints... Secondary structure from input PDB file: 267 helices and 30 sheets defined 54.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.020A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 removed outlier: 4.311A pdb=" N CYS A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.927A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.644A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.241A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 264 Processing helix chain 'A' and resid 275 through 291 removed outlier: 3.661A pdb=" N MET A 279 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 283 " --> pdb=" O MET A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 317 through 347 removed outlier: 3.537A pdb=" N GLN A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 369 removed outlier: 4.580A pdb=" N GLY A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA A 366 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.515A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 433 removed outlier: 4.556A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.614A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.618A pdb=" N GLU B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 49 through 59 removed outlier: 3.531A pdb=" N GLN B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.995A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.211A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 127 through 143 removed outlier: 3.507A pdb=" N LYS B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 removed outlier: 3.711A pdb=" N PHE B 165 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 209 Processing helix chain 'B' and resid 233 through 246 removed outlier: 3.809A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 3.521A pdb=" N THR B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.989A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 5 through 20 removed outlier: 4.240A pdb=" N VAL C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 removed outlier: 4.301A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 85 through 92 removed outlier: 4.580A pdb=" N GLY C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 92 " --> pdb=" O CYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.601A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 4.136A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.304A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.293A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 211' Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.716A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 5.864A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 283 " --> pdb=" O MET C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 343 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 344 through 346 No H-bonds generated for 'chain 'C' and resid 344 through 346' Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.547A pdb=" N ILE C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY C 365 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA C 366 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 394 removed outlier: 3.556A pdb=" N TYR C 387 " --> pdb=" O HIS C 383 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 427 through 433 Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 4.003A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 31 Processing helix chain 'D' and resid 36 through 48 removed outlier: 3.507A pdb=" N THR D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 71 through 80 removed outlier: 3.627A pdb=" N ALA D 75 " --> pdb=" O GLN D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.205A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.578A pdb=" N VAL D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 125 " --> pdb=" O ASP D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.940A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 283 Processing helix chain 'D' and resid 284 through 287 Processing helix chain 'D' and resid 299 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.308A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 4.100A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.535A pdb=" N ARG D 481 " --> pdb=" O HIS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'E' and resid 15 through 30 removed outlier: 3.713A pdb=" N GLU E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N MET E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 51 Processing helix chain 'E' and resid 57 through 65 Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 72 through 77 Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.768A pdb=" N ILE E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 155 through 172 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 216 through 225 removed outlier: 3.832A pdb=" N ILE E 223 " --> pdb=" O GLN E 219 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG E 224 " --> pdb=" O ARG E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 235 through 250 Processing helix chain 'E' and resid 261 through 272 removed outlier: 3.669A pdb=" N PHE E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 30 removed outlier: 3.561A pdb=" N GLU F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 51 Processing helix chain 'F' and resid 57 through 66 Processing helix chain 'F' and resid 72 through 77 Processing helix chain 'F' and resid 100 through 114 Processing helix chain 'F' and resid 137 through 142 Processing helix chain 'F' and resid 155 through 172 removed outlier: 3.539A pdb=" N TYR F 172 " --> pdb=" O GLY F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 205 Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.578A pdb=" N ARG F 220 " --> pdb=" O ASN F 216 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG F 224 " --> pdb=" O ARG F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 235 through 250 Processing helix chain 'F' and resid 261 through 272 removed outlier: 3.794A pdb=" N PHE F 272 " --> pdb=" O LEU F 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 34 Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.919A pdb=" N ILE G 62 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'H' and resid 5 through 17 removed outlier: 3.541A pdb=" N VAL H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 20 No H-bonds generated for 'chain 'H' and resid 18 through 20' Processing helix chain 'H' and resid 21 through 30 removed outlier: 4.011A pdb=" N LYS H 30 " --> pdb=" O LYS H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 45 removed outlier: 3.520A pdb=" N LYS H 44 " --> pdb=" O GLN H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 86 through 92 Processing helix chain 'H' and resid 119 through 125 Processing helix chain 'H' and resid 127 through 142 Processing helix chain 'H' and resid 153 through 160 removed outlier: 4.309A pdb=" N GLY H 157 " --> pdb=" O GLU H 153 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU H 158 " --> pdb=" O CYS H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 175 removed outlier: 3.639A pdb=" N VAL H 166 " --> pdb=" O ASP H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 206 removed outlier: 3.516A pdb=" N HIS H 196 " --> pdb=" O SER H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 245 removed outlier: 3.776A pdb=" N LEU H 241 " --> pdb=" O SER H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 265 Processing helix chain 'H' and resid 266 through 268 No H-bonds generated for 'chain 'H' and resid 266 through 268' Processing helix chain 'H' and resid 275 through 290 removed outlier: 5.822A pdb=" N TYR H 281 " --> pdb=" O ARG H 277 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE H 282 " --> pdb=" O SER H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 314 Processing helix chain 'H' and resid 317 through 347 removed outlier: 3.580A pdb=" N GLN H 321 " --> pdb=" O ASP H 317 " (cutoff:3.500A) Proline residue: H 333 - end of helix Proline residue: H 344 - end of helix Processing helix chain 'H' and resid 358 through 369 removed outlier: 3.728A pdb=" N ILE H 364 " --> pdb=" O PRO H 360 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY H 365 " --> pdb=" O ARG H 361 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA H 366 " --> pdb=" O HIS H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 391 removed outlier: 3.566A pdb=" N MET H 391 " --> pdb=" O TYR H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 417 Processing helix chain 'H' and resid 424 through 434 removed outlier: 4.397A pdb=" N PHE H 429 " --> pdb=" O ILE H 425 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ILE H 430 " --> pdb=" O LYS H 426 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE H 431 " --> pdb=" O GLU H 427 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET H 434 " --> pdb=" O ILE H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 447 Processing helix chain 'H' and resid 451 through 468 removed outlier: 3.713A pdb=" N ALA H 457 " --> pdb=" O PHE H 453 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE H 458 " --> pdb=" O ASP H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 474 Processing helix chain 'I' and resid 10 through 15 Processing helix chain 'I' and resid 17 through 32 Processing helix chain 'I' and resid 36 through 47 Processing helix chain 'I' and resid 49 through 57 Processing helix chain 'I' and resid 70 through 80 removed outlier: 4.028A pdb=" N GLY I 74 " --> pdb=" O CYS I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 108 removed outlier: 4.464A pdb=" N VAL I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 126 Processing helix chain 'I' and resid 127 through 143 Processing helix chain 'I' and resid 152 through 158 Processing helix chain 'I' and resid 161 through 172 Processing helix chain 'I' and resid 192 through 210 removed outlier: 3.677A pdb=" N LEU I 210 " --> pdb=" O ARG I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 213 No H-bonds generated for 'chain 'I' and resid 211 through 213' Processing helix chain 'I' and resid 233 through 247 removed outlier: 3.800A pdb=" N PHE I 237 " --> pdb=" O TYR I 233 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE I 240 " --> pdb=" O ASN I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 283 removed outlier: 3.574A pdb=" N MET I 281 " --> pdb=" O THR I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 287 Processing helix chain 'I' and resid 294 through 297 removed outlier: 3.529A pdb=" N HIS I 297 " --> pdb=" O GLN I 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 294 through 297' Processing helix chain 'I' and resid 298 through 308 Processing helix chain 'I' and resid 322 through 337 Processing helix chain 'I' and resid 341 through 358 Processing helix chain 'I' and resid 358 through 363 Processing helix chain 'I' and resid 372 through 386 Processing helix chain 'I' and resid 399 through 412 Processing helix chain 'I' and resid 413 through 417 removed outlier: 4.036A pdb=" N LYS I 417 " --> pdb=" O PRO I 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 437 Processing helix chain 'I' and resid 445 through 447 No H-bonds generated for 'chain 'I' and resid 445 through 447' Processing helix chain 'I' and resid 448 through 459 Processing helix chain 'I' and resid 460 through 463 Processing helix chain 'I' and resid 478 through 482 Processing helix chain 'I' and resid 485 through 509 Processing helix chain 'I' and resid 515 through 519 Processing helix chain 'J' and resid 5 through 17 Processing helix chain 'J' and resid 18 through 20 No H-bonds generated for 'chain 'J' and resid 18 through 20' Processing helix chain 'J' and resid 21 through 31 removed outlier: 4.143A pdb=" N LYS J 30 " --> pdb=" O LYS J 26 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS J 31 " --> pdb=" O ASP J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 46 removed outlier: 4.021A pdb=" N CYS J 45 " --> pdb=" O GLN J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 68 Processing helix chain 'J' and resid 86 through 92 removed outlier: 3.648A pdb=" N SER J 92 " --> pdb=" O CYS J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 126 Processing helix chain 'J' and resid 127 through 142 Processing helix chain 'J' and resid 153 through 159 removed outlier: 4.196A pdb=" N GLY J 157 " --> pdb=" O GLU J 153 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU J 158 " --> pdb=" O CYS J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 175 removed outlier: 4.120A pdb=" N VAL J 166 " --> pdb=" O ASP J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 206 Processing helix chain 'J' and resid 233 through 245 removed outlier: 3.548A pdb=" N LEU J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 264 Processing helix chain 'J' and resid 265 through 268 Processing helix chain 'J' and resid 275 through 291 removed outlier: 5.905A pdb=" N TYR J 281 " --> pdb=" O ARG J 277 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE J 282 " --> pdb=" O SER J 278 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER J 283 " --> pdb=" O MET J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 314 Processing helix chain 'J' and resid 317 through 347 removed outlier: 3.540A pdb=" N GLN J 321 " --> pdb=" O ASP J 317 " (cutoff:3.500A) Proline residue: J 333 - end of helix Proline residue: J 344 - end of helix Processing helix chain 'J' and resid 357 through 370 removed outlier: 4.510A pdb=" N ARG J 361 " --> pdb=" O GLY J 357 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY J 365 " --> pdb=" O ARG J 361 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA J 366 " --> pdb=" O HIS J 362 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU J 370 " --> pdb=" O ALA J 366 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 394 removed outlier: 4.110A pdb=" N ARG J 389 " --> pdb=" O ASP J 385 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS J 392 " --> pdb=" O ASP J 388 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU J 393 " --> pdb=" O ARG J 389 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 417 Processing helix chain 'J' and resid 424 through 426 No H-bonds generated for 'chain 'J' and resid 424 through 426' Processing helix chain 'J' and resid 427 through 434 removed outlier: 3.547A pdb=" N PHE J 431 " --> pdb=" O GLU J 427 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS J 433 " --> pdb=" O PHE J 429 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET J 434 " --> pdb=" O ILE J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 447 Processing helix chain 'J' and resid 451 through 468 removed outlier: 3.839A pdb=" N ALA J 457 " --> pdb=" O PHE J 453 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE J 458 " --> pdb=" O ASP J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 469 through 474 removed outlier: 3.564A pdb=" N LYS J 473 " --> pdb=" O PRO J 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 15 Processing helix chain 'K' and resid 17 through 31 Processing helix chain 'K' and resid 36 through 49 removed outlier: 3.544A pdb=" N THR K 48 " --> pdb=" O PHE K 44 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR K 49 " --> pdb=" O GLN K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 57 Processing helix chain 'K' and resid 70 through 80 removed outlier: 4.100A pdb=" N GLY K 74 " --> pdb=" O CYS K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 94 No H-bonds generated for 'chain 'K' and resid 92 through 94' Processing helix chain 'K' and resid 95 through 108 Processing helix chain 'K' and resid 119 through 126 Processing helix chain 'K' and resid 127 through 143 Processing helix chain 'K' and resid 152 through 159 Processing helix chain 'K' and resid 161 through 172 Processing helix chain 'K' and resid 192 through 209 Processing helix chain 'K' and resid 233 through 248 removed outlier: 3.938A pdb=" N PHE K 237 " --> pdb=" O TYR K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 283 Processing helix chain 'K' and resid 284 through 287 Processing helix chain 'K' and resid 294 through 297 removed outlier: 3.502A pdb=" N HIS K 297 " --> pdb=" O GLN K 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 294 through 297' Processing helix chain 'K' and resid 298 through 308 Processing helix chain 'K' and resid 322 through 337 Processing helix chain 'K' and resid 341 through 363 removed outlier: 5.234A pdb=" N THR K 360 " --> pdb=" O THR K 356 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TRP K 361 " --> pdb=" O ASP K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 386 Processing helix chain 'K' and resid 399 through 412 Processing helix chain 'K' and resid 413 through 417 removed outlier: 4.096A pdb=" N LYS K 417 " --> pdb=" O PRO K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 426 through 437 Processing helix chain 'K' and resid 445 through 447 No H-bonds generated for 'chain 'K' and resid 445 through 447' Processing helix chain 'K' and resid 448 through 459 Processing helix chain 'K' and resid 460 through 463 Processing helix chain 'K' and resid 478 through 482 removed outlier: 3.565A pdb=" N ARG K 481 " --> pdb=" O HIS K 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 485 through 509 Processing helix chain 'K' and resid 515 through 519 Processing helix chain 'L' and resid 15 through 30 Processing helix chain 'L' and resid 57 through 65 Processing helix chain 'L' and resid 67 through 71 Processing helix chain 'L' and resid 100 through 114 removed outlier: 3.708A pdb=" N ILE L 104 " --> pdb=" O GLY L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 142 Processing helix chain 'L' and resid 155 through 172 Processing helix chain 'L' and resid 193 through 205 Processing helix chain 'L' and resid 216 through 225 removed outlier: 3.558A pdb=" N ARG L 224 " --> pdb=" O ARG L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 232 Processing helix chain 'L' and resid 235 through 250 removed outlier: 3.524A pdb=" N ARG L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 271 Processing helix chain 'M' and resid 15 through 30 Processing helix chain 'M' and resid 46 through 51 Processing helix chain 'M' and resid 57 through 65 Processing helix chain 'M' and resid 72 through 77 removed outlier: 3.765A pdb=" N VAL M 76 " --> pdb=" O GLU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 114 removed outlier: 3.546A pdb=" N ILE M 104 " --> pdb=" O GLY M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 136 Processing helix chain 'M' and resid 137 through 142 Processing helix chain 'M' and resid 155 through 172 Processing helix chain 'M' and resid 193 through 205 Processing helix chain 'M' and resid 216 through 224 removed outlier: 3.808A pdb=" N ARG M 224 " --> pdb=" O ARG M 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 232 Processing helix chain 'M' and resid 235 through 250 Processing helix chain 'M' and resid 261 through 271 Processing helix chain 'N' and resid 26 through 34 Processing helix chain 'N' and resid 68 through 78 Processing helix chain 'N' and resid 82 through 93 Processing helix chain 'N' and resid 102 through 104 No H-bonds generated for 'chain 'N' and resid 102 through 104' Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.197A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.975A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 8.048A pdb=" N VAL A 223 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN A 252 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 225 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N SER A 254 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLY A 227 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.485A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE B 367 " --> pdb=" O PRO B 390 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B 392 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.895A pdb=" N LEU C 399 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU C 353 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR C 377 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.737A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE C 79 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLN C 151 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE C 81 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.633A pdb=" N VAL C 223 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA C 251 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 removed outlier: 8.701A pdb=" N VAL D 114 " --> pdb=" O THR D 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.319A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.726A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE D 367 " --> pdb=" O HIS D 392 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU D 394 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU D 369 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 85 through 88 removed outlier: 4.106A pdb=" N GLY E 10 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN E 5 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N TYR E 149 " --> pdb=" O GLN E 5 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA E 7 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL E 151 " --> pdb=" O ALA E 7 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR E 9 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE E 148 " --> pdb=" O GLY E 182 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE E 184 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE E 150 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN E 186 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS E 152 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE E 209 " --> pdb=" O GLY E 181 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU E 183 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE E 211 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS E 185 " --> pdb=" O PHE E 211 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 78 through 80 removed outlier: 6.407A pdb=" N MET F 35 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASP F 126 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL F 37 " --> pdb=" O ASP F 126 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY F 10 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN F 5 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N TYR F 149 " --> pdb=" O GLN F 5 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA F 7 " --> pdb=" O TYR F 149 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL F 151 " --> pdb=" O ALA F 7 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR F 9 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE F 148 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY F 182 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 13.017A pdb=" N MET F 208 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N GLY F 181 " --> pdb=" O MET F 208 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N HIS F 210 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU F 183 " --> pdb=" O HIS F 210 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL F 212 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYS F 185 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 15 through 18 removed outlier: 6.695A pdb=" N THR G 3 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL G 113 " --> pdb=" O THR G 3 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR G 5 " --> pdb=" O VAL G 113 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 32 through 34 removed outlier: 6.173A pdb=" N VAL H 351 " --> pdb=" O VAL H 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY H 376 " --> pdb=" O VAL H 351 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE H 421 " --> pdb=" O ARG H 439 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 178 through 181 removed outlier: 4.216A pdb=" N PHE H 114 " --> pdb=" O HIS H 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 248 through 254 removed outlier: 6.478A pdb=" N VAL H 223 " --> pdb=" O CYS H 249 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA H 251 " --> pdb=" O VAL H 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 114 through 115 Processing sheet with id=AC2, first strand: chain 'I' and resid 251 through 253 removed outlier: 6.399A pdb=" N ASN I 225 " --> pdb=" O VAL I 291 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 420 through 423 removed outlier: 8.538A pdb=" N THR I 420 " --> pdb=" O GLU I 389 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL I 391 " --> pdb=" O THR I 420 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N TYR I 422 " --> pdb=" O VAL I 391 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE I 393 " --> pdb=" O TYR I 422 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N PHE I 367 " --> pdb=" O HIS I 392 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU I 394 " --> pdb=" O PHE I 367 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU I 369 " --> pdb=" O LEU I 394 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG I 366 " --> pdb=" O PHE I 441 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE I 443 " --> pdb=" O ARG I 366 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA I 368 " --> pdb=" O ILE I 443 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET I 442 " --> pdb=" O ILE I 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'J' and resid 32 through 34 removed outlier: 4.015A pdb=" N LEU J 399 " --> pdb=" O VAL J 375 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR J 401 " --> pdb=" O THR J 377 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL J 351 " --> pdb=" O VAL J 374 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY J 376 " --> pdb=" O VAL J 351 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE J 421 " --> pdb=" O ARG J 439 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 178 through 181 removed outlier: 6.187A pdb=" N ILE J 79 " --> pdb=" O SER J 149 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLN J 151 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE J 81 " --> pdb=" O GLN J 151 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE J 114 " --> pdb=" O HIS J 80 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 248 through 254 removed outlier: 6.498A pdb=" N VAL J 223 " --> pdb=" O CYS J 249 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA J 251 " --> pdb=" O VAL J 223 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN J 271 " --> pdb=" O MET J 295 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 114 through 115 Processing sheet with id=AC8, first strand: chain 'K' and resid 251 through 253 removed outlier: 6.364A pdb=" N ASN K 225 " --> pdb=" O VAL K 291 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 420 through 423 removed outlier: 8.615A pdb=" N THR K 420 " --> pdb=" O GLU K 389 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL K 391 " --> pdb=" O THR K 420 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N TYR K 422 " --> pdb=" O VAL K 391 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE K 393 " --> pdb=" O TYR K 422 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE K 367 " --> pdb=" O HIS K 392 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU K 394 " --> pdb=" O PHE K 367 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU K 369 " --> pdb=" O LEU K 394 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG K 366 " --> pdb=" O PHE K 441 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE K 443 " --> pdb=" O ARG K 366 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA K 368 " --> pdb=" O ILE K 443 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N MET K 442 " --> pdb=" O ILE K 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'L' and resid 78 through 79 removed outlier: 3.885A pdb=" N LEU L 128 " --> pdb=" O CYS L 39 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY L 10 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN L 5 " --> pdb=" O GLU L 147 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N TYR L 149 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA L 7 " --> pdb=" O TYR L 149 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL L 151 " --> pdb=" O ALA L 7 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR L 9 " --> pdb=" O VAL L 151 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE L 148 " --> pdb=" O GLY L 181 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU L 183 " --> pdb=" O ILE L 148 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE L 150 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N CYS L 185 " --> pdb=" O ILE L 150 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS L 152 " --> pdb=" O CYS L 185 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL L 212 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N CYS L 185 " --> pdb=" O VAL L 212 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 78 through 80 removed outlier: 6.490A pdb=" N MET M 35 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASP M 126 " --> pdb=" O MET M 35 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL M 37 " --> pdb=" O ASP M 126 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLN M 5 " --> pdb=" O GLU M 147 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N TYR M 149 " --> pdb=" O GLN M 5 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA M 7 " --> pdb=" O TYR M 149 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL M 151 " --> pdb=" O ALA M 7 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR M 9 " --> pdb=" O VAL M 151 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE M 148 " --> pdb=" O GLY M 181 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU M 183 " --> pdb=" O ILE M 148 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE M 150 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N CYS M 185 " --> pdb=" O ILE M 150 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS M 152 " --> pdb=" O CYS M 185 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N HIS M 210 " --> pdb=" O GLY M 181 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU M 183 " --> pdb=" O HIS M 210 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL M 212 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS M 185 " --> pdb=" O VAL M 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 15 through 18 removed outlier: 6.670A pdb=" N THR N 3 " --> pdb=" O LEU N 111 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL N 113 " --> pdb=" O THR N 3 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR N 5 " --> pdb=" O VAL N 113 " (cutoff:3.500A) 1981 hydrogen bonds defined for protein. 5709 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.62 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.84: 43169 1.84 - 2.48: 238 2.48 - 3.12: 42 3.12 - 3.76: 16 3.76 - 4.40: 8 Bond restraints: 43473 Sorted by residual: bond pdb="FE2 CLF B 602 " pdb="FE8 CLF B 602 " ideal model delta sigma weight residual 2.200 4.400 -2.200 2.00e-02 2.50e+03 1.21e+04 bond pdb="FE2 CLF D 601 " pdb="FE8 CLF D 601 " ideal model delta sigma weight residual 2.200 4.395 -2.195 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE2 CLF H 503 " pdb="FE8 CLF H 503 " ideal model delta sigma weight residual 2.200 4.394 -2.194 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE2 CLF K 602 " pdb="FE8 CLF K 602 " ideal model delta sigma weight residual 2.200 4.388 -2.188 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE5 CLF D 601 " pdb="FE6 CLF D 601 " ideal model delta sigma weight residual 2.200 3.915 -1.715 2.00e-02 2.50e+03 7.35e+03 ... (remaining 43468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.83: 58647 6.83 - 13.66: 14 13.66 - 20.49: 4 20.49 - 27.32: 0 27.32 - 34.15: 8 Bond angle restraints: 58673 Sorted by residual: angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.85 34.15 3.00e+00 1.11e-01 1.30e+02 angle pdb=" S1 CLF D 601 " pdb="FE2 CLF D 601 " pdb="FE4 CLF D 601 " ideal model delta sigma weight residual 90.00 55.97 34.03 3.00e+00 1.11e-01 1.29e+02 angle pdb=" S1 CLF H 503 " pdb="FE2 CLF H 503 " pdb="FE4 CLF H 503 " ideal model delta sigma weight residual 90.00 56.04 33.96 3.00e+00 1.11e-01 1.28e+02 angle pdb=" S1 CLF K 602 " pdb="FE2 CLF K 602 " pdb="FE4 CLF K 602 " ideal model delta sigma weight residual 90.00 56.06 33.94 3.00e+00 1.11e-01 1.28e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE1 CLF B 602 " ideal model delta sigma weight residual 90.00 61.08 28.92 3.00e+00 1.11e-01 9.29e+01 ... (remaining 58668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.81: 22848 19.81 - 39.62: 2784 39.62 - 59.43: 835 59.43 - 79.24: 118 79.24 - 99.05: 58 Dihedral angle restraints: 26643 sinusoidal: 11336 harmonic: 15307 Sorted by residual: dihedral pdb=" CA GLU E 117 " pdb=" C GLU E 117 " pdb=" N ASP E 118 " pdb=" CA ASP E 118 " ideal model delta harmonic sigma weight residual 180.00 148.88 31.12 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" C5' ADP F 302 " pdb=" O5' ADP F 302 " pdb=" PA ADP F 302 " pdb=" O2A ADP F 302 " ideal model delta sinusoidal sigma weight residual -60.00 39.06 -99.05 1 2.00e+01 2.50e-03 2.78e+01 dihedral pdb=" CA SER E 187 " pdb=" C SER E 187 " pdb=" N ARG E 188 " pdb=" CA ARG E 188 " ideal model delta harmonic sigma weight residual 180.00 154.45 25.55 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 26640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5196 0.066 - 0.131: 915 0.131 - 0.197: 126 0.197 - 0.263: 47 0.263 - 0.329: 10 Chirality restraints: 6294 Sorted by residual: chirality pdb=" CB VAL M 84 " pdb=" CA VAL M 84 " pdb=" CG1 VAL M 84 " pdb=" CG2 VAL M 84 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CB VAL H 250 " pdb=" CA VAL H 250 " pdb=" CG1 VAL H 250 " pdb=" CG2 VAL H 250 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA LEU F 196 " pdb=" N LEU F 196 " pdb=" C LEU F 196 " pdb=" CB LEU F 196 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 6291 not shown) Planarity restraints: 7553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY H 356 " -0.019 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C GLY H 356 " 0.068 2.00e-02 2.50e+03 pdb=" O GLY H 356 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY H 357 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 357 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C GLY H 357 " -0.051 2.00e-02 2.50e+03 pdb=" O GLY H 357 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU H 358 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 94 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.65e+00 pdb=" C ALA J 94 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA J 94 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY J 95 " -0.016 2.00e-02 2.50e+03 ... (remaining 7550 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 1202 2.63 - 3.20: 41154 3.20 - 3.77: 80586 3.77 - 4.33: 118567 4.33 - 4.90: 179985 Nonbonded interactions: 421494 Sorted by model distance: nonbonded pdb=" N GLU C 22 " pdb=" OE1 GLU C 22 " model vdw 2.065 3.120 nonbonded pdb=" O2B ADP M 302 " pdb="MG MG M 303 " model vdw 2.079 2.170 nonbonded pdb=" OE2 GLU K 109 " pdb="FE FE I 601 " model vdw 2.089 2.260 nonbonded pdb=" O2B ADP F 302 " pdb="MG MG F 303 " model vdw 2.090 2.170 nonbonded pdb=" OD2 ASP I 266 " pdb=" NH2 ARG I 270 " model vdw 2.124 3.120 ... (remaining 421489 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 248 or resid 250 through 502)) selection = (chain 'C' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) selection = (chain 'H' and (resid 4 through 248 or resid 250 through 502)) selection = (chain 'J' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) } ncs_group { reference = (chain 'B' and resid 2 through 523) selection = (chain 'D' and resid 2 through 523) selection = (chain 'I' and resid 2 through 523) selection = (chain 'K' and resid 2 through 523) } ncs_group { reference = (chain 'E' and (resid 3 through 82 or resid 84 through 274 or resid 301 through \ 302)) selection = (chain 'F' and (resid 3 through 274 or resid 302 through 303)) selection = (chain 'L' and (resid 3 through 82 or resid 84 through 302)) selection = (chain 'M' and (resid 3 through 82 or resid 84 through 274 or resid 302 through \ 303)) } ncs_group { reference = (chain 'G' and (resid 2 through 26 or resid 29 through 201)) selection = (chain 'N' and (resid 2 through 26 or resid 29 through 201)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 48.940 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.039 2.200 43521 Z= 1.982 Angle : 0.922 34.148 58709 Z= 0.550 Chirality : 0.055 0.329 6294 Planarity : 0.004 0.050 7553 Dihedral : 18.862 99.055 16867 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.65 % Allowed : 26.06 % Favored : 70.29 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.11), residues: 5322 helix: 0.42 (0.10), residues: 2523 sheet: 0.38 (0.21), residues: 591 loop : -0.89 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG M 224 TYR 0.021 0.002 TYR A 354 PHE 0.027 0.001 PHE B 57 TRP 0.034 0.002 TRP J 335 HIS 0.008 0.001 HIS L 210 Details of bonding type rmsd covalent geometry : bond 0.03882 (43473) covalent geometry : angle 0.88767 (58673) hydrogen bonds : bond 0.21027 ( 1981) hydrogen bonds : angle 7.43942 ( 5709) metal coordination : bond 0.01007 ( 16) metal coordination : angle 10.12149 ( 36) Misc. bond : bond 0.15870 ( 32) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 550 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.6955 (mp0) cc_final: 0.6555 (mp0) REVERT: A 245 MET cc_start: 0.8384 (ttp) cc_final: 0.8146 (ttm) REVERT: B 7 LYS cc_start: 0.7745 (tttp) cc_final: 0.6860 (tptp) REVERT: B 330 MET cc_start: 0.8086 (mtt) cc_final: 0.7281 (mtt) REVERT: B 417 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7670 (mmtm) REVERT: C 4 MET cc_start: 0.5570 (pp-130) cc_final: 0.5247 (ppp) REVERT: C 362 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.7963 (m90) REVERT: D 26 LYS cc_start: 0.8362 (mtpt) cc_final: 0.7695 (mttt) REVERT: D 112 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8549 (m) REVERT: D 404 LYS cc_start: 0.7943 (mttt) cc_final: 0.7409 (tmmt) REVERT: F 61 MET cc_start: 0.7709 (mmm) cc_final: 0.7334 (mmp) REVERT: F 174 ASN cc_start: 0.7687 (m-40) cc_final: 0.7473 (m110) REVERT: F 191 ASP cc_start: 0.5530 (OUTLIER) cc_final: 0.4209 (t70) REVERT: F 220 ARG cc_start: 0.7356 (mtm-85) cc_final: 0.6499 (mtm-85) REVERT: G 37 LYS cc_start: 0.8984 (mptt) cc_final: 0.8568 (mmtm) REVERT: H 245 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8333 (ttm) REVERT: H 288 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7080 (pt0) REVERT: H 318 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7312 (pm20) REVERT: I 7 LYS cc_start: 0.7973 (tmtt) cc_final: 0.7361 (tptp) REVERT: I 54 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7081 (pt0) REVERT: I 283 ASP cc_start: 0.7830 (m-30) cc_final: 0.7579 (t70) REVERT: J 43 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.5985 (pttm) REVERT: J 47 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7687 (tt) REVERT: J 176 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6492 (ttmm) REVERT: J 221 TYR cc_start: 0.6883 (m-80) cc_final: 0.6631 (m-80) REVERT: K 26 LYS cc_start: 0.8458 (mtpp) cc_final: 0.7756 (mttt) REVERT: K 42 GLU cc_start: 0.8228 (tt0) cc_final: 0.7964 (tm-30) REVERT: K 171 LYS cc_start: 0.7382 (ptmm) cc_final: 0.7005 (pttm) REVERT: K 404 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7759 (tmmt) REVERT: M 3 MET cc_start: 0.6201 (tpt) cc_final: 0.5934 (tpp) outliers start: 166 outliers final: 36 residues processed: 656 average time/residue: 0.8770 time to fit residues: 698.2623 Evaluate side-chains 526 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 482 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 359 ARG Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain J residue 286 MET Chi-restraints excluded: chain J residue 359 ARG Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 222 GLU Chi-restraints excluded: chain L residue 226 MET Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 258 ASN Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 127 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 265 optimal weight: 10.0000 chunk 523 optimal weight: 0.8980 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 199 ASN C 383 HIS C 432 GLN ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN E 216 ASN J 41 GLN J 98 ASN J 199 ASN J 384 ASN ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 167 ASN M 5 GLN M 51 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.147382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.107104 restraints weight = 64923.600| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.51 r_work: 0.3163 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.358 43521 Z= 0.286 Angle : 0.784 30.648 58709 Z= 0.365 Chirality : 0.047 0.239 6294 Planarity : 0.005 0.057 7553 Dihedral : 7.064 119.365 6620 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.51 % Allowed : 23.59 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.11), residues: 5322 helix: 0.88 (0.10), residues: 2560 sheet: 0.00 (0.19), residues: 650 loop : -0.88 (0.12), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 96 TYR 0.021 0.002 TYR A 379 PHE 0.017 0.002 PHE D 44 TRP 0.024 0.002 TRP J 335 HIS 0.008 0.001 HIS K 297 Details of bonding type rmsd covalent geometry : bond 0.00581 (43473) covalent geometry : angle 0.74891 (58673) hydrogen bonds : bond 0.05953 ( 1981) hydrogen bonds : angle 5.56930 ( 5709) metal coordination : bond 0.01249 ( 16) metal coordination : angle 9.44190 ( 36) Misc. bond : bond 0.16583 ( 32) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 496 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7284 (mp0) cc_final: 0.6834 (mp0) REVERT: B 7 LYS cc_start: 0.7974 (tttp) cc_final: 0.7118 (tptp) REVERT: B 50 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7694 (tttt) REVERT: B 330 MET cc_start: 0.8265 (mtt) cc_final: 0.7530 (mtt) REVERT: B 453 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7367 (ttm-80) REVERT: B 503 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8018 (tm-30) REVERT: C 4 MET cc_start: 0.5673 (pp-130) cc_final: 0.5369 (ppp) REVERT: C 25 ARG cc_start: 0.6985 (ttp-110) cc_final: 0.6719 (ttp-110) REVERT: C 98 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8143 (m110) REVERT: C 362 HIS cc_start: 0.8452 (OUTLIER) cc_final: 0.8048 (m90) REVERT: D 7 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7024 (mmmt) REVERT: D 26 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7707 (mttt) REVERT: D 51 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: D 258 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7468 (pp20) REVERT: D 404 LYS cc_start: 0.7858 (mttt) cc_final: 0.7363 (tmmt) REVERT: D 461 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: E 4 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6906 (ptp-170) REVERT: E 159 MET cc_start: 0.7661 (mtp) cc_final: 0.7335 (mtp) REVERT: F 33 LYS cc_start: 0.6966 (mtmp) cc_final: 0.6729 (mtmp) REVERT: F 61 MET cc_start: 0.7554 (mmm) cc_final: 0.7076 (mpm) REVERT: F 191 ASP cc_start: 0.5766 (OUTLIER) cc_final: 0.4264 (t70) REVERT: F 197 ILE cc_start: 0.6579 (OUTLIER) cc_final: 0.5992 (mp) REVERT: F 220 ARG cc_start: 0.6910 (mtm-85) cc_final: 0.6142 (mtm-85) REVERT: G 37 LYS cc_start: 0.9131 (mptt) cc_final: 0.8704 (mmtm) REVERT: G 92 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.7899 (mtm-85) REVERT: H 6 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6739 (ptm160) REVERT: H 15 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7215 (mp0) REVERT: H 17 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8738 (mp) REVERT: H 26 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8740 (ttpp) REVERT: H 245 MET cc_start: 0.8694 (ttp) cc_final: 0.8480 (ttm) REVERT: H 288 GLU cc_start: 0.7779 (tt0) cc_final: 0.7041 (pt0) REVERT: H 318 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7280 (pm20) REVERT: H 393 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7982 (mm-30) REVERT: I 7 LYS cc_start: 0.8189 (tmtt) cc_final: 0.7604 (tptp) REVERT: I 38 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: I 51 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: I 283 ASP cc_start: 0.8041 (m-30) cc_final: 0.7776 (t70) REVERT: I 461 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: J 98 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8202 (m110) REVERT: J 288 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6480 (mt-10) REVERT: J 345 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7384 (mtm180) REVERT: J 415 ARG cc_start: 0.7416 (mmm160) cc_final: 0.6730 (tpt90) REVERT: K 26 LYS cc_start: 0.8385 (mtpp) cc_final: 0.7594 (mttt) REVERT: K 42 GLU cc_start: 0.8164 (tt0) cc_final: 0.7862 (tm-30) REVERT: K 51 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: K 128 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: K 171 LYS cc_start: 0.7200 (ptmm) cc_final: 0.6940 (pttp) REVERT: K 177 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6901 (t70) REVERT: K 404 LYS cc_start: 0.7857 (mtmt) cc_final: 0.7344 (tmmt) REVERT: K 461 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8285 (pm20) REVERT: L 5 GLN cc_start: 0.8070 (mt0) cc_final: 0.7798 (mt0) REVERT: L 111 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: L 138 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7071 (tmt) REVERT: L 171 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7778 (tppt) REVERT: L 271 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6737 (pp20) REVERT: M 226 MET cc_start: 0.6727 (ptm) cc_final: 0.6384 (ptm) REVERT: M 278 GLU cc_start: 0.2807 (OUTLIER) cc_final: 0.2483 (mm-30) outliers start: 205 outliers final: 85 residues processed: 656 average time/residue: 0.8133 time to fit residues: 651.5338 Evaluate side-chains 591 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 474 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 461 GLU Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain I residue 38 ASP Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 360 THR Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain J residue 286 MET Chi-restraints excluded: chain J residue 288 GLU Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain J residue 359 ARG Chi-restraints excluded: chain J residue 377 THR Chi-restraints excluded: chain J residue 423 SER Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 258 GLU Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain K residue 461 GLU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 222 GLU Chi-restraints excluded: chain L residue 258 ASN Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 152 CYS Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain M residue 278 GLU Chi-restraints excluded: chain N residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 327 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 368 optimal weight: 8.9990 chunk 344 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 293 optimal weight: 0.4980 chunk 479 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 383 HIS ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN J 31 HIS ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN M 5 GLN M 51 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108477 restraints weight = 66605.750| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.75 r_work: 0.3163 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.342 43521 Z= 0.245 Angle : 0.745 30.876 58709 Z= 0.339 Chirality : 0.045 0.190 6294 Planarity : 0.004 0.055 7553 Dihedral : 6.512 91.769 6586 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.49 % Allowed : 23.31 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.11), residues: 5322 helix: 1.10 (0.10), residues: 2557 sheet: -0.01 (0.20), residues: 614 loop : -0.90 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 97 TYR 0.021 0.002 TYR C 99 PHE 0.013 0.001 PHE D 44 TRP 0.018 0.002 TRP J 335 HIS 0.007 0.001 HIS K 297 Details of bonding type rmsd covalent geometry : bond 0.00497 (43473) covalent geometry : angle 0.70780 (58673) hydrogen bonds : bond 0.05059 ( 1981) hydrogen bonds : angle 5.31711 ( 5709) metal coordination : bond 0.01081 ( 16) metal coordination : angle 9.43843 ( 36) Misc. bond : bond 0.14587 ( 32) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 497 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7289 (mp0) cc_final: 0.6821 (mp0) REVERT: A 215 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7890 (t) REVERT: A 480 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: B 7 LYS cc_start: 0.7925 (tttp) cc_final: 0.7043 (tptp) REVERT: B 330 MET cc_start: 0.8240 (mtt) cc_final: 0.7501 (mtt) REVERT: B 453 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7337 (ttm-80) REVERT: B 503 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: C 4 MET cc_start: 0.5665 (pp-130) cc_final: 0.5269 (ppp) REVERT: C 362 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.7961 (m90) REVERT: D 7 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7011 (mmmt) REVERT: D 26 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7673 (mttt) REVERT: D 51 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: D 133 ASP cc_start: 0.8156 (m-30) cc_final: 0.7902 (m-30) REVERT: D 404 LYS cc_start: 0.7860 (mttt) cc_final: 0.7341 (tmmt) REVERT: E 4 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6932 (ptp-170) REVERT: E 111 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7400 (mt-10) REVERT: E 112 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7095 (tp30) REVERT: E 138 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7066 (tmt) REVERT: E 142 GLU cc_start: 0.8374 (mp0) cc_final: 0.7971 (mp0) REVERT: E 155 GLU cc_start: 0.6142 (mt-10) cc_final: 0.5597 (mt-10) REVERT: E 159 MET cc_start: 0.7663 (mtp) cc_final: 0.7365 (mtp) REVERT: F 33 LYS cc_start: 0.6917 (mtmp) cc_final: 0.6702 (mtmp) REVERT: F 61 MET cc_start: 0.7487 (mmm) cc_final: 0.7030 (mpm) REVERT: F 191 ASP cc_start: 0.5596 (OUTLIER) cc_final: 0.4099 (t70) REVERT: F 197 ILE cc_start: 0.6414 (OUTLIER) cc_final: 0.5827 (mp) REVERT: F 220 ARG cc_start: 0.6842 (mtm-85) cc_final: 0.6029 (mtm-85) REVERT: F 282 ILE cc_start: 0.5543 (OUTLIER) cc_final: 0.5253 (mp) REVERT: G 37 LYS cc_start: 0.9138 (mptt) cc_final: 0.8708 (mmtm) REVERT: H 15 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7236 (mp0) REVERT: H 17 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8604 (mp) REVERT: H 26 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8716 (ttpp) REVERT: H 288 GLU cc_start: 0.7785 (tt0) cc_final: 0.7022 (pt0) REVERT: H 318 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7224 (pm20) REVERT: H 393 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7995 (mm-30) REVERT: I 7 LYS cc_start: 0.8174 (tmtt) cc_final: 0.7570 (tptp) REVERT: I 283 ASP cc_start: 0.8047 (m-30) cc_final: 0.7784 (t70) REVERT: I 299 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8315 (mt-10) REVERT: I 461 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8353 (pm20) REVERT: J 22 GLU cc_start: 0.6831 (mp0) cc_final: 0.6597 (mm-30) REVERT: J 152 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8118 (m) REVERT: J 288 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6451 (mt-10) REVERT: J 345 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7357 (mtm180) REVERT: J 415 ARG cc_start: 0.7456 (mmm160) cc_final: 0.6760 (tpt90) REVERT: K 26 LYS cc_start: 0.8376 (mtpp) cc_final: 0.7575 (mttt) REVERT: K 42 GLU cc_start: 0.8151 (tt0) cc_final: 0.7788 (tm-30) REVERT: K 51 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: K 120 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6857 (mt-10) REVERT: K 128 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: K 171 LYS cc_start: 0.7196 (ptmm) cc_final: 0.6931 (pttp) REVERT: K 177 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6870 (t70) REVERT: K 404 LYS cc_start: 0.7845 (mtmt) cc_final: 0.7302 (tmmt) REVERT: L 44 ASP cc_start: 0.7653 (p0) cc_final: 0.6756 (p0) REVERT: L 117 GLU cc_start: 0.5416 (OUTLIER) cc_final: 0.4984 (pm20) REVERT: L 138 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7042 (tmt) REVERT: L 171 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7718 (tppt) REVERT: L 271 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6654 (pp20) REVERT: M 111 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7192 (mt-10) REVERT: M 226 MET cc_start: 0.6507 (ptm) cc_final: 0.6273 (ptm) REVERT: M 229 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6569 (pp) REVERT: M 278 GLU cc_start: 0.2854 (OUTLIER) cc_final: 0.2527 (mm-30) outliers start: 204 outliers final: 92 residues processed: 655 average time/residue: 0.7419 time to fit residues: 596.4686 Evaluate side-chains 598 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 473 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 258 GLU Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 GLU Chi-restraints excluded: chain I residue 360 THR Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain J residue 288 GLU Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain J residue 423 SER Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain J residue 467 LEU Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 120 GLU Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 222 GLU Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 258 ASN Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 190 THR Chi-restraints excluded: chain M residue 229 ILE Chi-restraints excluded: chain M residue 278 GLU Chi-restraints excluded: chain N residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 406 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 343 optimal weight: 4.9990 chunk 7 optimal weight: 0.0570 chunk 170 optimal weight: 1.9990 chunk 373 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 278 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 344 optimal weight: 4.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 383 HIS ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN F 51 HIS F 174 ASN ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN M 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105852 restraints weight = 68639.136| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.58 r_work: 0.3144 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.354 43521 Z= 0.276 Angle : 0.770 30.848 58709 Z= 0.354 Chirality : 0.047 0.213 6294 Planarity : 0.005 0.069 7553 Dihedral : 6.460 90.914 6577 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.19 % Allowed : 22.32 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.11), residues: 5322 helix: 1.05 (0.10), residues: 2564 sheet: -0.09 (0.20), residues: 610 loop : -0.93 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 96 TYR 0.023 0.002 TYR A 379 PHE 0.015 0.002 PHE D 44 TRP 0.017 0.002 TRP A 335 HIS 0.008 0.001 HIS K 297 Details of bonding type rmsd covalent geometry : bond 0.00578 (43473) covalent geometry : angle 0.73537 (58673) hydrogen bonds : bond 0.05436 ( 1981) hydrogen bonds : angle 5.29811 ( 5709) metal coordination : bond 0.01319 ( 16) metal coordination : angle 9.29267 ( 36) Misc. bond : bond 0.15332 ( 32) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 489 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7268 (mp0) cc_final: 0.6823 (mp0) REVERT: B 7 LYS cc_start: 0.7968 (tttp) cc_final: 0.7097 (tptp) REVERT: B 283 ASP cc_start: 0.8270 (t70) cc_final: 0.7912 (t70) REVERT: B 330 MET cc_start: 0.8296 (mtt) cc_final: 0.7578 (mtt) REVERT: B 453 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7334 (ttm-80) REVERT: B 503 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: C 4 MET cc_start: 0.5675 (pp-130) cc_final: 0.5280 (ppp) REVERT: C 19 VAL cc_start: 0.7553 (OUTLIER) cc_final: 0.7338 (t) REVERT: C 98 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8291 (m110) REVERT: D 7 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7063 (mmmt) REVERT: D 26 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7695 (mttt) REVERT: D 51 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: D 133 ASP cc_start: 0.8253 (m-30) cc_final: 0.8012 (m-30) REVERT: D 177 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6750 (t70) REVERT: D 258 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7697 (pp20) REVERT: D 404 LYS cc_start: 0.7885 (mttt) cc_final: 0.7381 (tmmt) REVERT: E 4 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6940 (ptp-170) REVERT: E 111 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: E 112 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7169 (tp30) REVERT: E 138 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7142 (tmt) REVERT: E 142 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: E 159 MET cc_start: 0.7687 (mtp) cc_final: 0.7429 (mtp) REVERT: F 61 MET cc_start: 0.7501 (mmm) cc_final: 0.7039 (mpm) REVERT: F 191 ASP cc_start: 0.5530 (OUTLIER) cc_final: 0.3914 (t70) REVERT: F 197 ILE cc_start: 0.6389 (OUTLIER) cc_final: 0.5799 (mp) REVERT: F 220 ARG cc_start: 0.6862 (mtm-85) cc_final: 0.6068 (mtm-85) REVERT: F 282 ILE cc_start: 0.5547 (OUTLIER) cc_final: 0.5265 (mp) REVERT: G 37 LYS cc_start: 0.9144 (mptt) cc_final: 0.8709 (mmtm) REVERT: G 92 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7871 (mtm-85) REVERT: H 15 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7184 (mp0) REVERT: H 17 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8644 (mp) REVERT: H 26 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8719 (ttpp) REVERT: H 288 GLU cc_start: 0.7805 (tt0) cc_final: 0.7059 (pt0) REVERT: H 318 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7234 (pm20) REVERT: H 393 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7995 (mm-30) REVERT: H 474 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8175 (mmtm) REVERT: I 7 LYS cc_start: 0.8175 (tmtt) cc_final: 0.7586 (tptp) REVERT: I 283 ASP cc_start: 0.8062 (m-30) cc_final: 0.7818 (t70) REVERT: I 299 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: I 461 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: J 98 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8275 (m110) REVERT: J 152 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8200 (m) REVERT: J 288 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: J 345 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7387 (mtm180) REVERT: J 415 ARG cc_start: 0.7406 (mmm160) cc_final: 0.6738 (tpt90) REVERT: K 4 GLN cc_start: 0.7101 (mm-40) cc_final: 0.6730 (mp-120) REVERT: K 7 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7213 (mmmt) REVERT: K 26 LYS cc_start: 0.8401 (mtpp) cc_final: 0.7500 (mttt) REVERT: K 42 GLU cc_start: 0.8100 (tt0) cc_final: 0.7703 (tm-30) REVERT: K 51 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: K 120 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6969 (mt-10) REVERT: K 128 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6948 (tt0) REVERT: K 171 LYS cc_start: 0.7236 (ptmm) cc_final: 0.6985 (pttp) REVERT: K 177 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6851 (t70) REVERT: K 247 MET cc_start: 0.8602 (ttp) cc_final: 0.8178 (ttt) REVERT: K 404 LYS cc_start: 0.7842 (mtmt) cc_final: 0.7299 (tmmt) REVERT: L 5 GLN cc_start: 0.8078 (mt0) cc_final: 0.7719 (mt0) REVERT: L 44 ASP cc_start: 0.7699 (p0) cc_final: 0.6753 (p0) REVERT: L 111 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: L 117 GLU cc_start: 0.5507 (OUTLIER) cc_final: 0.5041 (pm20) REVERT: L 171 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7778 (tppt) REVERT: L 195 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5857 (pm20) REVERT: L 208 MET cc_start: 0.6642 (ttt) cc_final: 0.6357 (ttt) REVERT: L 271 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6712 (pp20) REVERT: M 108 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8144 (t0) REVERT: M 111 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: M 229 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6764 (pp) REVERT: M 240 GLU cc_start: 0.6754 (tt0) cc_final: 0.6191 (tt0) outliers start: 236 outliers final: 114 residues processed: 680 average time/residue: 0.6172 time to fit residues: 514.8224 Evaluate side-chains 631 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 477 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 258 GLU Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 GLU Chi-restraints excluded: chain I residue 360 THR Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain J residue 288 GLU Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain J residue 362 HIS Chi-restraints excluded: chain J residue 423 SER Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain J residue 467 LEU Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 120 GLU Chi-restraints excluded: chain K residue 128 GLN Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 258 GLU Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 222 GLU Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 258 ASN Chi-restraints excluded: chain L residue 263 ASP Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 166 SER Chi-restraints excluded: chain M residue 190 THR Chi-restraints excluded: chain M residue 229 ILE Chi-restraints excluded: chain M residue 274 ILE Chi-restraints excluded: chain N residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 27 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 517 optimal weight: 0.9990 chunk 413 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 158 optimal weight: 0.5980 chunk 389 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 404 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS C 98 ASN C 383 HIS D 128 GLN ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 GLN J 98 ASN K 104 ASN K 286 ASN L 237 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.110469 restraints weight = 57549.977| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.64 r_work: 0.3209 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.298 43521 Z= 0.206 Angle : 0.707 30.789 58709 Z= 0.314 Chirality : 0.043 0.152 6294 Planarity : 0.004 0.067 7553 Dihedral : 6.101 88.328 6577 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.25 % Allowed : 23.42 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.11), residues: 5322 helix: 1.32 (0.11), residues: 2555 sheet: -0.02 (0.20), residues: 614 loop : -0.83 (0.12), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 97 TYR 0.024 0.001 TYR C 99 PHE 0.014 0.001 PHE M 109 TRP 0.017 0.001 TRP J 335 HIS 0.008 0.001 HIS J 362 Details of bonding type rmsd covalent geometry : bond 0.00407 (43473) covalent geometry : angle 0.66793 (58673) hydrogen bonds : bond 0.04033 ( 1981) hydrogen bonds : angle 5.07597 ( 5709) metal coordination : bond 0.00810 ( 16) metal coordination : angle 9.43006 ( 36) Misc. bond : bond 0.12024 ( 32) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 504 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7199 (mp0) cc_final: 0.6823 (mp0) REVERT: B 7 LYS cc_start: 0.7887 (tttp) cc_final: 0.7055 (tptp) REVERT: B 283 ASP cc_start: 0.8115 (t70) cc_final: 0.7761 (t70) REVERT: B 330 MET cc_start: 0.8199 (mtt) cc_final: 0.7453 (mtt) REVERT: B 453 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7316 (ttm-80) REVERT: B 503 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: C 4 MET cc_start: 0.5575 (pp-130) cc_final: 0.5271 (ppp) REVERT: C 362 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.7701 (m90) REVERT: D 7 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.6969 (mmmt) REVERT: D 26 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7708 (mttt) REVERT: D 51 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: D 133 ASP cc_start: 0.8123 (m-30) cc_final: 0.7881 (m-30) REVERT: D 177 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6763 (t70) REVERT: D 404 LYS cc_start: 0.7877 (mttt) cc_final: 0.7367 (tmmt) REVERT: E 4 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7119 (ptp-170) REVERT: E 111 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: E 112 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7102 (tp30) REVERT: E 138 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7147 (tmt) REVERT: E 142 GLU cc_start: 0.8355 (mp0) cc_final: 0.7955 (mp0) REVERT: E 159 MET cc_start: 0.7664 (mtp) cc_final: 0.7438 (mtp) REVERT: F 61 MET cc_start: 0.7407 (mmm) cc_final: 0.6971 (mpm) REVERT: F 191 ASP cc_start: 0.5438 (OUTLIER) cc_final: 0.3850 (t70) REVERT: F 197 ILE cc_start: 0.6359 (OUTLIER) cc_final: 0.5807 (mp) REVERT: F 200 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6315 (tp) REVERT: F 220 ARG cc_start: 0.6912 (mtm-85) cc_final: 0.6106 (mtm-85) REVERT: F 282 ILE cc_start: 0.5528 (OUTLIER) cc_final: 0.5282 (mp) REVERT: G 37 LYS cc_start: 0.9111 (mptt) cc_final: 0.8703 (mmtm) REVERT: G 92 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7839 (mtm-85) REVERT: H 6 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6473 (ptm160) REVERT: H 15 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7216 (mp0) REVERT: H 17 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8507 (mp) REVERT: H 26 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8655 (ttpp) REVERT: H 288 GLU cc_start: 0.7727 (tt0) cc_final: 0.7048 (pt0) REVERT: H 318 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7194 (pm20) REVERT: H 332 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7909 (tptt) REVERT: H 393 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7957 (mm-30) REVERT: I 7 LYS cc_start: 0.8140 (tmtt) cc_final: 0.7586 (tptp) REVERT: I 283 ASP cc_start: 0.7981 (m-30) cc_final: 0.7752 (t70) REVERT: I 299 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8248 (mt-10) REVERT: J 8 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5943 (pt0) REVERT: J 22 GLU cc_start: 0.6797 (mp0) cc_final: 0.6376 (pm20) REVERT: J 98 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8196 (m110) REVERT: J 152 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.7986 (m) REVERT: J 243 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: J 394 MET cc_start: 0.7284 (tpt) cc_final: 0.7083 (tpt) REVERT: J 415 ARG cc_start: 0.7359 (mmm160) cc_final: 0.6702 (tpt90) REVERT: K 4 GLN cc_start: 0.7066 (mm-40) cc_final: 0.6754 (mp-120) REVERT: K 7 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7248 (mmmt) REVERT: K 26 LYS cc_start: 0.8389 (mtpp) cc_final: 0.7492 (mttt) REVERT: K 42 GLU cc_start: 0.8143 (tt0) cc_final: 0.7746 (tm-30) REVERT: K 51 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: K 120 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6842 (mt-10) REVERT: K 177 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6878 (t70) REVERT: K 247 MET cc_start: 0.8533 (ttp) cc_final: 0.8146 (ttt) REVERT: K 404 LYS cc_start: 0.7817 (mtmt) cc_final: 0.7294 (tmmt) REVERT: L 30 MET cc_start: 0.5682 (mtt) cc_final: 0.5458 (mtt) REVERT: L 44 ASP cc_start: 0.7633 (p0) cc_final: 0.6708 (p0) REVERT: L 111 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: L 117 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.4927 (pm20) REVERT: L 138 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7054 (tmt) REVERT: L 157 MET cc_start: 0.7804 (mmm) cc_final: 0.7572 (mmm) REVERT: L 195 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5832 (pm20) REVERT: L 208 MET cc_start: 0.6527 (ttt) cc_final: 0.6174 (ttt) REVERT: L 271 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6559 (pp20) REVERT: M 111 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7030 (mt-10) REVERT: M 120 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7024 (mp) REVERT: M 156 MET cc_start: 0.7423 (tpp) cc_final: 0.7068 (tmm) REVERT: M 226 MET cc_start: 0.6470 (ptm) cc_final: 0.6213 (ptm) REVERT: M 240 GLU cc_start: 0.6664 (tt0) cc_final: 0.6167 (tt0) REVERT: N 92 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.7920 (mtm-85) outliers start: 193 outliers final: 70 residues processed: 658 average time/residue: 0.5192 time to fit residues: 422.5294 Evaluate side-chains 582 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 475 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 332 LYS Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 401 TYR Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 GLU Chi-restraints excluded: chain I residue 360 THR Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain J residue 243 GLU Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 120 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 345 THR Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 222 GLU Chi-restraints excluded: chain L residue 258 ASN Chi-restraints excluded: chain L residue 263 ASP Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 92 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 26 optimal weight: 0.9990 chunk 242 optimal weight: 9.9990 chunk 424 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 501 optimal weight: 9.9990 chunk 523 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 365 optimal weight: 0.9990 chunk 3 optimal weight: 0.0060 chunk 372 optimal weight: 0.9990 overall best weight: 0.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN C 98 ASN C 383 HIS ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN J 151 GLN ** K 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110998 restraints weight = 58922.822| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.68 r_work: 0.3203 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.278 43521 Z= 0.200 Angle : 0.701 30.798 58709 Z= 0.308 Chirality : 0.043 0.153 6294 Planarity : 0.004 0.047 7553 Dihedral : 5.811 85.248 6573 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.61 % Allowed : 24.14 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.11), residues: 5322 helix: 1.45 (0.11), residues: 2538 sheet: -0.02 (0.20), residues: 614 loop : -0.78 (0.12), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 97 TYR 0.017 0.001 TYR J 99 PHE 0.015 0.001 PHE C 431 TRP 0.016 0.001 TRP J 335 HIS 0.009 0.001 HIS J 362 Details of bonding type rmsd covalent geometry : bond 0.00397 (43473) covalent geometry : angle 0.66176 (58673) hydrogen bonds : bond 0.03833 ( 1981) hydrogen bonds : angle 4.99362 ( 5709) metal coordination : bond 0.00712 ( 16) metal coordination : angle 9.38714 ( 36) Misc. bond : bond 0.11219 ( 32) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 492 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7203 (mp0) cc_final: 0.6818 (mp0) REVERT: A 215 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7904 (t) REVERT: B 7 LYS cc_start: 0.7874 (tttp) cc_final: 0.6995 (tptp) REVERT: B 175 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8440 (pt) REVERT: B 283 ASP cc_start: 0.8091 (t70) cc_final: 0.7722 (t70) REVERT: B 330 MET cc_start: 0.8169 (mtt) cc_final: 0.7454 (mtt) REVERT: B 453 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7291 (ttm-80) REVERT: B 503 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: C 4 MET cc_start: 0.5617 (pp-130) cc_final: 0.5317 (ppp) REVERT: C 18 GLU cc_start: 0.7126 (pt0) cc_final: 0.6891 (tp30) REVERT: C 98 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8118 (m110) REVERT: C 362 HIS cc_start: 0.8419 (OUTLIER) cc_final: 0.7678 (m90) REVERT: D 26 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7654 (mttt) REVERT: D 51 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: D 133 ASP cc_start: 0.8049 (m-30) cc_final: 0.7799 (m-30) REVERT: D 172 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6656 (mt-10) REVERT: D 177 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6764 (t70) REVERT: D 404 LYS cc_start: 0.7843 (mttt) cc_final: 0.7319 (tmmt) REVERT: E 4 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.7093 (ptp-170) REVERT: E 112 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7071 (tp30) REVERT: E 138 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7039 (tmt) REVERT: E 142 GLU cc_start: 0.8327 (mp0) cc_final: 0.7782 (mp0) REVERT: E 159 MET cc_start: 0.7616 (mtp) cc_final: 0.7390 (mtp) REVERT: F 61 MET cc_start: 0.7346 (mmm) cc_final: 0.6920 (mpm) REVERT: F 191 ASP cc_start: 0.5341 (OUTLIER) cc_final: 0.3733 (t70) REVERT: F 197 ILE cc_start: 0.6287 (OUTLIER) cc_final: 0.5745 (mp) REVERT: F 200 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6268 (tp) REVERT: F 210 HIS cc_start: 0.8012 (t70) cc_final: 0.7342 (t70) REVERT: F 220 ARG cc_start: 0.6893 (mtm-85) cc_final: 0.6101 (mtm-85) REVERT: F 282 ILE cc_start: 0.5526 (OUTLIER) cc_final: 0.5310 (mp) REVERT: G 37 LYS cc_start: 0.9100 (mptt) cc_final: 0.8663 (mmtm) REVERT: G 92 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7804 (mtm-85) REVERT: H 6 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6449 (ptm160) REVERT: H 15 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7201 (mp0) REVERT: H 17 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8443 (mp) REVERT: H 25 ARG cc_start: 0.8170 (ttm110) cc_final: 0.7951 (ttm110) REVERT: H 26 LYS cc_start: 0.8900 (mtpt) cc_final: 0.8622 (ttpp) REVERT: H 288 GLU cc_start: 0.7752 (tt0) cc_final: 0.7028 (pt0) REVERT: H 318 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7148 (pm20) REVERT: H 332 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7852 (tptt) REVERT: H 393 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: H 473 LYS cc_start: 0.7783 (mtmm) cc_final: 0.7179 (mtmt) REVERT: H 480 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: I 7 LYS cc_start: 0.8120 (tmtt) cc_final: 0.7563 (tptp) REVERT: I 283 ASP cc_start: 0.7934 (m-30) cc_final: 0.7695 (t70) REVERT: I 299 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8247 (mt-10) REVERT: I 461 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8251 (pm20) REVERT: J 22 GLU cc_start: 0.6901 (mp0) cc_final: 0.6420 (pm20) REVERT: J 152 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7884 (m) REVERT: J 243 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.5985 (mp0) REVERT: J 345 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7324 (mtm180) REVERT: J 394 MET cc_start: 0.7185 (tpt) cc_final: 0.6960 (tpt) REVERT: J 415 ARG cc_start: 0.7290 (mmm160) cc_final: 0.6579 (tpt90) REVERT: J 476 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7932 (mm-40) REVERT: K 4 GLN cc_start: 0.7040 (mm-40) cc_final: 0.6713 (mp-120) REVERT: K 7 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7207 (mmmt) REVERT: K 26 LYS cc_start: 0.8358 (mtpp) cc_final: 0.7418 (mttt) REVERT: K 42 GLU cc_start: 0.8111 (tt0) cc_final: 0.7790 (tm-30) REVERT: K 51 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: K 120 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6855 (mt-10) REVERT: K 177 ASP cc_start: 0.7124 (OUTLIER) cc_final: 0.6856 (t70) REVERT: K 247 MET cc_start: 0.8513 (ttp) cc_final: 0.8126 (ttt) REVERT: K 404 LYS cc_start: 0.7768 (mtmt) cc_final: 0.7230 (tmmt) REVERT: L 16 LYS cc_start: 0.6707 (OUTLIER) cc_final: 0.6498 (ttpp) REVERT: L 44 ASP cc_start: 0.7651 (p0) cc_final: 0.6694 (p0) REVERT: L 111 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: L 138 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7005 (tmt) REVERT: L 155 GLU cc_start: 0.6138 (OUTLIER) cc_final: 0.5922 (tm-30) REVERT: L 195 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.5782 (pm20) REVERT: L 208 MET cc_start: 0.6616 (ttt) cc_final: 0.6227 (ttt) REVERT: L 271 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6566 (pp20) REVERT: M 33 LYS cc_start: 0.6855 (tttt) cc_final: 0.6411 (mtmm) REVERT: M 93 GLU cc_start: 0.7501 (mp0) cc_final: 0.7243 (tt0) REVERT: M 108 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8010 (t0) REVERT: M 111 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: M 156 MET cc_start: 0.7420 (tpp) cc_final: 0.7102 (tmm) REVERT: M 226 MET cc_start: 0.6406 (ptm) cc_final: 0.6176 (ptm) REVERT: M 240 GLU cc_start: 0.6630 (tt0) cc_final: 0.6154 (tt0) REVERT: M 268 LEU cc_start: 0.7372 (tp) cc_final: 0.7110 (tt) REVERT: M 271 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6211 (pt0) REVERT: N 92 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7852 (mtm-85) outliers start: 164 outliers final: 71 residues processed: 625 average time/residue: 0.5333 time to fit residues: 409.2124 Evaluate side-chains 592 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 479 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 332 LYS Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 258 GLU Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 GLU Chi-restraints excluded: chain I residue 360 THR Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain J residue 243 GLU Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain J residue 476 GLN Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 120 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 222 GLU Chi-restraints excluded: chain L residue 258 ASN Chi-restraints excluded: chain L residue 263 ASP Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 271 GLU Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 92 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 312 optimal weight: 0.5980 chunk 392 optimal weight: 3.9990 chunk 460 optimal weight: 6.9990 chunk 378 optimal weight: 10.0000 chunk 423 optimal weight: 0.6980 chunk 436 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 269 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 476 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 383 HIS ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 ASN ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN I 104 ASN ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.148813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110007 restraints weight = 60503.861| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.60 r_work: 0.3187 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.300 43521 Z= 0.225 Angle : 0.721 30.817 58709 Z= 0.321 Chirality : 0.044 0.162 6294 Planarity : 0.004 0.061 7553 Dihedral : 5.805 84.451 6570 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.74 % Allowed : 23.97 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.11), residues: 5322 helix: 1.43 (0.11), residues: 2546 sheet: -0.02 (0.20), residues: 610 loop : -0.78 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 97 TYR 0.022 0.002 TYR J 407 PHE 0.020 0.001 PHE M 109 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS J 362 Details of bonding type rmsd covalent geometry : bond 0.00456 (43473) covalent geometry : angle 0.68368 (58673) hydrogen bonds : bond 0.04307 ( 1981) hydrogen bonds : angle 5.02600 ( 5709) metal coordination : bond 0.00904 ( 16) metal coordination : angle 9.24966 ( 36) Misc. bond : bond 0.12541 ( 32) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 480 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7231 (mp0) cc_final: 0.6841 (mp0) REVERT: A 215 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.7913 (t) REVERT: B 7 LYS cc_start: 0.7948 (tttp) cc_final: 0.7097 (tptp) REVERT: B 175 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8471 (pt) REVERT: B 283 ASP cc_start: 0.8187 (t70) cc_final: 0.7838 (t70) REVERT: B 330 MET cc_start: 0.8243 (mtt) cc_final: 0.7499 (mtt) REVERT: B 453 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7318 (ttm-80) REVERT: B 503 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7927 (tm-30) REVERT: C 4 MET cc_start: 0.5609 (pp-130) cc_final: 0.5314 (ppp) REVERT: C 221 TYR cc_start: 0.6769 (m-80) cc_final: 0.6551 (m-80) REVERT: C 467 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8683 (tp) REVERT: D 4 GLN cc_start: 0.7048 (mm-40) cc_final: 0.6724 (mp-120) REVERT: D 7 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.6994 (mmmt) REVERT: D 26 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7703 (mttt) REVERT: D 51 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: D 133 ASP cc_start: 0.8127 (m-30) cc_final: 0.7886 (m-30) REVERT: D 172 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6741 (mt-10) REVERT: D 177 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6769 (t70) REVERT: D 404 LYS cc_start: 0.7890 (mttt) cc_final: 0.7382 (tmmt) REVERT: E 4 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7105 (ptp-170) REVERT: E 112 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7116 (tp30) REVERT: E 138 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7162 (tmt) REVERT: E 142 GLU cc_start: 0.8320 (mp0) cc_final: 0.7899 (mp0) REVERT: E 159 MET cc_start: 0.7658 (mtp) cc_final: 0.7426 (mtp) REVERT: E 222 GLU cc_start: 0.5925 (mm-30) cc_final: 0.5533 (tp30) REVERT: F 61 MET cc_start: 0.7422 (mmm) cc_final: 0.6984 (mpm) REVERT: F 191 ASP cc_start: 0.5359 (OUTLIER) cc_final: 0.3742 (t70) REVERT: F 197 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.5773 (mp) REVERT: F 200 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6290 (tp) REVERT: F 210 HIS cc_start: 0.8015 (t70) cc_final: 0.7324 (t70) REVERT: F 220 ARG cc_start: 0.6910 (mtm-85) cc_final: 0.6076 (mtm-85) REVERT: F 282 ILE cc_start: 0.5520 (OUTLIER) cc_final: 0.5310 (mp) REVERT: G 37 LYS cc_start: 0.9127 (mptt) cc_final: 0.8710 (mmtm) REVERT: G 92 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7869 (mtm-85) REVERT: H 6 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6622 (ptm160) REVERT: H 26 LYS cc_start: 0.8983 (mtpt) cc_final: 0.8706 (ttpp) REVERT: H 288 GLU cc_start: 0.7783 (tt0) cc_final: 0.7081 (pt0) REVERT: H 318 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7182 (pm20) REVERT: H 332 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7904 (tptt) REVERT: H 393 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7993 (mm-30) REVERT: H 480 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: I 7 LYS cc_start: 0.8156 (tmtt) cc_final: 0.7568 (tptp) REVERT: I 283 ASP cc_start: 0.8003 (m-30) cc_final: 0.7772 (t70) REVERT: I 299 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8281 (mt-10) REVERT: I 461 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8296 (pm20) REVERT: J 15 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6407 (tm-30) REVERT: J 22 GLU cc_start: 0.6916 (mp0) cc_final: 0.6435 (pm20) REVERT: J 152 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8029 (m) REVERT: J 175 SER cc_start: 0.8583 (t) cc_final: 0.8367 (t) REVERT: J 221 TYR cc_start: 0.6728 (m-80) cc_final: 0.6499 (m-80) REVERT: J 243 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.5994 (mp0) REVERT: J 345 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7352 (mtm180) REVERT: J 394 MET cc_start: 0.7229 (tpt) cc_final: 0.7024 (tpt) REVERT: J 415 ARG cc_start: 0.7316 (mmm160) cc_final: 0.6598 (tpt90) REVERT: K 4 GLN cc_start: 0.7101 (mm-40) cc_final: 0.6800 (mp-120) REVERT: K 7 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7236 (mmmt) REVERT: K 26 LYS cc_start: 0.8415 (mtpp) cc_final: 0.7481 (mttt) REVERT: K 42 GLU cc_start: 0.8131 (tt0) cc_final: 0.7809 (tm-30) REVERT: K 51 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: K 120 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6847 (mt-10) REVERT: K 177 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6806 (t70) REVERT: K 247 MET cc_start: 0.8557 (ttp) cc_final: 0.8197 (ttt) REVERT: K 404 LYS cc_start: 0.7818 (mtmt) cc_final: 0.7287 (tmmt) REVERT: L 44 ASP cc_start: 0.7716 (p0) cc_final: 0.6783 (p0) REVERT: L 111 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: L 117 GLU cc_start: 0.5396 (OUTLIER) cc_final: 0.5187 (mt-10) REVERT: L 138 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7383 (tmt) REVERT: L 155 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5895 (tm-30) REVERT: L 157 MET cc_start: 0.7836 (mmm) cc_final: 0.7431 (mmm) REVERT: L 195 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5809 (pm20) REVERT: L 208 MET cc_start: 0.6660 (ttt) cc_final: 0.6273 (ttt) REVERT: L 271 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6570 (pp20) REVERT: M 33 LYS cc_start: 0.6899 (tttt) cc_final: 0.6531 (mtmm) REVERT: M 93 GLU cc_start: 0.7521 (mp0) cc_final: 0.7266 (tt0) REVERT: M 111 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: M 120 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6867 (mp) REVERT: M 156 MET cc_start: 0.7498 (tpp) cc_final: 0.7185 (tmm) REVERT: M 240 GLU cc_start: 0.6660 (tt0) cc_final: 0.6217 (tt0) REVERT: M 268 LEU cc_start: 0.7390 (tp) cc_final: 0.7139 (tt) REVERT: M 271 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6157 (pt0) REVERT: N 92 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7924 (mtm-85) outliers start: 170 outliers final: 76 residues processed: 623 average time/residue: 0.5415 time to fit residues: 416.0443 Evaluate side-chains 597 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 479 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain E residue 4 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 332 LYS Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 258 GLU Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 GLU Chi-restraints excluded: chain I residue 360 THR Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain J residue 243 GLU Chi-restraints excluded: chain J residue 334 GLU Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain J residue 362 HIS Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 120 GLU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain L residue 16 LYS Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 155 GLU Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 222 GLU Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 258 ASN Chi-restraints excluded: chain L residue 263 ASP Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 271 GLU Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 92 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 253 optimal weight: 7.9990 chunk 446 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 268 optimal weight: 9.9990 chunk 219 optimal weight: 0.0770 chunk 359 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 152 optimal weight: 30.0000 chunk 317 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 252 GLN C 383 HIS D 128 GLN ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS E 146 GLN ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN M 108 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.151347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112427 restraints weight = 67463.200| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.84 r_work: 0.3217 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.265 43521 Z= 0.192 Angle : 0.691 30.759 58709 Z= 0.301 Chirality : 0.042 0.154 6294 Planarity : 0.004 0.051 7553 Dihedral : 5.584 81.189 6570 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.17 % Allowed : 24.41 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.11), residues: 5322 helix: 1.53 (0.11), residues: 2544 sheet: -0.06 (0.20), residues: 618 loop : -0.75 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 206 TYR 0.022 0.001 TYR J 407 PHE 0.015 0.001 PHE C 431 TRP 0.017 0.001 TRP J 335 HIS 0.008 0.001 HIS J 362 Details of bonding type rmsd covalent geometry : bond 0.00380 (43473) covalent geometry : angle 0.65175 (58673) hydrogen bonds : bond 0.03563 ( 1981) hydrogen bonds : angle 4.90318 ( 5709) metal coordination : bond 0.00665 ( 16) metal coordination : angle 9.30666 ( 36) Misc. bond : bond 0.10481 ( 32) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 502 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7208 (mp0) cc_final: 0.6806 (mp0) REVERT: A 215 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7896 (t) REVERT: B 7 LYS cc_start: 0.7900 (tttp) cc_final: 0.7031 (tptp) REVERT: B 175 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8429 (pt) REVERT: B 283 ASP cc_start: 0.8116 (t70) cc_final: 0.7759 (t70) REVERT: B 330 MET cc_start: 0.8197 (mtt) cc_final: 0.7512 (mtt) REVERT: B 503 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7944 (tm-30) REVERT: C 4 MET cc_start: 0.5456 (pp-130) cc_final: 0.5181 (ppp) REVERT: C 18 GLU cc_start: 0.6995 (pt0) cc_final: 0.6393 (tp30) REVERT: C 221 TYR cc_start: 0.6728 (m-80) cc_final: 0.6513 (m-80) REVERT: C 362 HIS cc_start: 0.8407 (OUTLIER) cc_final: 0.7699 (m90) REVERT: D 4 GLN cc_start: 0.6936 (mm-40) cc_final: 0.6606 (mp-120) REVERT: D 7 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6837 (mmmt) REVERT: D 26 LYS cc_start: 0.8306 (mtpt) cc_final: 0.7671 (mttt) REVERT: D 51 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: D 172 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6692 (mt-10) REVERT: D 404 LYS cc_start: 0.7881 (mttt) cc_final: 0.7361 (tmmt) REVERT: E 111 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: E 112 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7137 (tp30) REVERT: E 138 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7159 (tmt) REVERT: E 142 GLU cc_start: 0.8336 (mp0) cc_final: 0.7897 (mp0) REVERT: E 214 ARG cc_start: 0.5668 (tpp-160) cc_final: 0.4753 (mmm-85) REVERT: E 270 MET cc_start: 0.6628 (mtm) cc_final: 0.5758 (tpt) REVERT: F 61 MET cc_start: 0.7359 (mmm) cc_final: 0.6917 (mpm) REVERT: F 186 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7513 (t0) REVERT: F 191 ASP cc_start: 0.5283 (OUTLIER) cc_final: 0.3601 (t70) REVERT: F 197 ILE cc_start: 0.6267 (OUTLIER) cc_final: 0.5716 (mp) REVERT: F 200 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6304 (tp) REVERT: F 210 HIS cc_start: 0.7989 (t70) cc_final: 0.7270 (t70) REVERT: F 220 ARG cc_start: 0.6880 (mtm-85) cc_final: 0.6081 (mtm-85) REVERT: G 37 LYS cc_start: 0.9110 (mptt) cc_final: 0.8697 (mmtm) REVERT: G 92 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7840 (mtm-85) REVERT: H 6 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6422 (ptm160) REVERT: H 15 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7691 (pt0) REVERT: H 26 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8699 (ttpp) REVERT: H 288 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7086 (pt0) REVERT: H 318 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7138 (pm20) REVERT: H 332 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7855 (tptt) REVERT: H 393 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: H 396 ASP cc_start: 0.8173 (t70) cc_final: 0.7950 (t70) REVERT: H 473 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7129 (mtmt) REVERT: H 480 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: I 7 LYS cc_start: 0.8101 (tmtt) cc_final: 0.7554 (tptp) REVERT: I 283 ASP cc_start: 0.7956 (m-30) cc_final: 0.7729 (t70) REVERT: I 299 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8284 (mt-10) REVERT: I 461 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8233 (pm20) REVERT: J 15 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6604 (mm-30) REVERT: J 22 GLU cc_start: 0.6950 (mp0) cc_final: 0.6462 (pm20) REVERT: J 152 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7836 (m) REVERT: J 175 SER cc_start: 0.8618 (t) cc_final: 0.8397 (t) REVERT: J 221 TYR cc_start: 0.6740 (m-80) cc_final: 0.6417 (m-80) REVERT: J 243 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6477 (mt-10) REVERT: J 345 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7344 (mtm180) REVERT: J 415 ARG cc_start: 0.7285 (mmm160) cc_final: 0.6584 (tpt90) REVERT: K 4 GLN cc_start: 0.7054 (mm-40) cc_final: 0.6735 (mp-120) REVERT: K 7 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7376 (mmmt) REVERT: K 26 LYS cc_start: 0.8357 (mtpp) cc_final: 0.7486 (mttt) REVERT: K 42 GLU cc_start: 0.8173 (tt0) cc_final: 0.7843 (tm-30) REVERT: K 51 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: K 177 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6808 (t70) REVERT: K 247 MET cc_start: 0.8514 (ttp) cc_final: 0.8141 (ttt) REVERT: K 404 LYS cc_start: 0.7791 (mtmt) cc_final: 0.7262 (tmmt) REVERT: L 44 ASP cc_start: 0.7702 (p0) cc_final: 0.6803 (p0) REVERT: L 111 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: L 138 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7073 (tmt) REVERT: L 157 MET cc_start: 0.7765 (mmm) cc_final: 0.7430 (mmt) REVERT: L 195 GLU cc_start: 0.6101 (OUTLIER) cc_final: 0.5839 (pm20) REVERT: L 208 MET cc_start: 0.6608 (ttt) cc_final: 0.6157 (ttt) REVERT: L 222 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.6084 (mp0) REVERT: L 271 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6486 (pp20) REVERT: M 33 LYS cc_start: 0.6852 (tttt) cc_final: 0.6573 (mtmm) REVERT: M 93 GLU cc_start: 0.7551 (mp0) cc_final: 0.7254 (tt0) REVERT: M 108 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7987 (t0) REVERT: M 111 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6990 (mt-10) REVERT: M 117 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5945 (pm20) REVERT: M 120 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6321 (mp) REVERT: M 156 MET cc_start: 0.7440 (tpp) cc_final: 0.7142 (tmm) REVERT: M 226 MET cc_start: 0.6578 (ptm) cc_final: 0.6322 (ptm) REVERT: M 240 GLU cc_start: 0.6557 (tt0) cc_final: 0.6128 (tt0) REVERT: M 268 LEU cc_start: 0.7294 (tp) cc_final: 0.7008 (tt) REVERT: M 271 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6134 (pt0) REVERT: N 92 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8047 (mtm-85) outliers start: 144 outliers final: 63 residues processed: 618 average time/residue: 0.5224 time to fit residues: 394.3709 Evaluate side-chains 590 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 487 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 288 GLU Chi-restraints excluded: chain H residue 332 LYS Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 258 GLU Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 GLU Chi-restraints excluded: chain I residue 360 THR Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain J residue 15 GLU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain J residue 243 GLU Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain J residue 362 HIS Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain K residue 417 LYS Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 222 GLU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 258 ASN Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 117 GLU Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 271 GLU Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 92 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 54 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 360 optimal weight: 0.8980 chunk 478 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 442 optimal weight: 1.9990 chunk 336 optimal weight: 7.9990 chunk 444 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 401 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN C 98 ASN C 383 HIS ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 GLN F 174 ASN ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.148470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109333 restraints weight = 61190.875| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.66 r_work: 0.3173 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.312 43521 Z= 0.235 Angle : 0.737 30.852 58709 Z= 0.331 Chirality : 0.045 0.225 6294 Planarity : 0.004 0.060 7553 Dihedral : 5.724 81.541 6567 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.95 % Allowed : 24.78 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.11), residues: 5322 helix: 1.43 (0.11), residues: 2561 sheet: -0.00 (0.20), residues: 610 loop : -0.78 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 401 TYR 0.021 0.002 TYR C 407 PHE 0.020 0.001 PHE M 109 TRP 0.014 0.001 TRP A 335 HIS 0.007 0.001 HIS E 210 Details of bonding type rmsd covalent geometry : bond 0.00478 (43473) covalent geometry : angle 0.70101 (58673) hydrogen bonds : bond 0.04516 ( 1981) hydrogen bonds : angle 5.01267 ( 5709) metal coordination : bond 0.00966 ( 16) metal coordination : angle 9.16358 ( 36) Misc. bond : bond 0.13183 ( 32) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 488 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7265 (mp0) cc_final: 0.6846 (mp0) REVERT: A 215 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7921 (t) REVERT: B 7 LYS cc_start: 0.7973 (tttp) cc_final: 0.7104 (tptp) REVERT: B 171 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7723 (pttm) REVERT: B 175 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8450 (pt) REVERT: B 279 GLU cc_start: 0.8088 (mp0) cc_final: 0.7588 (mm-30) REVERT: B 330 MET cc_start: 0.8255 (mtt) cc_final: 0.7517 (mtt) REVERT: B 503 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: C 4 MET cc_start: 0.5560 (pp-130) cc_final: 0.5297 (ppp) REVERT: C 221 TYR cc_start: 0.6739 (m-80) cc_final: 0.6525 (m-80) REVERT: C 388 ASP cc_start: 0.7661 (m-30) cc_final: 0.7411 (m-30) REVERT: D 4 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6816 (mp-120) REVERT: D 7 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7001 (mmmt) REVERT: D 26 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7730 (mttt) REVERT: D 51 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: D 172 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: D 404 LYS cc_start: 0.7893 (mttt) cc_final: 0.7376 (tmmt) REVERT: E 111 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: E 112 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7179 (tp30) REVERT: E 138 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7117 (tmt) REVERT: E 142 GLU cc_start: 0.8286 (mp0) cc_final: 0.7916 (mp0) REVERT: E 202 ASN cc_start: 0.6796 (t0) cc_final: 0.6065 (t0) REVERT: E 214 ARG cc_start: 0.5724 (tpp-160) cc_final: 0.4771 (mmm-85) REVERT: F 61 MET cc_start: 0.7410 (mmm) cc_final: 0.6953 (mpm) REVERT: F 186 ASN cc_start: 0.7916 (OUTLIER) cc_final: 0.7476 (t0) REVERT: F 191 ASP cc_start: 0.5314 (OUTLIER) cc_final: 0.3649 (t70) REVERT: F 197 ILE cc_start: 0.6353 (OUTLIER) cc_final: 0.5748 (mp) REVERT: F 200 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6333 (tp) REVERT: F 210 HIS cc_start: 0.8013 (t70) cc_final: 0.7086 (t-90) REVERT: F 220 ARG cc_start: 0.6896 (mtm-85) cc_final: 0.6075 (mtm-85) REVERT: G 37 LYS cc_start: 0.9130 (mptt) cc_final: 0.8716 (mmtm) REVERT: G 92 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7883 (mtm-85) REVERT: H 6 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6868 (ptm160) REVERT: H 26 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8769 (ttpp) REVERT: H 288 GLU cc_start: 0.7839 (tt0) cc_final: 0.7154 (pt0) REVERT: H 318 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7176 (pm20) REVERT: H 332 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7922 (tptt) REVERT: H 393 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7987 (mm-30) REVERT: H 480 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: I 7 LYS cc_start: 0.8134 (tmtt) cc_final: 0.7552 (tptp) REVERT: I 50 LYS cc_start: 0.8446 (mmmt) cc_final: 0.8227 (mmmm) REVERT: I 51 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: I 283 ASP cc_start: 0.7980 (m-30) cc_final: 0.7735 (t70) REVERT: I 299 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8303 (mt-10) REVERT: J 22 GLU cc_start: 0.6937 (mp0) cc_final: 0.6431 (pm20) REVERT: J 152 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8071 (m) REVERT: J 175 SER cc_start: 0.8606 (t) cc_final: 0.8381 (t) REVERT: J 221 TYR cc_start: 0.6791 (m-80) cc_final: 0.6482 (m-80) REVERT: J 243 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: J 345 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7406 (mtm180) REVERT: J 415 ARG cc_start: 0.7271 (mmm160) cc_final: 0.6589 (tpt90) REVERT: K 4 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6824 (mp-120) REVERT: K 7 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7249 (mmmt) REVERT: K 26 LYS cc_start: 0.8425 (mtpp) cc_final: 0.7490 (mttt) REVERT: K 42 GLU cc_start: 0.8140 (tt0) cc_final: 0.7810 (tm-30) REVERT: K 51 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: K 177 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6783 (t70) REVERT: K 247 MET cc_start: 0.8564 (ttp) cc_final: 0.8227 (ttt) REVERT: K 404 LYS cc_start: 0.7825 (mtmt) cc_final: 0.7297 (tmmt) REVERT: L 5 GLN cc_start: 0.8203 (mt0) cc_final: 0.7937 (mt0) REVERT: L 44 ASP cc_start: 0.7727 (p0) cc_final: 0.6841 (p0) REVERT: L 111 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: L 157 MET cc_start: 0.7759 (mmm) cc_final: 0.7471 (mmm) REVERT: L 195 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5828 (pm20) REVERT: L 208 MET cc_start: 0.6672 (ttt) cc_final: 0.6247 (ttt) REVERT: L 222 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5959 (mp0) REVERT: L 271 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6539 (pp20) REVERT: M 33 LYS cc_start: 0.6858 (tttt) cc_final: 0.6507 (mtmm) REVERT: M 93 GLU cc_start: 0.7544 (mp0) cc_final: 0.7268 (tt0) REVERT: M 108 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8097 (t0) REVERT: M 111 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: M 120 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6797 (mp) REVERT: M 156 MET cc_start: 0.7417 (tpp) cc_final: 0.7089 (tmm) REVERT: M 240 GLU cc_start: 0.6637 (tt0) cc_final: 0.6252 (tt0) REVERT: M 271 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6525 (tt0) REVERT: N 92 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7954 (mtm-85) outliers start: 134 outliers final: 71 residues processed: 597 average time/residue: 0.4993 time to fit residues: 364.8154 Evaluate side-chains 587 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 479 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 186 ASN Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 177 THR Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 332 LYS Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 258 GLU Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 GLU Chi-restraints excluded: chain I residue 360 THR Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain J residue 243 GLU Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain J residue 362 HIS Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 222 GLU Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 258 ASN Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 271 GLU Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 185 optimal weight: 5.9990 chunk 296 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 263 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 258 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 353 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 383 HIS ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 174 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107750 restraints weight = 58417.004| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.64 r_work: 0.3144 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.338 43521 Z= 0.285 Angle : 0.783 30.759 58709 Z= 0.360 Chirality : 0.048 0.211 6294 Planarity : 0.005 0.073 7553 Dihedral : 5.977 83.897 6567 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.82 % Allowed : 24.85 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.11), residues: 5322 helix: 1.26 (0.10), residues: 2540 sheet: -0.10 (0.20), residues: 610 loop : -0.88 (0.12), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 96 TYR 0.022 0.002 TYR A 379 PHE 0.019 0.002 PHE C 431 TRP 0.015 0.002 TRP H 335 HIS 0.008 0.001 HIS E 210 Details of bonding type rmsd covalent geometry : bond 0.00608 (43473) covalent geometry : angle 0.75005 (58673) hydrogen bonds : bond 0.05304 ( 1981) hydrogen bonds : angle 5.15810 ( 5709) metal coordination : bond 0.01342 ( 16) metal coordination : angle 9.06322 ( 36) Misc. bond : bond 0.14933 ( 32) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10644 Ramachandran restraints generated. 5322 Oldfield, 0 Emsley, 5322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 483 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7237 (mp0) cc_final: 0.6816 (mp0) REVERT: B 7 LYS cc_start: 0.7978 (tttp) cc_final: 0.7084 (tptp) REVERT: B 171 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7786 (pttm) REVERT: B 175 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8454 (pt) REVERT: B 283 ASP cc_start: 0.8270 (t70) cc_final: 0.7889 (t70) REVERT: B 330 MET cc_start: 0.8310 (mtt) cc_final: 0.7591 (mtt) REVERT: B 503 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: C 4 MET cc_start: 0.5574 (pp-130) cc_final: 0.5305 (ppp) REVERT: C 60 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7965 (ptp-170) REVERT: C 221 TYR cc_start: 0.6747 (m-80) cc_final: 0.6533 (m-80) REVERT: D 4 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6826 (mp-120) REVERT: D 7 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7022 (mmmt) REVERT: D 26 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7682 (mttt) REVERT: D 51 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: D 172 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6857 (mt-10) REVERT: D 404 LYS cc_start: 0.7880 (mttt) cc_final: 0.7353 (tmmt) REVERT: E 111 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7372 (mt-10) REVERT: E 112 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7177 (tp30) REVERT: E 138 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7177 (tmt) REVERT: E 142 GLU cc_start: 0.8293 (mp0) cc_final: 0.7990 (mp0) REVERT: E 202 ASN cc_start: 0.6893 (t0) cc_final: 0.6112 (t0) REVERT: F 61 MET cc_start: 0.7426 (mmm) cc_final: 0.6953 (mpm) REVERT: F 191 ASP cc_start: 0.5338 (OUTLIER) cc_final: 0.3639 (t70) REVERT: F 197 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.5824 (mp) REVERT: F 200 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6376 (tp) REVERT: F 210 HIS cc_start: 0.8020 (t70) cc_final: 0.7317 (t70) REVERT: F 220 ARG cc_start: 0.6835 (mtm-85) cc_final: 0.5995 (mtm-85) REVERT: F 229 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6694 (pp) REVERT: G 37 LYS cc_start: 0.9146 (mptt) cc_final: 0.8710 (mmtm) REVERT: G 92 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.7907 (mtm-85) REVERT: H 26 LYS cc_start: 0.9044 (mtpt) cc_final: 0.8824 (ttpp) REVERT: H 288 GLU cc_start: 0.7866 (tt0) cc_final: 0.7188 (pt0) REVERT: H 318 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7190 (pm20) REVERT: H 332 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7963 (tptt) REVERT: H 393 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8014 (mm-30) REVERT: I 7 LYS cc_start: 0.8113 (tmtt) cc_final: 0.7505 (tptp) REVERT: I 51 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: I 283 ASP cc_start: 0.8076 (m-30) cc_final: 0.7794 (t70) REVERT: I 299 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: I 461 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8362 (pm20) REVERT: J 22 GLU cc_start: 0.6865 (mp0) cc_final: 0.6380 (pm20) REVERT: J 152 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8182 (m) REVERT: J 175 SER cc_start: 0.8620 (t) cc_final: 0.8393 (t) REVERT: J 221 TYR cc_start: 0.6785 (m-80) cc_final: 0.6455 (m-80) REVERT: J 243 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6053 (mp0) REVERT: J 345 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7354 (mtm180) REVERT: J 415 ARG cc_start: 0.7260 (mmm160) cc_final: 0.6614 (tpt90) REVERT: K 4 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6845 (mp-120) REVERT: K 7 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7226 (mmmt) REVERT: K 26 LYS cc_start: 0.8400 (mtpp) cc_final: 0.7489 (mttt) REVERT: K 42 GLU cc_start: 0.8107 (tt0) cc_final: 0.7770 (tm-30) REVERT: K 51 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: K 177 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6782 (t70) REVERT: K 247 MET cc_start: 0.8617 (ttp) cc_final: 0.8259 (ttt) REVERT: K 404 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7302 (tmmt) REVERT: L 5 GLN cc_start: 0.8218 (mt0) cc_final: 0.7912 (mt0) REVERT: L 44 ASP cc_start: 0.7752 (p0) cc_final: 0.6882 (p0) REVERT: L 111 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: L 195 GLU cc_start: 0.6106 (OUTLIER) cc_final: 0.5836 (pm20) REVERT: L 208 MET cc_start: 0.6797 (ttt) cc_final: 0.6461 (ttt) REVERT: L 271 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6538 (pp20) REVERT: M 108 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8168 (t0) REVERT: M 111 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: M 120 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6887 (mp) REVERT: M 156 MET cc_start: 0.7473 (tpp) cc_final: 0.7173 (tmm) REVERT: M 240 GLU cc_start: 0.6738 (tt0) cc_final: 0.6267 (tt0) REVERT: M 271 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6573 (tt0) REVERT: N 92 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7966 (mtm-85) outliers start: 128 outliers final: 76 residues processed: 589 average time/residue: 0.5342 time to fit residues: 384.5171 Evaluate side-chains 585 residues out of total 4540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 474 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 4 GLN Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 138 MET Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 92 ARG Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 44 LYS Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 332 LYS Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 355 ILE Chi-restraints excluded: chain H residue 362 HIS Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain H residue 393 GLU Chi-restraints excluded: chain H residue 480 GLU Chi-restraints excluded: chain I residue 51 GLU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 258 GLU Chi-restraints excluded: chain I residue 276 THR Chi-restraints excluded: chain I residue 299 GLU Chi-restraints excluded: chain I residue 360 THR Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 420 THR Chi-restraints excluded: chain I residue 461 GLU Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 152 SER Chi-restraints excluded: chain J residue 176 LYS Chi-restraints excluded: chain J residue 243 GLU Chi-restraints excluded: chain J residue 345 ARG Chi-restraints excluded: chain J residue 362 HIS Chi-restraints excluded: chain J residue 423 SER Chi-restraints excluded: chain J residue 463 MET Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 51 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 360 THR Chi-restraints excluded: chain K residue 369 LEU Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 222 GLU Chi-restraints excluded: chain L residue 227 THR Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 258 ASN Chi-restraints excluded: chain L residue 271 GLU Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain M residue 271 GLU Chi-restraints excluded: chain N residue 68 THR Chi-restraints excluded: chain N residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 131 optimal weight: 0.8980 chunk 211 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 130 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 chunk 465 optimal weight: 20.0000 chunk 277 optimal weight: 1.9990 chunk 109 optimal weight: 0.0870 chunk 507 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 128 GLN ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN M 108 ASN M 174 ASN N 32 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.149901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110710 restraints weight = 64812.963| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.69 r_work: 0.3205 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.292 43521 Z= 0.204 Angle : 0.718 30.742 58709 Z= 0.318 Chirality : 0.043 0.195 6294 Planarity : 0.004 0.052 7553 Dihedral : 5.725 82.275 6567 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.42 % Allowed : 25.42 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.11), residues: 5322 helix: 1.44 (0.11), residues: 2537 sheet: -0.06 (0.20), residues: 614 loop : -0.81 (0.12), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 220 TYR 0.021 0.001 TYR J 407 PHE 0.015 0.001 PHE C 431 TRP 0.017 0.001 TRP J 335 HIS 0.008 0.001 HIS J 362 Details of bonding type rmsd covalent geometry : bond 0.00407 (43473) covalent geometry : angle 0.68040 (58673) hydrogen bonds : bond 0.03876 ( 1981) hydrogen bonds : angle 4.99305 ( 5709) metal coordination : bond 0.00785 ( 16) metal coordination : angle 9.22740 ( 36) Misc. bond : bond 0.11819 ( 32) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20015.00 seconds wall clock time: 339 minutes 33.00 seconds (20373.00 seconds total)