Starting phenix.real_space_refine on Mon Jan 20 00:34:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rif_19186/01_2025/8rif_19186.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rif_19186/01_2025/8rif_19186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rif_19186/01_2025/8rif_19186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rif_19186/01_2025/8rif_19186.map" model { file = "/net/cci-nas-00/data/ceres_data/8rif_19186/01_2025/8rif_19186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rif_19186/01_2025/8rif_19186.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 124 5.49 5 Mg 8 5.21 5 S 288 5.16 5 C 39968 2.51 5 N 11205 2.21 5 O 12522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 64125 Number of models: 1 Model: "" Number of chains: 26 Chain: "2" Number of atoms: 4938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4938 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 25, 'TRANS': 598} Chain breaks: 2 Chain: "3" Number of atoms: 4811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4811 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 28, 'TRANS': 585} Chain breaks: 4 Chain: "4" Number of atoms: 5120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5120 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 23, 'TRANS': 621} Chain breaks: 3 Chain: "5" Number of atoms: 5136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5136 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 28, 'TRANS': 627} Chain breaks: 3 Chain: "6" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4874 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 22, 'TRANS': 592} Chain breaks: 5 Chain: "7" Number of atoms: 5976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5976 Classifications: {'peptide': 755} Link IDs: {'PTRANS': 31, 'TRANS': 723} Chain breaks: 3 Chain: "X" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1086 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "Y" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1087 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain: "A" Number of atoms: 4938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4938 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 25, 'TRANS': 598} Chain breaks: 2 Chain: "B" Number of atoms: 4811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4811 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 28, 'TRANS': 585} Chain breaks: 4 Chain: "C" Number of atoms: 5120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5120 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 23, 'TRANS': 621} Chain breaks: 3 Chain: "D" Number of atoms: 5136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5136 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 28, 'TRANS': 627} Chain breaks: 3 Chain: "E" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4874 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 22, 'TRANS': 592} Chain breaks: 5 Chain: "F" Number of atoms: 5976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5976 Classifications: {'peptide': 755} Link IDs: {'PTRANS': 31, 'TRANS': 723} Chain breaks: 3 Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" 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: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1302 SG CYS 2 341 124.887 113.090 82.674 1.00 64.40 S ATOM 1325 SG CYS 2 344 124.198 116.367 82.760 1.00 30.00 S ATOM 1483 SG CYS 2 364 123.496 114.757 86.048 1.00 65.56 S ATOM 1504 SG CYS 2 367 120.829 113.448 83.326 1.00 30.00 S ATOM 10992 SG CYS 4 349 119.951 66.103 101.420 1.00 63.04 S ATOM 11013 SG CYS 4 352 118.817 63.979 103.700 1.00 65.41 S ATOM 11160 SG CYS 4 371 118.008 63.116 100.591 1.00 66.16 S ATOM 11202 SG CYS 4 376 116.013 66.280 102.264 1.00 70.35 S ATOM 16141 SG CYS 5 183 120.935 103.408 59.469 1.00 56.45 S ATOM 16166 SG CYS 5 186 118.186 105.507 58.463 1.00 59.29 S ATOM 16337 SG CYS 5 211 119.580 106.331 61.475 1.00 59.79 S ATOM 16520 SG CYS 5 236 117.471 102.914 61.295 1.00 61.49 S ATOM 21251 SG CYS 6 311 120.540 86.310 100.149 1.00 71.92 S ATOM 21273 SG CYS 6 314 118.408 87.682 102.584 1.00 73.57 S ATOM 21430 SG CYS 6 333 119.044 84.031 102.995 1.00 75.00 S ATOM 21464 SG CYS 6 338 116.836 85.291 100.015 1.00 80.22 S ATOM 26679 SG CYS 7 262 117.901 54.557 74.631 1.00 60.00 S ATOM 26702 SG CYS 7 265 115.923 53.319 72.118 1.00 60.06 S ATOM 26856 SG CYS 7 284 117.576 56.997 71.946 1.00 61.17 S ATOM 26893 SG CYS 7 289 114.559 56.312 74.218 1.00 60.60 S ATOM 34330 SG CYS A 341 114.919 77.022 82.668 1.00 64.40 S ATOM 34353 SG CYS A 344 115.608 73.745 82.754 1.00 30.00 S ATOM 34511 SG CYS A 364 116.311 75.355 86.042 1.00 65.56 S ATOM 34532 SG CYS A 367 118.977 76.665 83.319 1.00 30.00 S ATOM 44020 SG CYS C 349 119.848 124.010 101.414 1.00 63.04 S ATOM 44041 SG CYS C 352 120.982 126.134 103.694 1.00 65.41 S ATOM 44188 SG CYS C 371 121.790 126.997 100.585 1.00 66.16 S ATOM 44230 SG CYS C 376 123.786 123.834 102.257 1.00 70.35 S ATOM 49169 SG CYS D 183 118.865 86.705 59.463 1.00 56.45 S ATOM 49194 SG CYS D 186 121.614 84.607 58.456 1.00 59.29 S ATOM 49365 SG CYS D 211 120.221 83.782 61.468 1.00 59.79 S ATOM 49548 SG CYS D 236 122.329 87.200 61.288 1.00 61.49 S ATOM 54279 SG CYS E 311 119.263 103.803 100.143 1.00 71.92 S ATOM 54301 SG CYS E 314 121.395 102.431 102.577 1.00 73.57 S ATOM 54458 SG CYS E 333 120.759 106.082 102.989 1.00 75.00 S ATOM 54492 SG CYS E 338 122.967 104.822 100.008 1.00 80.22 S ATOM 59707 SG CYS F 262 121.891 135.557 74.625 1.00 60.00 S ATOM 59730 SG CYS F 265 123.868 136.795 72.112 1.00 60.06 S ATOM 59884 SG CYS F 284 122.216 133.117 71.940 1.00 61.17 S ATOM 59921 SG CYS F 289 125.233 133.802 74.211 1.00 60.60 S Time building chain proxies: 33.95, per 1000 atoms: 0.53 Number of scatterers: 64125 At special positions: 0 Unit cell: (240.84, 191.16, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 288 16.00 P 124 15.00 Mg 8 11.99 O 12522 8.00 N 11205 7.00 C 39968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.00 Conformation dependent library (CDL) restraints added in 6.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21002 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 364 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 367 " pdb=" ZN 41001 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 371 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 41001 " - pdb=" SG CYS 4 376 " pdb=" ZN 51002 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 186 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 51002 " - pdb=" SG CYS 5 183 " pdb=" ZN 61101 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 61101 " - pdb=" SG CYS 6 333 " pdb=" ZN 71002 " pdb="ZN ZN 71002 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 71002 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 71002 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 71002 " - pdb=" SG CYS 7 289 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 344 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 364 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 341 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 367 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 349 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 371 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 352 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 376 " pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 186 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 236 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 211 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 183 " pdb=" ZN E1101 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 338 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 314 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 311 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 333 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 262 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 265 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 284 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 289 " Number of angles added : 60 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14856 Finding SS restraints... Secondary structure from input PDB file: 316 helices and 80 sheets defined 44.4% alpha, 12.7% beta 29 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 16.77 Creating SS restraints... Processing helix chain '2' and resid 182 through 187 removed outlier: 3.877A pdb=" N SER 2 187 " --> pdb=" O LEU 2 183 " (cutoff:3.500A) Processing helix chain '2' and resid 193 through 200 removed outlier: 3.756A pdb=" N GLN 2 200 " --> pdb=" O GLU 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 200 through 217 Processing helix chain '2' and resid 225 through 238 removed outlier: 3.591A pdb=" N ARG 2 230 " --> pdb=" O VAL 2 226 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY 2 235 " --> pdb=" O ILE 2 231 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU 2 236 " --> pdb=" O ARG 2 232 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET 2 237 " --> pdb=" O THR 2 233 " (cutoff:3.500A) Processing helix chain '2' and resid 245 through 253 Processing helix chain '2' and resid 253 through 263 removed outlier: 3.674A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 283 removed outlier: 3.501A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE 2 270 " --> pdb=" O GLU 2 266 " (cutoff:3.500A) Processing helix chain '2' and resid 285 through 290 removed outlier: 4.256A pdb=" N ILE 2 289 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 removed outlier: 3.770A pdb=" N LEU 2 314 " --> pdb=" O GLU 2 311 " (cutoff:3.500A) Processing helix chain '2' and resid 393 through 397 Processing helix chain '2' and resid 413 through 415 No H-bonds generated for 'chain '2' and resid 413 through 415' Processing helix chain '2' and resid 477 through 489 removed outlier: 4.239A pdb=" N ARG 2 482 " --> pdb=" O GLU 2 478 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU 2 483 " --> pdb=" O GLU 2 479 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 501 removed outlier: 3.513A pdb=" N LYS 2 496 " --> pdb=" O GLY 2 492 " (cutoff:3.500A) Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 560 removed outlier: 4.027A pdb=" N ILE 2 552 " --> pdb=" O ALA 2 548 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 599 Processing helix chain '2' and resid 613 through 627 Processing helix chain '2' and resid 662 through 666 Processing helix chain '2' and resid 670 through 675 Processing helix chain '2' and resid 688 through 706 removed outlier: 3.662A pdb=" N ASP 2 692 " --> pdb=" O ASP 2 688 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU 2 693 " --> pdb=" O GLU 2 689 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG 2 694 " --> pdb=" O GLU 2 690 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 774 removed outlier: 3.603A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS 2 768 " --> pdb=" O MET 2 764 " (cutoff:3.500A) Processing helix chain '2' and resid 779 through 782 removed outlier: 3.798A pdb=" N ASP 2 782 " --> pdb=" O HIS 2 779 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 779 through 782' Processing helix chain '2' and resid 783 through 801 removed outlier: 3.616A pdb=" N ARG 2 788 " --> pdb=" O ASP 2 784 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE 2 798 " --> pdb=" O ARG 2 794 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER 2 799 " --> pdb=" O ARG 2 795 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 4.182A pdb=" N LEU 2 810 " --> pdb=" O THR 2 806 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER 2 819 " --> pdb=" O ARG 2 815 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG 2 824 " --> pdb=" O PHE 2 820 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 848 removed outlier: 3.664A pdb=" N LYS 2 839 " --> pdb=" O ASP 2 835 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL 2 840 " --> pdb=" O ARG 2 836 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL 2 841 " --> pdb=" O ALA 2 837 " (cutoff:3.500A) Processing helix chain '2' and resid 850 through 861 removed outlier: 3.672A pdb=" N ARG 2 859 " --> pdb=" O ARG 2 855 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 35 Processing helix chain '3' and resid 38 through 52 removed outlier: 3.528A pdb=" N ILE 3 45 " --> pdb=" O SER 3 41 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN 3 46 " --> pdb=" O VAL 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 107 removed outlier: 3.653A pdb=" N ARG 3 104 " --> pdb=" O LEU 3 100 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 117 Processing helix chain '3' and resid 117 through 137 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 281 through 283 No H-bonds generated for 'chain '3' and resid 281 through 283' Processing helix chain '3' and resid 343 through 356 removed outlier: 3.864A pdb=" N SER 3 354 " --> pdb=" O ILE 3 350 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS 3 356 " --> pdb=" O LYS 3 352 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 366 Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 426 Processing helix chain '3' and resid 435 through 437 No H-bonds generated for 'chain '3' and resid 435 through 437' Processing helix chain '3' and resid 438 through 442 Processing helix chain '3' and resid 460 through 465 Processing helix chain '3' and resid 474 through 478 removed outlier: 3.660A pdb=" N MET 3 478 " --> pdb=" O PHE 3 475 " (cutoff:3.500A) Processing helix chain '3' and resid 479 through 491 removed outlier: 3.809A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 533 removed outlier: 3.600A pdb=" N ASN 3 532 " --> pdb=" O ASP 3 528 " (cutoff:3.500A) Processing helix chain '3' and resid 536 through 542 removed outlier: 3.576A pdb=" N ARG 3 542 " --> pdb=" O SER 3 538 " (cutoff:3.500A) Processing helix chain '3' and resid 555 through 569 Processing helix chain '3' and resid 652 through 667 removed outlier: 3.833A pdb=" N ARG 3 657 " --> pdb=" O ILE 3 653 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL 3 667 " --> pdb=" O ALA 3 663 " (cutoff:3.500A) Processing helix chain '3' and resid 674 through 688 removed outlier: 4.283A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 717 removed outlier: 3.723A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE 3 706 " --> pdb=" O LEU 3 702 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 Processing helix chain '4' and resid 186 through 200 removed outlier: 3.542A pdb=" N ASN 4 196 " --> pdb=" O THR 4 192 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE 4 197 " --> pdb=" O ASN 4 193 " (cutoff:3.500A) Processing helix chain '4' and resid 225 through 237 removed outlier: 3.632A pdb=" N GLN 4 229 " --> pdb=" O TYR 4 225 " (cutoff:3.500A) Processing helix chain '4' and resid 245 through 250 removed outlier: 3.946A pdb=" N ALA 4 250 " --> pdb=" O ASN 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 262 Processing helix chain '4' and resid 264 through 283 removed outlier: 3.866A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE 4 271 " --> pdb=" O GLU 4 267 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN 4 274 " --> pdb=" O SER 4 270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE 4 276 " --> pdb=" O MET 4 272 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL 4 281 " --> pdb=" O LYS 4 277 " (cutoff:3.500A) Processing helix chain '4' and resid 313 through 317 Processing helix chain '4' and resid 318 through 322 removed outlier: 3.504A pdb=" N ILE 4 322 " --> pdb=" O PRO 4 319 " (cutoff:3.500A) Processing helix chain '4' and resid 386 through 389 Processing helix chain '4' and resid 477 through 480 Processing helix chain '4' and resid 481 through 492 Processing helix chain '4' and resid 502 through 514 Processing helix chain '4' and resid 517 through 526 Processing helix chain '4' and resid 533 through 546 removed outlier: 3.551A pdb=" N LYS 4 537 " --> pdb=" O LEU 4 533 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE 4 540 " --> pdb=" O VAL 4 536 " (cutoff:3.500A) Processing helix chain '4' and resid 573 through 585 removed outlier: 3.597A pdb=" N ILE 4 577 " --> pdb=" O SER 4 573 " (cutoff:3.500A) Processing helix chain '4' and resid 592 through 596 removed outlier: 4.167A pdb=" N GLY 4 595 " --> pdb=" O SER 4 592 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER 4 596 " --> pdb=" O GLY 4 593 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 592 through 596' Processing helix chain '4' and resid 597 through 602 Processing helix chain '4' and resid 619 through 624 Processing helix chain '4' and resid 634 through 637 Processing helix chain '4' and resid 638 through 644 removed outlier: 4.163A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) Processing helix chain '4' and resid 644 through 651 removed outlier: 3.915A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 691 Processing helix chain '4' and resid 695 through 700 removed outlier: 3.840A pdb=" N SER 4 700 " --> pdb=" O PRO 4 696 " (cutoff:3.500A) Processing helix chain '4' and resid 713 through 727 removed outlier: 3.760A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) Processing helix chain '4' and resid 743 through 757 Processing helix chain '4' and resid 763 through 780 removed outlier: 3.704A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) Processing helix chain '4' and resid 794 through 811 removed outlier: 3.968A pdb=" N LEU 4 798 " --> pdb=" O THR 4 794 " (cutoff:3.500A) Processing helix chain '4' and resid 818 through 834 removed outlier: 3.730A pdb=" N VAL 4 822 " --> pdb=" O GLU 4 818 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) Processing helix chain '4' and resid 846 through 850 Processing helix chain '5' and resid 23 through 38 removed outlier: 3.523A pdb=" N LEU 5 36 " --> pdb=" O LYS 5 32 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 56 Processing helix chain '5' and resid 66 through 68 No H-bonds generated for 'chain '5' and resid 66 through 68' Processing helix chain '5' and resid 72 through 82 Processing helix chain '5' and resid 82 through 105 Proline residue: 5 88 - end of helix removed outlier: 3.798A pdb=" N ALA 5 93 " --> pdb=" O LEU 5 89 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE 5 94 " --> pdb=" O PHE 5 90 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR 5 95 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 221 through 226 Processing helix chain '5' and resid 245 through 248 Processing helix chain '5' and resid 281 through 283 No H-bonds generated for 'chain '5' and resid 281 through 283' Processing helix chain '5' and resid 350 through 362 removed outlier: 3.642A pdb=" N ARG 5 362 " --> pdb=" O LEU 5 358 " (cutoff:3.500A) Processing helix chain '5' and resid 366 through 374 Processing helix chain '5' and resid 381 through 392 Processing helix chain '5' and resid 421 through 432 removed outlier: 3.596A pdb=" N LEU 5 425 " --> pdb=" O ALA 5 421 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU 5 426 " --> pdb=" O LYS 5 422 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS 5 431 " --> pdb=" O LYS 5 427 " (cutoff:3.500A) Processing helix chain '5' and resid 467 through 472 Processing helix chain '5' and resid 486 through 500 removed outlier: 3.598A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU 5 495 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) Processing helix chain '5' and resid 536 through 540 removed outlier: 3.553A pdb=" N ILE 5 540 " --> pdb=" O GLY 5 537 " (cutoff:3.500A) Processing helix chain '5' and resid 543 through 550 removed outlier: 3.628A pdb=" N ILE 5 546 " --> pdb=" O GLN 5 543 " (cutoff:3.500A) Processing helix chain '5' and resid 561 through 578 Processing helix chain '5' and resid 579 through 582 Processing helix chain '5' and resid 586 through 591 removed outlier: 3.827A pdb=" N GLY 5 591 " --> pdb=" O GLU 5 588 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 608 Processing helix chain '5' and resid 615 through 640 removed outlier: 4.447A pdb=" N GLU 5 620 " --> pdb=" O PRO 5 616 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS 5 621 " --> pdb=" O GLN 5 617 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN 5 632 " --> pdb=" O THR 5 628 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU 5 633 " --> pdb=" O ILE 5 629 " (cutoff:3.500A) Processing helix chain '5' and resid 649 through 666 removed outlier: 3.865A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU 5 654 " --> pdb=" O ILE 5 650 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE 5 656 " --> pdb=" O GLN 5 652 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU 5 661 " --> pdb=" O ILE 5 657 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU 5 666 " --> pdb=" O SER 5 662 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 688 removed outlier: 3.907A pdb=" N VAL 5 677 " --> pdb=" O GLN 5 673 " (cutoff:3.500A) Processing helix chain '5' and resid 689 through 698 removed outlier: 6.093A pdb=" N ASP 5 695 " --> pdb=" O ALA 5 692 " (cutoff:3.500A) Proline residue: 5 696 - end of helix Processing helix chain '6' and resid 105 through 121 Processing helix chain '6' and resid 134 through 147 removed outlier: 3.517A pdb=" N GLU 6 141 " --> pdb=" O ARG 6 137 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS 6 144 " --> pdb=" O ILE 6 140 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR 6 146 " --> pdb=" O PHE 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 161 removed outlier: 3.809A pdb=" N MET 6 160 " --> pdb=" O GLN 6 156 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) Processing helix chain '6' and resid 165 through 173 Processing helix chain '6' and resid 173 through 193 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 194 through 198 removed outlier: 3.668A pdb=" N ASN 6 198 " --> pdb=" O GLU 6 195 " (cutoff:3.500A) Processing helix chain '6' and resid 275 through 279 removed outlier: 3.636A pdb=" N ILE 6 279 " --> pdb=" O ILE 6 276 " (cutoff:3.500A) Processing helix chain '6' and resid 280 through 284 removed outlier: 3.719A pdb=" N LYS 6 283 " --> pdb=" O ARG 6 280 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE 6 284 " --> pdb=" O SER 6 281 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 280 through 284' Processing helix chain '6' and resid 364 through 368 removed outlier: 3.709A pdb=" N ILE 6 368 " --> pdb=" O ALA 6 365 " (cutoff:3.500A) Processing helix chain '6' and resid 384 through 386 No H-bonds generated for 'chain '6' and resid 384 through 386' Processing helix chain '6' and resid 407 through 410 removed outlier: 3.823A pdb=" N LEU 6 410 " --> pdb=" O VAL 6 407 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 407 through 410' Processing helix chain '6' and resid 513 through 522 removed outlier: 3.693A pdb=" N LYS 6 521 " --> pdb=" O LYS 6 517 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP 6 522 " --> pdb=" O GLU 6 518 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 532 Processing helix chain '6' and resid 540 through 553 Processing helix chain '6' and resid 581 through 592 removed outlier: 4.018A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 604 through 609 Processing helix chain '6' and resid 640 through 644 Processing helix chain '6' and resid 645 through 658 removed outlier: 3.593A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 708 removed outlier: 3.772A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) Processing helix chain '6' and resid 720 through 738 Processing helix chain '6' and resid 747 through 759 removed outlier: 3.575A pdb=" N ARG 6 753 " --> pdb=" O GLU 6 749 " (cutoff:3.500A) Processing helix chain '6' and resid 766 through 784 removed outlier: 3.736A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 815 removed outlier: 3.702A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 835 removed outlier: 3.535A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE 6 835 " --> pdb=" O LEU 6 831 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 26 removed outlier: 3.675A pdb=" N ASN 7 19 " --> pdb=" O ASN 7 15 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU 7 20 " --> pdb=" O ASN 7 16 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 removed outlier: 3.643A pdb=" N ASN 7 72 " --> pdb=" O GLN 7 68 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 95 removed outlier: 3.526A pdb=" N PHE 7 93 " --> pdb=" O GLN 7 89 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN 7 95 " --> pdb=" O GLU 7 91 " (cutoff:3.500A) Processing helix chain '7' and resid 101 through 109 removed outlier: 3.596A pdb=" N ALA 7 105 " --> pdb=" O ASP 7 101 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 124 removed outlier: 4.361A pdb=" N PHE 7 113 " --> pdb=" O ASN 7 109 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR 7 114 " --> pdb=" O ALA 7 110 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 137 through 165 removed outlier: 3.676A pdb=" N ILE 7 142 " --> pdb=" O VAL 7 138 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG 7 147 " --> pdb=" O LEU 7 143 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU 7 148 " --> pdb=" O ASN 7 144 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET 7 153 " --> pdb=" O ARG 7 149 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU 7 154 " --> pdb=" O ASN 7 150 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU 7 164 " --> pdb=" O GLU 7 160 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN 7 165 " --> pdb=" O ILE 7 161 " (cutoff:3.500A) Processing helix chain '7' and resid 179 through 189 removed outlier: 3.594A pdb=" N GLU 7 183 " --> pdb=" O ASP 7 179 " (cutoff:3.500A) Processing helix chain '7' and resid 194 through 198 Processing helix chain '7' and resid 208 through 215 removed outlier: 3.522A pdb=" N TYR 7 215 " --> pdb=" O CYS 7 211 " (cutoff:3.500A) Processing helix chain '7' and resid 231 through 235 removed outlier: 3.638A pdb=" N LEU 7 235 " --> pdb=" O GLY 7 232 " (cutoff:3.500A) Processing helix chain '7' and resid 286 through 292 Processing helix chain '7' and resid 318 through 322 removed outlier: 3.532A pdb=" N VAL 7 322 " --> pdb=" O SER 7 319 " (cutoff:3.500A) Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain '7' and resid 363 through 367 Processing helix chain '7' and resid 394 through 407 removed outlier: 3.587A pdb=" N SER 7 407 " --> pdb=" O GLU 7 403 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 416 Processing helix chain '7' and resid 425 through 438 Processing helix chain '7' and resid 465 through 477 Processing helix chain '7' and resid 489 through 493 removed outlier: 3.638A pdb=" N GLY 7 492 " --> pdb=" O SER 7 489 " (cutoff:3.500A) Processing helix chain '7' and resid 511 through 516 Processing helix chain '7' and resid 525 through 529 removed outlier: 3.647A pdb=" N MET 7 529 " --> pdb=" O PHE 7 526 " (cutoff:3.500A) Processing helix chain '7' and resid 530 through 544 removed outlier: 3.550A pdb=" N ALA 7 536 " --> pdb=" O SER 7 532 " (cutoff:3.500A) Processing helix chain '7' and resid 579 through 583 Processing helix chain '7' and resid 587 through 592 Processing helix chain '7' and resid 605 through 622 removed outlier: 3.914A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 647 Processing helix chain '7' and resid 653 through 677 removed outlier: 3.502A pdb=" N TYR 7 659 " --> pdb=" O ALA 7 655 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS 7 672 " --> pdb=" O ARG 7 668 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG 7 673 " --> pdb=" O GLN 7 669 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU 7 674 " --> pdb=" O ASP 7 670 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER 7 677 " --> pdb=" O ARG 7 673 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 704 removed outlier: 3.720A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 723 removed outlier: 3.779A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) Processing helix chain '7' and resid 724 through 729 removed outlier: 3.618A pdb=" N LEU 7 727 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN 7 729 " --> pdb=" O SER 7 726 " (cutoff:3.500A) Processing helix chain '7' and resid 741 through 753 Processing helix chain '7' and resid 762 through 773 Processing helix chain '7' and resid 775 through 789 Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.877A pdb=" N SER A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 200 removed outlier: 3.756A pdb=" N GLN A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 217 Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.591A pdb=" N ARG A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 253 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.674A pdb=" N ALA A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 283 removed outlier: 3.501A pdb=" N MET A 267 " --> pdb=" O CYS A 263 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.256A pdb=" N ILE A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.770A pdb=" N LEU A 314 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 477 through 489 removed outlier: 4.239A pdb=" N ARG A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.513A pdb=" N LYS A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 548 through 560 removed outlier: 4.026A pdb=" N ILE A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 613 through 627 Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 670 through 675 Processing helix chain 'A' and resid 688 through 706 removed outlier: 3.662A pdb=" N ASP A 692 " --> pdb=" O ASP A 688 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 774 removed outlier: 3.603A pdb=" N LYS A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 768 " --> pdb=" O MET A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 782 removed outlier: 3.798A pdb=" N ASP A 782 " --> pdb=" O HIS A 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 779 through 782' Processing helix chain 'A' and resid 783 through 801 removed outlier: 3.616A pdb=" N ARG A 788 " --> pdb=" O ASP A 784 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 798 " --> pdb=" O ARG A 794 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 799 " --> pdb=" O ARG A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 824 removed outlier: 4.182A pdb=" N LEU A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG A 824 " --> pdb=" O PHE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 848 removed outlier: 3.664A pdb=" N LYS A 839 " --> pdb=" O ASP A 835 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 840 " --> pdb=" O ARG A 836 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 861 removed outlier: 3.672A pdb=" N ARG A 859 " --> pdb=" O ARG A 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 35 Processing helix chain 'B' and resid 38 through 52 removed outlier: 3.529A pdb=" N ILE B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 removed outlier: 3.652A pdb=" N ARG B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 117 Processing helix chain 'B' and resid 117 through 137 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 343 through 356 removed outlier: 3.863A pdb=" N SER B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS B 356 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 374 through 387 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 442 Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.660A pdb=" N MET B 478 " --> pdb=" O PHE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.809A pdb=" N GLU B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 491 " --> pdb=" O HIS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.599A pdb=" N ASN B 532 " --> pdb=" O ASP B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.576A pdb=" N ARG B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 569 Processing helix chain 'B' and resid 652 through 667 removed outlier: 3.832A pdb=" N ARG B 657 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 658 " --> pdb=" O PRO B 654 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 688 removed outlier: 4.283A pdb=" N VAL B 678 " --> pdb=" O GLU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 717 removed outlier: 3.722A pdb=" N LEU B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 738 Processing helix chain 'C' and resid 186 through 200 removed outlier: 3.542A pdb=" N ASN C 196 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE C 197 " --> pdb=" O ASN C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 237 removed outlier: 3.632A pdb=" N GLN C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 removed outlier: 3.947A pdb=" N ALA C 250 " --> pdb=" O ASN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 264 through 283 removed outlier: 3.866A pdb=" N SER C 270 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN C 274 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 276 " --> pdb=" O MET C 272 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL C 281 " --> pdb=" O LYS C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.504A pdb=" N ILE C 322 " --> pdb=" O PRO C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 477 through 480 Processing helix chain 'C' and resid 481 through 492 Processing helix chain 'C' and resid 502 through 514 Processing helix chain 'C' and resid 517 through 526 Processing helix chain 'C' and resid 533 through 546 removed outlier: 3.550A pdb=" N LYS C 537 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 585 removed outlier: 3.597A pdb=" N ILE C 577 " --> pdb=" O SER C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 596 removed outlier: 4.167A pdb=" N GLY C 595 " --> pdb=" O SER C 592 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER C 596 " --> pdb=" O GLY C 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 592 through 596' Processing helix chain 'C' and resid 597 through 602 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 634 through 637 Processing helix chain 'C' and resid 638 through 644 removed outlier: 4.163A pdb=" N VAL C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 651 removed outlier: 3.915A pdb=" N VAL C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 691 Processing helix chain 'C' and resid 695 through 700 removed outlier: 3.841A pdb=" N SER C 700 " --> pdb=" O PRO C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 727 removed outlier: 3.760A pdb=" N LEU C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 757 Processing helix chain 'C' and resid 763 through 780 removed outlier: 3.704A pdb=" N GLU C 769 " --> pdb=" O ALA C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 811 removed outlier: 3.968A pdb=" N LEU C 798 " --> pdb=" O THR C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 834 removed outlier: 3.730A pdb=" N VAL C 822 " --> pdb=" O GLU C 818 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 833 " --> pdb=" O ILE C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 850 Processing helix chain 'D' and resid 23 through 38 removed outlier: 3.523A pdb=" N LEU D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 56 Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 72 through 82 Processing helix chain 'D' and resid 82 through 105 Proline residue: D 88 - end of helix removed outlier: 3.798A pdb=" N ALA D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 245 through 248 Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 350 through 362 removed outlier: 3.642A pdb=" N ARG D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 374 Processing helix chain 'D' and resid 381 through 392 Processing helix chain 'D' and resid 421 through 432 removed outlier: 3.595A pdb=" N LEU D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 426 " --> pdb=" O LYS D 422 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 472 Processing helix chain 'D' and resid 486 through 500 removed outlier: 3.598A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU D 495 " --> pdb=" O VAL D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 540 removed outlier: 3.552A pdb=" N ILE D 540 " --> pdb=" O GLY D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 550 removed outlier: 3.629A pdb=" N ILE D 546 " --> pdb=" O GLN D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 578 Processing helix chain 'D' and resid 579 through 582 Processing helix chain 'D' and resid 586 through 591 removed outlier: 3.827A pdb=" N GLY D 591 " --> pdb=" O GLU D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 608 Processing helix chain 'D' and resid 615 through 640 removed outlier: 4.447A pdb=" N GLU D 620 " --> pdb=" O PRO D 616 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS D 621 " --> pdb=" O GLN D 617 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN D 632 " --> pdb=" O THR D 628 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 633 " --> pdb=" O ILE D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 666 removed outlier: 3.865A pdb=" N LEU D 653 " --> pdb=" O THR D 649 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU D 654 " --> pdb=" O ILE D 650 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 661 " --> pdb=" O ILE D 657 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU D 666 " --> pdb=" O SER D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 688 removed outlier: 3.907A pdb=" N VAL D 677 " --> pdb=" O GLN D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 698 removed outlier: 6.093A pdb=" N ASP D 695 " --> pdb=" O ALA D 692 " (cutoff:3.500A) Proline residue: D 696 - end of helix Processing helix chain 'E' and resid 105 through 121 Processing helix chain 'E' and resid 134 through 147 removed outlier: 3.517A pdb=" N GLU E 141 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 161 removed outlier: 3.809A pdb=" N MET E 160 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG E 161 " --> pdb=" O HIS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 173 Processing helix chain 'E' and resid 173 through 193 Proline residue: E 179 - end of helix Processing helix chain 'E' and resid 194 through 198 removed outlier: 3.668A pdb=" N ASN E 198 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.636A pdb=" N ILE E 279 " --> pdb=" O ILE E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 284 removed outlier: 3.719A pdb=" N LYS E 283 " --> pdb=" O ARG E 280 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE E 284 " --> pdb=" O SER E 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 280 through 284' Processing helix chain 'E' and resid 364 through 368 removed outlier: 3.710A pdb=" N ILE E 368 " --> pdb=" O ALA E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 407 through 410 removed outlier: 3.823A pdb=" N LEU E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 407 through 410' Processing helix chain 'E' and resid 513 through 522 removed outlier: 3.693A pdb=" N LYS E 521 " --> pdb=" O LYS E 517 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP E 522 " --> pdb=" O GLU E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 532 Processing helix chain 'E' and resid 540 through 553 Processing helix chain 'E' and resid 581 through 592 removed outlier: 4.018A pdb=" N LEU E 585 " --> pdb=" O LYS E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 609 Processing helix chain 'E' and resid 640 through 644 Processing helix chain 'E' and resid 645 through 658 removed outlier: 3.594A pdb=" N ALA E 651 " --> pdb=" O SER E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 694 through 699 Processing helix chain 'E' and resid 702 through 708 removed outlier: 3.772A pdb=" N ARG E 708 " --> pdb=" O PRO E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 720 through 738 Processing helix chain 'E' and resid 747 through 759 removed outlier: 3.574A pdb=" N ARG E 753 " --> pdb=" O GLU E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 766 through 784 removed outlier: 3.736A pdb=" N SER E 771 " --> pdb=" O LYS E 767 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 815 removed outlier: 3.702A pdb=" N LEU E 800 " --> pdb=" O THR E 796 " (cutoff:3.500A) Processing helix chain 'E' and resid 820 through 835 removed outlier: 3.536A pdb=" N ILE E 824 " --> pdb=" O THR E 820 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE E 835 " --> pdb=" O LEU E 831 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 26 removed outlier: 3.674A pdb=" N ASN F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU F 20 " --> pdb=" O ASN F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 72 removed outlier: 3.643A pdb=" N ASN F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.526A pdb=" N PHE F 93 " --> pdb=" O GLN F 89 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 109 removed outlier: 3.595A pdb=" N ALA F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 124 removed outlier: 4.361A pdb=" N PHE F 113 " --> pdb=" O ASN F 109 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU F 115 " --> pdb=" O ASN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 165 removed outlier: 3.676A pdb=" N ILE F 142 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 154 " --> pdb=" O ASN F 150 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN F 165 " --> pdb=" O ILE F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 189 removed outlier: 3.594A pdb=" N GLU F 183 " --> pdb=" O ASP F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 198 Processing helix chain 'F' and resid 208 through 215 removed outlier: 3.522A pdb=" N TYR F 215 " --> pdb=" O CYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 235 removed outlier: 3.638A pdb=" N LEU F 235 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 292 Processing helix chain 'F' and resid 318 through 322 removed outlier: 3.531A pdb=" N VAL F 322 " --> pdb=" O SER F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 363 through 367 Processing helix chain 'F' and resid 394 through 407 removed outlier: 3.586A pdb=" N SER F 407 " --> pdb=" O GLU F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 416 Processing helix chain 'F' and resid 425 through 438 Processing helix chain 'F' and resid 465 through 477 Processing helix chain 'F' and resid 489 through 493 removed outlier: 3.638A pdb=" N GLY F 492 " --> pdb=" O SER F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 516 Processing helix chain 'F' and resid 525 through 529 removed outlier: 3.647A pdb=" N MET F 529 " --> pdb=" O PHE F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 544 removed outlier: 3.550A pdb=" N ALA F 536 " --> pdb=" O SER F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 583 Processing helix chain 'F' and resid 587 through 592 Processing helix chain 'F' and resid 605 through 622 removed outlier: 3.915A pdb=" N GLU F 610 " --> pdb=" O ARG F 606 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS F 611 " --> pdb=" O ASP F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 647 Processing helix chain 'F' and resid 653 through 677 removed outlier: 3.501A pdb=" N TYR F 659 " --> pdb=" O ALA F 655 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS F 672 " --> pdb=" O ARG F 668 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG F 673 " --> pdb=" O GLN F 669 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU F 674 " --> pdb=" O ASP F 670 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER F 677 " --> pdb=" O ARG F 673 " (cutoff:3.500A) Processing helix chain 'F' and resid 685 through 704 removed outlier: 3.721A pdb=" N LEU F 689 " --> pdb=" O THR F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 709 through 723 removed outlier: 3.778A pdb=" N VAL F 713 " --> pdb=" O ASP F 709 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 729 removed outlier: 3.618A pdb=" N LEU F 727 " --> pdb=" O LYS F 724 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN F 729 " --> pdb=" O SER F 726 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 753 Processing helix chain 'F' and resid 762 through 773 Processing helix chain 'F' and resid 775 through 789 Processing sheet with id=AA1, first strand: chain '2' and resid 241 through 244 Processing sheet with id=AA2, first strand: chain '2' and resid 317 through 327 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 317 through 327 current: chain '2' and resid 346 through 352 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 346 through 352 current: chain '2' and resid 405 through 411 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 405 through 411 current: chain '2' and resid 448 through 458 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '2' and resid 525 through 526 Processing sheet with id=AA4, first strand: chain '2' and resid 563 through 567 removed outlier: 3.505A pdb=" N ALA 2 649 " --> pdb=" O ILE 2 606 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL 2 683 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU 2 542 " --> pdb=" O VAL 2 683 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 579 through 582 Processing sheet with id=AA6, first strand: chain '2' and resid 628 through 633 Processing sheet with id=AA7, first strand: chain '3' and resid 95 through 99 Processing sheet with id=AA8, first strand: chain '3' and resid 165 through 166 removed outlier: 3.520A pdb=" N GLU 3 183 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '3' and resid 179 through 189 current: chain '3' and resid 209 through 213 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 209 through 213 current: chain '3' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 273 through 279 current: chain '3' and resid 318 through 330 Processing sheet with id=AA9, first strand: chain '3' and resid 391 through 392 removed outlier: 3.579A pdb=" N LYS 3 391 " --> pdb=" O LEU 3 399 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 429 through 433 removed outlier: 6.406A pdb=" N GLY 3 468 " --> pdb=" O SER 3 511 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE 3 513 " --> pdb=" O GLY 3 468 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL 3 470 " --> pdb=" O ILE 3 513 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ALA 3 515 " --> pdb=" O VAL 3 470 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE 3 472 " --> pdb=" O ALA 3 515 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE 3 405 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ALA 3 516 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N MET 3 407 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU 3 406 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 444 through 448 Processing sheet with id=AB3, first strand: chain '3' and resid 494 through 498 Processing sheet with id=AB4, first strand: chain '4' and resid 240 through 243 Processing sheet with id=AB5, first strand: chain '4' and resid 325 through 335 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 325 through 335 current: chain '4' and resid 355 through 359 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 355 through 359 current: chain '4' and resid 414 through 420 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 414 through 420 current: chain '4' and resid 458 through 467 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '4' and resid 364 through 367 Processing sheet with id=AB7, first strand: chain '4' and resid 453 through 454 Processing sheet with id=AB8, first strand: chain '4' and resid 550 through 551 Processing sheet with id=AB9, first strand: chain '4' and resid 588 through 591 removed outlier: 3.791A pdb=" N VAL 4 589 " --> pdb=" O VAL 4 628 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY 4 568 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL 4 708 " --> pdb=" O LEU 4 565 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N CYS 4 567 " --> pdb=" O VAL 4 708 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 603 through 607 removed outlier: 3.553A pdb=" N TYR 4 604 " --> pdb=" O GLU 4 617 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 653 through 658 Processing sheet with id=AC3, first strand: chain '4' and resid 761 through 762 removed outlier: 7.110A pdb=" N ILE 4 761 " --> pdb=" O VAL 4 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '5' and resid 8 through 12 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 8 through 12 current: chain 'F' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 267 through 272 current: chain 'F' and resid 330 through 336 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 330 through 336 current: chain 'F' and resid 372 through 383 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain '5' and resid 60 through 64 removed outlier: 6.072A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASN 5 140 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL 5 63 " --> pdb=" O ASN 5 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain '5' and resid 159 through 169 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 159 through 169 current: chain '5' and resid 189 through 193 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 189 through 193 current: chain '5' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 273 through 279 current: chain '5' and resid 325 through 335 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain '5' and resid 398 through 399 Processing sheet with id=AC8, first strand: chain '5' and resid 436 through 440 removed outlier: 7.050A pdb=" N VAL 5 437 " --> pdb=" O CYS 5 478 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASP 5 480 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR 5 439 " --> pdb=" O ASP 5 480 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY 5 416 " --> pdb=" O ALA 5 523 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN 5 411 " --> pdb=" O MET 5 552 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE 5 554 " --> pdb=" O ASN 5 411 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU 5 413 " --> pdb=" O PHE 5 554 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL 5 556 " --> pdb=" O LEU 5 413 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU 5 415 " --> pdb=" O VAL 5 556 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 452 through 455 removed outlier: 6.803A pdb=" N SER 5 452 " --> pdb=" O GLU 5 465 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 501 through 505 Processing sheet with id=AD2, first strand: chain '6' and resid 150 through 154 removed outlier: 3.661A pdb=" N PHE 6 268 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 287 through 297 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 287 through 297 current: chain '6' and resid 317 through 322 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 317 through 322 current: chain '6' and resid 376 through 382 WARNING: can't find start of bonding for strands! previous: chain '6' and resid 376 through 382 current: chain '6' and resid 450 through 461 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain '6' and resid 557 through 558 Processing sheet with id=AD5, first strand: chain '6' and resid 595 through 599 removed outlier: 6.129A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '6' and resid 610 through 614 Processing sheet with id=AD7, first strand: chain '6' and resid 660 through 665 Processing sheet with id=AD8, first strand: chain '7' and resid 77 through 81 Processing sheet with id=AD9, first strand: chain '7' and resid 238 through 248 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 238 through 248 current: chain '7' and resid 267 through 272 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 267 through 272 current: chain '7' and resid 330 through 336 WARNING: can't find start of bonding for strands! previous: chain '7' and resid 330 through 336 current: chain '7' and resid 372 through 383 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain '7' and resid 442 through 445 removed outlier: 6.600A pdb=" N MET 7 448 " --> pdb=" O VAL 7 444 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '7' and resid 480 through 484 removed outlier: 6.517A pdb=" N CYS 7 457 " --> pdb=" O PHE 7 598 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N MET 7 600 " --> pdb=" O CYS 7 457 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET 7 459 " --> pdb=" O MET 7 600 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '7' and resid 495 through 499 Processing sheet with id=AE4, first strand: chain '7' and resid 545 through 550 removed outlier: 3.532A pdb=" N THR 7 555 " --> pdb=" O ILE 7 548 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '7' and resid 759 through 761 Processing sheet with id=AE6, first strand: chain 'A' and resid 241 through 244 Processing sheet with id=AE7, first strand: chain 'A' and resid 317 through 327 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 317 through 327 current: chain 'A' and resid 346 through 352 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 346 through 352 current: chain 'A' and resid 405 through 411 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 405 through 411 current: chain 'A' and resid 448 through 458 No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'A' and resid 525 through 526 Processing sheet with id=AE9, first strand: chain 'A' and resid 563 through 567 removed outlier: 3.505A pdb=" N ALA A 649 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 540 " --> pdb=" O CYS A 681 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL A 683 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A 542 " --> pdb=" O VAL A 683 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 579 through 582 Processing sheet with id=AF2, first strand: chain 'A' and resid 628 through 633 Processing sheet with id=AF3, first strand: chain 'B' and resid 95 through 99 Processing sheet with id=AF4, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.520A pdb=" N GLU B 183 " --> pdb=" O LEU B 166 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 179 through 189 current: chain 'B' and resid 209 through 213 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 209 through 213 current: chain 'B' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 273 through 279 current: chain 'B' and resid 318 through 330 Processing sheet with id=AF5, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.579A pdb=" N LYS B 391 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 429 through 433 removed outlier: 6.406A pdb=" N GLY B 468 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE B 513 " --> pdb=" O GLY B 468 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL B 470 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ALA B 515 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE B 472 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE B 405 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA B 516 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N MET B 407 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 406 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 444 through 448 Processing sheet with id=AF8, first strand: chain 'B' and resid 494 through 498 Processing sheet with id=AF9, first strand: chain 'C' and resid 240 through 243 Processing sheet with id=AG1, first strand: chain 'C' and resid 325 through 335 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 325 through 335 current: chain 'C' and resid 355 through 359 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 355 through 359 current: chain 'C' and resid 414 through 420 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 414 through 420 current: chain 'C' and resid 458 through 467 No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'C' and resid 364 through 367 Processing sheet with id=AG3, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AG4, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AG5, first strand: chain 'C' and resid 588 through 591 removed outlier: 3.791A pdb=" N VAL C 589 " --> pdb=" O VAL C 628 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY C 568 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU C 565 " --> pdb=" O TYR C 706 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL C 708 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS C 567 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 603 through 607 removed outlier: 3.553A pdb=" N TYR C 604 " --> pdb=" O GLU C 617 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 653 through 658 Processing sheet with id=AG8, first strand: chain 'C' and resid 761 through 762 removed outlier: 7.110A pdb=" N ILE C 761 " --> pdb=" O VAL C 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'D' and resid 60 through 64 removed outlier: 6.073A pdb=" N LEU D 61 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASN D 140 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL D 63 " --> pdb=" O ASN D 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'D' and resid 159 through 169 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 159 through 169 current: chain 'D' and resid 189 through 193 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 189 through 193 current: chain 'D' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 273 through 279 current: chain 'D' and resid 325 through 335 No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'D' and resid 398 through 399 Processing sheet with id=AH3, first strand: chain 'D' and resid 436 through 440 removed outlier: 7.050A pdb=" N VAL D 437 " --> pdb=" O CYS D 478 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASP D 480 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR D 439 " --> pdb=" O ASP D 480 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 416 " --> pdb=" O ALA D 523 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN D 411 " --> pdb=" O MET D 552 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE D 554 " --> pdb=" O ASN D 411 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU D 413 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL D 556 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU D 415 " --> pdb=" O VAL D 556 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 452 through 455 removed outlier: 6.803A pdb=" N SER D 452 " --> pdb=" O GLU D 465 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 501 through 505 Processing sheet with id=AH6, first strand: chain 'E' and resid 150 through 154 removed outlier: 3.661A pdb=" N PHE E 268 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 287 through 297 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 287 through 297 current: chain 'E' and resid 317 through 322 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 317 through 322 current: chain 'E' and resid 376 through 382 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 376 through 382 current: chain 'E' and resid 450 through 461 No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'E' and resid 557 through 558 Processing sheet with id=AH9, first strand: chain 'E' and resid 595 through 599 removed outlier: 6.129A pdb=" N VAL E 596 " --> pdb=" O CYS E 637 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASP E 639 " --> pdb=" O VAL E 596 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR E 598 " --> pdb=" O ASP E 639 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 610 through 614 Processing sheet with id=AI2, first strand: chain 'E' and resid 660 through 665 Processing sheet with id=AI3, first strand: chain 'F' and resid 77 through 81 Processing sheet with id=AI4, first strand: chain 'F' and resid 442 through 445 removed outlier: 6.601A pdb=" N MET F 448 " --> pdb=" O VAL F 444 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 480 through 484 removed outlier: 6.517A pdb=" N CYS F 457 " --> pdb=" O PHE F 598 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N MET F 600 " --> pdb=" O CYS F 457 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET F 459 " --> pdb=" O MET F 600 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 495 through 499 Processing sheet with id=AI7, first strand: chain 'F' and resid 545 through 550 removed outlier: 3.531A pdb=" N THR F 555 " --> pdb=" O ILE F 548 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 759 through 761 2282 hydrogen bonds defined for protein. 6450 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 26.41 Time building geometry restraints manager: 17.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 10574 1.28 - 1.41: 15306 1.41 - 1.55: 38636 1.55 - 1.68: 378 1.68 - 1.82: 464 Bond restraints: 65358 Sorted by residual: bond pdb=" C GLN D 584 " pdb=" O GLN D 584 " ideal model delta sigma weight residual 1.237 1.141 0.096 1.36e-02 5.41e+03 4.95e+01 bond pdb=" C GLN 5 584 " pdb=" O GLN 5 584 " ideal model delta sigma weight residual 1.237 1.141 0.096 1.36e-02 5.41e+03 4.95e+01 bond pdb=" C ARG D 658 " pdb=" O ARG D 658 " ideal model delta sigma weight residual 1.236 1.163 0.072 1.19e-02 7.06e+03 3.70e+01 bond pdb=" C ARG 5 658 " pdb=" O ARG 5 658 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.19e-02 7.06e+03 3.62e+01 bond pdb=" C4 ADP F1000 " pdb=" C5 ADP F1000 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.24e+01 ... (remaining 65353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 86180 2.81 - 5.63: 2414 5.63 - 8.44: 221 8.44 - 11.26: 40 11.26 - 14.07: 4 Bond angle restraints: 88859 Sorted by residual: angle pdb=" PA ATP A1000 " pdb=" O3A ATP A1000 " pdb=" PB ATP A1000 " ideal model delta sigma weight residual 136.83 126.95 9.88 1.00e+00 1.00e+00 9.76e+01 angle pdb=" PA ATP 21000 " pdb=" O3A ATP 21000 " pdb=" PB ATP 21000 " ideal model delta sigma weight residual 136.83 126.97 9.86 1.00e+00 1.00e+00 9.72e+01 angle pdb=" N GLN 7 753 " pdb=" CA GLN 7 753 " pdb=" C GLN 7 753 " ideal model delta sigma weight residual 110.53 101.08 9.45 1.32e+00 5.74e-01 5.13e+01 angle pdb=" N GLN F 753 " pdb=" CA GLN F 753 " pdb=" C GLN F 753 " ideal model delta sigma weight residual 110.53 101.09 9.44 1.32e+00 5.74e-01 5.12e+01 angle pdb=" CA ASP 4 256 " pdb=" CB ASP 4 256 " pdb=" CG ASP 4 256 " ideal model delta sigma weight residual 112.60 119.68 -7.08 1.00e+00 1.00e+00 5.01e+01 ... (remaining 88854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 38786 33.87 - 67.73: 1073 67.73 - 101.60: 93 101.60 - 135.46: 2 135.46 - 169.33: 6 Dihedral angle restraints: 39960 sinusoidal: 17086 harmonic: 22874 Sorted by residual: dihedral pdb=" C5' ADP F1000 " pdb=" O5' ADP F1000 " pdb=" PA ADP F1000 " pdb=" O2A ADP F1000 " ideal model delta sinusoidal sigma weight residual 300.00 156.07 143.93 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" C5' ADP 71000 " pdb=" O5' ADP 71000 " pdb=" PA ADP 71000 " pdb=" O2A ADP 71000 " ideal model delta sinusoidal sigma weight residual 300.00 156.07 143.93 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" C5' ADP B1000 " pdb=" O5' ADP B1000 " pdb=" PA ADP B1000 " pdb=" O2A ADP B1000 " ideal model delta sinusoidal sigma weight residual 300.00 162.06 137.94 1 2.00e+01 2.50e-03 4.18e+01 ... (remaining 39957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 8072 0.053 - 0.106: 1662 0.106 - 0.160: 483 0.160 - 0.213: 84 0.213 - 0.266: 13 Chirality restraints: 10314 Sorted by residual: chirality pdb=" CA ILE B 359 " pdb=" N ILE B 359 " pdb=" C ILE B 359 " pdb=" CB ILE B 359 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ILE 3 359 " pdb=" N ILE 3 359 " pdb=" C ILE 3 359 " pdb=" CB ILE 3 359 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ASP 4 278 " pdb=" N ASP 4 278 " pdb=" C ASP 4 278 " pdb=" CB ASP 4 278 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 10311 not shown) Planarity restraints: 11040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 459 " 0.023 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C MET F 459 " -0.081 2.00e-02 2.50e+03 pdb=" O MET F 459 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY F 460 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET 7 459 " -0.023 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" C MET 7 459 " 0.080 2.00e-02 2.50e+03 pdb=" O MET 7 459 " -0.029 2.00e-02 2.50e+03 pdb=" N GLY 7 460 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS 5 609 " 0.023 2.00e-02 2.50e+03 4.51e-02 2.03e+01 pdb=" C LYS 5 609 " -0.078 2.00e-02 2.50e+03 pdb=" O LYS 5 609 " 0.029 2.00e-02 2.50e+03 pdb=" N CYS 5 610 " 0.026 2.00e-02 2.50e+03 ... (remaining 11037 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 20163 2.85 - 3.36: 56880 3.36 - 3.87: 97940 3.87 - 4.39: 114015 4.39 - 4.90: 195176 Nonbonded interactions: 484174 Sorted by model distance: nonbonded pdb=" O ARG 2 485 " pdb=" OG SER 2 488 " model vdw 2.334 3.040 nonbonded pdb=" O ARG A 485 " pdb=" OG SER A 488 " model vdw 2.335 3.040 nonbonded pdb=" O GLU 7 160 " pdb=" OG SER 7 163 " model vdw 2.335 3.040 nonbonded pdb=" O GLU F 160 " pdb=" OG SER F 163 " model vdw 2.335 3.040 nonbonded pdb=" OE1 GLU 5 91 " pdb=" O PHE 5 135 " model vdw 2.338 3.040 ... (remaining 484169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '2' selection = chain 'A' } ncs_group { reference = chain '3' selection = chain 'B' } ncs_group { reference = chain '4' selection = chain 'C' } ncs_group { reference = chain '5' selection = chain 'D' } ncs_group { reference = chain '6' selection = chain 'E' } ncs_group { reference = chain '7' selection = chain 'F' } ncs_group { reference = (chain 'X' and (resid 1 through 25 or resid 29 through 53)) selection = (chain 'Y' and (resid 1 through 25 or resid 29 through 53)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 2.190 Check model and map are aligned: 0.360 Set scattering table: 0.460 Process input model: 143.550 Find NCS groups from input model: 3.780 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 65358 Z= 0.434 Angle : 0.994 14.073 88859 Z= 0.654 Chirality : 0.050 0.266 10314 Planarity : 0.006 0.063 11040 Dihedral : 15.373 169.328 25104 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.95 % Favored : 94.89 % Rotamer: Outliers : 0.87 % Allowed : 1.58 % Favored : 97.56 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.09), residues: 7714 helix: -0.48 (0.09), residues: 2946 sheet: 0.13 (0.13), residues: 1558 loop : -1.76 (0.10), residues: 3210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP 7 792 HIS 0.008 0.001 HIS E 730 PHE 0.041 0.002 PHE 5 31 TYR 0.034 0.002 TYR C 519 ARG 0.010 0.001 ARG F 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 474 time to evaluate : 5.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 491 ASP cc_start: 0.7448 (t0) cc_final: 0.7239 (t0) REVERT: 4 811 MET cc_start: 0.7325 (ttp) cc_final: 0.6838 (ttm) REVERT: A 624 MET cc_start: 0.8240 (mtp) cc_final: 0.8005 (mtp) REVERT: C 491 ASP cc_start: 0.7415 (t0) cc_final: 0.7194 (t0) REVERT: C 811 MET cc_start: 0.7379 (ttp) cc_final: 0.7004 (ttm) outliers start: 60 outliers final: 11 residues processed: 530 average time/residue: 1.4210 time to fit residues: 973.4137 Evaluate side-chains 267 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 256 time to evaluate : 5.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 266 GLN Chi-restraints excluded: chain 4 residue 553 THR Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 5 residue 585 ASN Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain D residue 585 ASN Chi-restraints excluded: chain F residue 285 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 663 optimal weight: 1.9990 chunk 595 optimal weight: 7.9990 chunk 330 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 401 optimal weight: 3.9990 chunk 318 optimal weight: 2.9990 chunk 616 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 374 optimal weight: 0.9980 chunk 458 optimal weight: 3.9990 chunk 713 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 188 ASN 2 405 HIS 3 253 HIS 4 259 HIS 4 808 HIS 5 571 HIS 5 625 ASN 5 632 GLN 6 347 ASN 6 730 HIS ** 7 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 405 HIS C 218 ASN C 259 HIS C 808 HIS D 571 HIS D 632 GLN E 730 HIS ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.083939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.065880 restraints weight = 198073.117| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.03 r_work: 0.3224 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 65358 Z= 0.259 Angle : 0.628 9.746 88859 Z= 0.328 Chirality : 0.045 0.162 10314 Planarity : 0.005 0.067 11040 Dihedral : 13.253 178.884 9831 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 1.23 % Allowed : 5.71 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.09), residues: 7714 helix: 0.37 (0.09), residues: 3030 sheet: 0.07 (0.13), residues: 1562 loop : -1.48 (0.10), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 792 HIS 0.007 0.001 HIS 6 730 PHE 0.015 0.002 PHE 6 122 TYR 0.030 0.002 TYR 4 519 ARG 0.007 0.001 ARG A 489 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 280 time to evaluate : 5.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 264 MET cc_start: 0.9057 (mtp) cc_final: 0.8727 (mtp) REVERT: 4 811 MET cc_start: 0.7728 (ttp) cc_final: 0.7328 (ttm) REVERT: 5 197 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: 5 404 MET cc_start: 0.7793 (mpm) cc_final: 0.7522 (mpm) REVERT: 5 585 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8272 (t0) REVERT: 6 313 MET cc_start: 0.8385 (mmt) cc_final: 0.8012 (mmt) REVERT: 7 459 MET cc_start: 0.8454 (mtp) cc_final: 0.8063 (mtm) REVERT: 7 666 ARG cc_start: 0.7987 (mpt180) cc_final: 0.7779 (mpt180) REVERT: 7 707 MET cc_start: 0.8635 (mpp) cc_final: 0.8325 (mpt) REVERT: 7 787 SER cc_start: 0.8647 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 264 MET cc_start: 0.9168 (mtt) cc_final: 0.8866 (mtt) REVERT: C 217 ASN cc_start: 0.8745 (m-40) cc_final: 0.8499 (p0) REVERT: C 491 ASP cc_start: 0.8206 (t0) cc_final: 0.7997 (t0) REVERT: C 811 MET cc_start: 0.7772 (ttp) cc_final: 0.7374 (ttm) REVERT: D 197 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: D 404 MET cc_start: 0.7766 (mpm) cc_final: 0.7503 (mpm) REVERT: D 585 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8335 (t0) REVERT: E 313 MET cc_start: 0.8260 (mmm) cc_final: 0.8006 (mmt) REVERT: F 459 MET cc_start: 0.8453 (mtp) cc_final: 0.8169 (mtm) REVERT: F 666 ARG cc_start: 0.7921 (mpt180) cc_final: 0.7701 (mpt180) REVERT: F 787 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8312 (p) outliers start: 85 outliers final: 16 residues processed: 331 average time/residue: 1.4061 time to fit residues: 608.3229 Evaluate side-chains 267 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 5.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 719 LYS Chi-restraints excluded: chain 4 residue 240 ASN Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 585 ASN Chi-restraints excluded: chain 7 residue 30 GLN Chi-restraints excluded: chain 7 residue 269 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 787 SER Chi-restraints excluded: chain 7 residue 803 PHE Chi-restraints excluded: chain B residue 719 LYS Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 585 ASN Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 787 SER Chi-restraints excluded: chain F residue 803 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 257 optimal weight: 7.9990 chunk 295 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 775 optimal weight: 9.9990 chunk 348 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 453 optimal weight: 3.9990 chunk 4 optimal weight: 0.1980 chunk 520 optimal weight: 6.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 487 HIS 4 218 ASN 5 49 GLN 5 411 ASN 6 139 GLN 6 357 GLN 7 210 ASN 7 334 HIS B 253 HIS B 487 HIS C 218 ASN D 411 ASN D 584 GLN E 139 GLN E 357 GLN F 210 ASN F 334 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.082174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.063923 restraints weight = 198691.369| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.95 r_work: 0.3175 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 65358 Z= 0.375 Angle : 0.633 9.110 88859 Z= 0.332 Chirality : 0.045 0.181 10314 Planarity : 0.005 0.065 11040 Dihedral : 13.248 179.067 9822 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.34 % Allowed : 8.31 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.09), residues: 7714 helix: 0.51 (0.09), residues: 3056 sheet: -0.19 (0.12), residues: 1618 loop : -1.39 (0.10), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 111 HIS 0.009 0.001 HIS C 413 PHE 0.022 0.002 PHE F 745 TYR 0.026 0.002 TYR C 519 ARG 0.004 0.000 ARG 3 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 256 time to evaluate : 5.773 Fit side-chains revert: symmetry clash REVERT: 4 780 MET cc_start: 0.8712 (tmm) cc_final: 0.8469 (tmm) REVERT: 4 811 MET cc_start: 0.8036 (ttp) cc_final: 0.7749 (ttm) REVERT: 5 197 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.6858 (m-80) REVERT: 5 404 MET cc_start: 0.7709 (mpm) cc_final: 0.7480 (mpm) REVERT: 5 480 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: 6 313 MET cc_start: 0.8481 (mmt) cc_final: 0.8245 (mmt) REVERT: 7 95 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7339 (pp30) REVERT: 7 707 MET cc_start: 0.8644 (mpp) cc_final: 0.8345 (mpp) REVERT: 7 787 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8286 (p) REVERT: C 491 ASP cc_start: 0.8207 (t0) cc_final: 0.7999 (t0) REVERT: C 780 MET cc_start: 0.8675 (tmm) cc_final: 0.8393 (tmm) REVERT: C 811 MET cc_start: 0.8049 (ttp) cc_final: 0.7816 (ttm) REVERT: D 197 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: D 404 MET cc_start: 0.7714 (mpm) cc_final: 0.7482 (mpm) REVERT: D 480 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8081 (m-30) REVERT: E 313 MET cc_start: 0.8415 (mmm) cc_final: 0.8183 (mmt) REVERT: F 459 MET cc_start: 0.8514 (mtp) cc_final: 0.8266 (mtm) REVERT: F 787 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8323 (p) outliers start: 93 outliers final: 24 residues processed: 309 average time/residue: 1.4279 time to fit residues: 581.0540 Evaluate side-chains 268 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 5.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 206 THR Chi-restraints excluded: chain 4 residue 215 PHE Chi-restraints excluded: chain 4 residue 240 ASN Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 480 ASP Chi-restraints excluded: chain 7 residue 30 GLN Chi-restraints excluded: chain 7 residue 95 GLN Chi-restraints excluded: chain 7 residue 211 CYS Chi-restraints excluded: chain 7 residue 269 VAL Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 782 CYS Chi-restraints excluded: chain 7 residue 787 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 749 MET Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 782 CYS Chi-restraints excluded: chain F residue 787 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 450 optimal weight: 8.9990 chunk 507 optimal weight: 1.9990 chunk 410 optimal weight: 5.9990 chunk 575 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 404 optimal weight: 7.9990 chunk 685 optimal weight: 4.9990 chunk 393 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 672 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 528 ASN 3 691 ASN 5 561 ASN 5 585 ASN ** 7 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 796 ASN A 528 ASN B 691 ASN D 561 ASN D 585 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 796 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.083173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.065020 restraints weight = 201001.778| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.03 r_work: 0.3201 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 65358 Z= 0.204 Angle : 0.541 10.078 88859 Z= 0.278 Chirality : 0.042 0.141 10314 Planarity : 0.004 0.059 11040 Dihedral : 13.001 177.821 9816 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.27 % Allowed : 9.32 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.09), residues: 7714 helix: 0.97 (0.10), residues: 3046 sheet: -0.13 (0.12), residues: 1554 loop : -1.18 (0.10), residues: 3114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 3 111 HIS 0.010 0.001 HIS F 622 PHE 0.019 0.001 PHE 7 745 TYR 0.021 0.001 TYR C 519 ARG 0.005 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 258 time to evaluate : 5.745 Fit side-chains REVERT: 4 491 ASP cc_start: 0.8181 (t0) cc_final: 0.7903 (t0) REVERT: 4 780 MET cc_start: 0.8660 (tmm) cc_final: 0.8421 (tmm) REVERT: 4 811 MET cc_start: 0.7973 (ttp) cc_final: 0.7607 (ttm) REVERT: 5 197 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.6730 (m-80) REVERT: 5 404 MET cc_start: 0.7592 (mpm) cc_final: 0.7233 (mpm) REVERT: 6 313 MET cc_start: 0.8525 (mmt) cc_final: 0.8140 (mmt) REVERT: 7 95 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6988 (pp30) REVERT: 7 787 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8256 (p) REVERT: C 491 ASP cc_start: 0.8177 (t0) cc_final: 0.7955 (t0) REVERT: C 780 MET cc_start: 0.8650 (tmm) cc_final: 0.8377 (tmm) REVERT: C 811 MET cc_start: 0.7977 (ttp) cc_final: 0.7628 (ttm) REVERT: D 404 MET cc_start: 0.7591 (mpm) cc_final: 0.7264 (mpm) REVERT: E 313 MET cc_start: 0.8377 (mmm) cc_final: 0.8108 (mmt) REVERT: F 459 MET cc_start: 0.8384 (mtp) cc_final: 0.8069 (mtm) REVERT: F 787 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8377 (p) outliers start: 88 outliers final: 22 residues processed: 310 average time/residue: 1.3146 time to fit residues: 541.8575 Evaluate side-chains 261 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 5.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 556 ILE Chi-restraints excluded: chain 4 residue 240 ASN Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 724 LEU Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 374 ILE Chi-restraints excluded: chain 5 residue 402 ASP Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 7 residue 95 GLN Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 782 CYS Chi-restraints excluded: chain 7 residue 787 SER Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 782 CYS Chi-restraints excluded: chain F residue 787 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 482 optimal weight: 6.9990 chunk 471 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 557 optimal weight: 9.9990 chunk 602 optimal weight: 6.9990 chunk 751 optimal weight: 20.0000 chunk 380 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 582 optimal weight: 3.9990 chunk 728 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 413 HIS ** 5 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 753 GLN C 413 HIS D 49 GLN ** D 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 753 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.081746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.063357 restraints weight = 198225.916| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.97 r_work: 0.3162 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 65358 Z= 0.427 Angle : 0.647 9.830 88859 Z= 0.335 Chirality : 0.046 0.183 10314 Planarity : 0.005 0.062 11040 Dihedral : 13.172 177.948 9815 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.56 % Allowed : 10.42 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.09), residues: 7714 helix: 0.77 (0.09), residues: 3038 sheet: -0.38 (0.12), residues: 1574 loop : -1.23 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 6 356 HIS 0.010 0.001 HIS C 413 PHE 0.021 0.002 PHE E 122 TYR 0.026 0.002 TYR 4 519 ARG 0.005 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 239 time to evaluate : 5.853 Fit side-chains REVERT: 2 258 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8301 (tt) REVERT: 3 264 MET cc_start: 0.9045 (mtp) cc_final: 0.8754 (mtt) REVERT: 3 462 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.8752 (mpp) REVERT: 4 491 ASP cc_start: 0.8250 (t0) cc_final: 0.7902 (t0) REVERT: 4 811 MET cc_start: 0.7960 (ttp) cc_final: 0.7669 (ttm) REVERT: 5 197 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: 5 404 MET cc_start: 0.7793 (mpm) cc_final: 0.7583 (mpm) REVERT: 5 480 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8177 (m-30) REVERT: 6 313 MET cc_start: 0.8563 (mmt) cc_final: 0.8270 (mmt) REVERT: 7 95 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7015 (pp30) REVERT: 7 787 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8199 (p) REVERT: A 258 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8305 (tt) REVERT: B 462 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8769 (mpp) REVERT: C 491 ASP cc_start: 0.8174 (t0) cc_final: 0.7943 (t0) REVERT: C 780 MET cc_start: 0.8642 (tmm) cc_final: 0.8427 (tmm) REVERT: C 811 MET cc_start: 0.7967 (ttp) cc_final: 0.7735 (ttm) REVERT: D 197 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.6782 (m-80) REVERT: D 480 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8154 (m-30) REVERT: F 459 MET cc_start: 0.8472 (mtp) cc_final: 0.8195 (mtm) REVERT: F 787 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8076 (p) outliers start: 108 outliers final: 43 residues processed: 322 average time/residue: 1.3283 time to fit residues: 569.3819 Evaluate side-chains 286 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 5.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 206 THR Chi-restraints excluded: chain 3 residue 359 ILE Chi-restraints excluded: chain 3 residue 395 ASN Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 556 ILE Chi-restraints excluded: chain 4 residue 215 PHE Chi-restraints excluded: chain 4 residue 240 ASN Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 501 ILE Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 724 LEU Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 402 ASP Chi-restraints excluded: chain 5 residue 480 ASP Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 7 residue 95 GLN Chi-restraints excluded: chain 7 residue 211 CYS Chi-restraints excluded: chain 7 residue 222 SER Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 459 MET Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 7 residue 782 CYS Chi-restraints excluded: chain 7 residue 787 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 541 MET Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 787 SER Chi-restraints excluded: chain F residue 789 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 291 optimal weight: 7.9990 chunk 211 optimal weight: 10.0000 chunk 649 optimal weight: 0.8980 chunk 55 optimal weight: 0.0000 chunk 297 optimal weight: 5.9990 chunk 761 optimal weight: 3.9990 chunk 681 optimal weight: 0.0970 chunk 214 optimal weight: 4.9990 chunk 664 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 585 ASN ** 7 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 583 ASN D 49 GLN D 585 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 583 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.083507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.065230 restraints weight = 196577.582| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.98 r_work: 0.3209 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 65358 Z= 0.190 Angle : 0.533 10.528 88859 Z= 0.272 Chirality : 0.042 0.145 10314 Planarity : 0.004 0.057 11040 Dihedral : 12.936 177.466 9815 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.56 % Allowed : 11.05 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.09), residues: 7714 helix: 1.15 (0.10), residues: 3046 sheet: -0.25 (0.13), residues: 1530 loop : -1.07 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 111 HIS 0.004 0.001 HIS 3 712 PHE 0.012 0.001 PHE 7 113 TYR 0.018 0.001 TYR 4 519 ARG 0.009 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 246 time to evaluate : 6.000 Fit side-chains REVERT: 2 258 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8253 (tt) REVERT: 3 264 MET cc_start: 0.9011 (mtp) cc_final: 0.8723 (mtt) REVERT: 3 462 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.8698 (mpp) REVERT: 4 811 MET cc_start: 0.7986 (ttp) cc_final: 0.7706 (ttm) REVERT: 5 197 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.6723 (m-80) REVERT: 5 404 MET cc_start: 0.7793 (mpm) cc_final: 0.7451 (mpm) REVERT: 6 313 MET cc_start: 0.8584 (mmt) cc_final: 0.8271 (mmt) REVERT: 7 95 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.6991 (pp30) REVERT: 7 787 SER cc_start: 0.8441 (t) cc_final: 0.8070 (p) REVERT: A 258 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8263 (tt) REVERT: B 462 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.8693 (mpp) REVERT: C 491 ASP cc_start: 0.8154 (t0) cc_final: 0.7932 (t0) REVERT: C 811 MET cc_start: 0.7986 (ttp) cc_final: 0.7706 (ttm) REVERT: D 197 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.6579 (m-80) REVERT: D 480 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8114 (m-30) REVERT: F 459 MET cc_start: 0.8420 (mtp) cc_final: 0.8121 (mtm) REVERT: F 666 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7791 (mpp-170) REVERT: F 787 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8187 (p) outliers start: 108 outliers final: 41 residues processed: 326 average time/residue: 1.2959 time to fit residues: 562.6229 Evaluate side-chains 281 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 230 time to evaluate : 5.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 206 THR Chi-restraints excluded: chain 3 residue 395 ASN Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 556 ILE Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 501 ILE Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 374 ILE Chi-restraints excluded: chain 5 residue 402 ASP Chi-restraints excluded: chain 5 residue 585 ASN Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 7 residue 95 GLN Chi-restraints excluded: chain 7 residue 222 SER Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 666 ARG Chi-restraints excluded: chain F residue 787 SER Chi-restraints excluded: chain F residue 789 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 455 optimal weight: 7.9990 chunk 187 optimal weight: 0.1980 chunk 340 optimal weight: 1.9990 chunk 661 optimal weight: 4.9990 chunk 523 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 490 optimal weight: 0.9990 chunk 463 optimal weight: 8.9990 chunk 408 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 625 ASN ** 7 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 585 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.083806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.065542 restraints weight = 196126.474| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.98 r_work: 0.3212 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 65358 Z= 0.180 Angle : 0.528 11.417 88859 Z= 0.267 Chirality : 0.041 0.207 10314 Planarity : 0.004 0.058 11040 Dihedral : 12.812 177.453 9814 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.43 % Allowed : 11.33 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.09), residues: 7714 helix: 1.36 (0.10), residues: 3030 sheet: -0.15 (0.13), residues: 1508 loop : -0.93 (0.10), residues: 3176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 111 HIS 0.004 0.001 HIS 7 538 PHE 0.013 0.001 PHE F 113 TYR 0.016 0.001 TYR 4 519 ARG 0.007 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 239 time to evaluate : 5.892 Fit side-chains REVERT: 2 258 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8245 (tt) REVERT: 3 264 MET cc_start: 0.9031 (mtp) cc_final: 0.8762 (mtt) REVERT: 3 462 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.8663 (mpp) REVERT: 4 780 MET cc_start: 0.8592 (tmm) cc_final: 0.8309 (tmm) REVERT: 4 811 MET cc_start: 0.8036 (ttp) cc_final: 0.7749 (ttm) REVERT: 5 197 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.6732 (m-80) REVERT: 5 404 MET cc_start: 0.7712 (mpm) cc_final: 0.7337 (mpm) REVERT: 5 480 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: 6 313 MET cc_start: 0.8617 (mmt) cc_final: 0.8195 (mmt) REVERT: 7 95 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6939 (pp30) REVERT: 7 666 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7485 (mpt180) REVERT: 7 787 SER cc_start: 0.8418 (t) cc_final: 0.8040 (p) REVERT: A 258 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8263 (tt) REVERT: B 462 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8659 (mpp) REVERT: C 491 ASP cc_start: 0.8133 (t0) cc_final: 0.7902 (t0) REVERT: C 811 MET cc_start: 0.8041 (ttp) cc_final: 0.7755 (ttm) REVERT: D 197 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.6550 (m-80) REVERT: D 480 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8044 (m-30) REVERT: F 787 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8196 (p) outliers start: 99 outliers final: 47 residues processed: 312 average time/residue: 1.3385 time to fit residues: 557.5293 Evaluate side-chains 289 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 231 time to evaluate : 5.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 473 VAL Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 206 THR Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 240 ASN Chi-restraints excluded: chain 4 residue 262 LEU Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 501 ILE Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 829 ILE Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 374 ILE Chi-restraints excluded: chain 5 residue 402 ASP Chi-restraints excluded: chain 5 residue 480 ASP Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 7 residue 95 GLN Chi-restraints excluded: chain 7 residue 222 SER Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 651 VAL Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 666 ARG Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 7 residue 789 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 782 CYS Chi-restraints excluded: chain F residue 787 SER Chi-restraints excluded: chain F residue 789 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 425 optimal weight: 9.9990 chunk 709 optimal weight: 0.9980 chunk 562 optimal weight: 2.9990 chunk 762 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 422 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 chunk 362 optimal weight: 8.9990 chunk 561 optimal weight: 0.2980 chunk 47 optimal weight: 8.9990 chunk 539 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.083916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.065620 restraints weight = 197767.333| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.98 r_work: 0.3218 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 65358 Z= 0.193 Angle : 0.530 12.644 88859 Z= 0.267 Chirality : 0.041 0.167 10314 Planarity : 0.004 0.059 11040 Dihedral : 12.728 177.360 9814 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.20 % Allowed : 11.72 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.09), residues: 7714 helix: 1.47 (0.10), residues: 3020 sheet: -0.19 (0.13), residues: 1510 loop : -0.86 (0.11), residues: 3184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 6 356 HIS 0.004 0.001 HIS 7 622 PHE 0.013 0.001 PHE F 745 TYR 0.025 0.001 TYR 7 786 ARG 0.006 0.000 ARG 7 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 240 time to evaluate : 5.739 Fit side-chains REVERT: 2 258 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8260 (tt) REVERT: 3 264 MET cc_start: 0.9012 (mtp) cc_final: 0.8732 (mtt) REVERT: 3 462 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.8614 (mpp) REVERT: 4 272 MET cc_start: 0.7834 (mmm) cc_final: 0.7502 (mtt) REVERT: 4 780 MET cc_start: 0.8593 (tmm) cc_final: 0.8317 (tmm) REVERT: 4 811 MET cc_start: 0.7975 (ttp) cc_final: 0.7684 (ttm) REVERT: 5 197 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: 5 404 MET cc_start: 0.7734 (mpm) cc_final: 0.7330 (mpm) REVERT: 6 313 MET cc_start: 0.8603 (mmt) cc_final: 0.8179 (mmt) REVERT: 7 95 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6813 (pp30) REVERT: 7 666 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7465 (mpt180) REVERT: 7 787 SER cc_start: 0.8399 (t) cc_final: 0.8041 (p) REVERT: B 462 MET cc_start: 0.9322 (OUTLIER) cc_final: 0.8617 (mpp) REVERT: C 272 MET cc_start: 0.7821 (mmm) cc_final: 0.7495 (mtt) REVERT: C 811 MET cc_start: 0.7976 (ttp) cc_final: 0.7712 (ttm) REVERT: D 65 MET cc_start: 0.8369 (ttp) cc_final: 0.8144 (ttp) REVERT: D 197 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.6553 (m-80) REVERT: D 480 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: E 313 MET cc_start: 0.8399 (mmm) cc_final: 0.8103 (mmt) REVERT: F 787 SER cc_start: 0.8434 (OUTLIER) cc_final: 0.8087 (p) outliers start: 83 outliers final: 56 residues processed: 304 average time/residue: 1.3253 time to fit residues: 538.0968 Evaluate side-chains 292 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 227 time to evaluate : 5.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 473 VAL Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 807 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 206 THR Chi-restraints excluded: chain 3 residue 359 ILE Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 501 ILE Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 724 LEU Chi-restraints excluded: chain 4 residue 829 ILE Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 374 ILE Chi-restraints excluded: chain 5 residue 402 ASP Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 7 residue 95 GLN Chi-restraints excluded: chain 7 residue 222 SER Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 651 VAL Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 666 ARG Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 7 residue 789 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 829 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 480 ASP Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 782 CYS Chi-restraints excluded: chain F residue 787 SER Chi-restraints excluded: chain F residue 789 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 385 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 432 optimal weight: 5.9990 chunk 541 optimal weight: 0.5980 chunk 381 optimal weight: 4.9990 chunk 714 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 621 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 585 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.083528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.065198 restraints weight = 197322.679| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.98 r_work: 0.3205 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 65358 Z= 0.226 Angle : 0.543 13.476 88859 Z= 0.274 Chirality : 0.042 0.156 10314 Planarity : 0.004 0.056 11040 Dihedral : 12.708 177.317 9814 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.26 % Allowed : 11.85 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.09), residues: 7714 helix: 1.44 (0.10), residues: 3026 sheet: -0.17 (0.13), residues: 1512 loop : -0.87 (0.11), residues: 3176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 6 356 HIS 0.005 0.001 HIS 7 538 PHE 0.015 0.001 PHE 7 113 TYR 0.017 0.001 TYR C 519 ARG 0.004 0.000 ARG F 400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 228 time to evaluate : 5.702 Fit side-chains REVERT: 2 258 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8307 (tt) REVERT: 3 264 MET cc_start: 0.9030 (mtp) cc_final: 0.8762 (mtt) REVERT: 3 462 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.8619 (mpp) REVERT: 4 780 MET cc_start: 0.8601 (tmm) cc_final: 0.8321 (tmm) REVERT: 4 811 MET cc_start: 0.7986 (ttp) cc_final: 0.7776 (ttm) REVERT: 5 197 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.6729 (m-80) REVERT: 5 404 MET cc_start: 0.7742 (mpm) cc_final: 0.7368 (mpm) REVERT: 5 480 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: 6 313 MET cc_start: 0.8626 (mmt) cc_final: 0.8188 (mmt) REVERT: 7 95 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6756 (pp30) REVERT: B 462 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.8626 (mpp) REVERT: C 811 MET cc_start: 0.7984 (ttp) cc_final: 0.7775 (ttm) REVERT: D 197 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.6584 (m-80) REVERT: D 552 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7341 (mtp) REVERT: E 313 MET cc_start: 0.8543 (mmm) cc_final: 0.8240 (mmt) REVERT: F 64 MET cc_start: 0.7181 (mmm) cc_final: 0.6840 (mmm) REVERT: F 787 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8112 (p) outliers start: 87 outliers final: 56 residues processed: 293 average time/residue: 1.3386 time to fit residues: 523.0848 Evaluate side-chains 290 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 225 time to evaluate : 5.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 473 VAL Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 3 residue 206 THR Chi-restraints excluded: chain 3 residue 359 ILE Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 501 ILE Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 724 LEU Chi-restraints excluded: chain 4 residue 829 ILE Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 374 ILE Chi-restraints excluded: chain 5 residue 402 ASP Chi-restraints excluded: chain 5 residue 480 ASP Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 7 residue 95 GLN Chi-restraints excluded: chain 7 residue 122 ASP Chi-restraints excluded: chain 7 residue 222 SER Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 651 VAL Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 7 residue 782 CYS Chi-restraints excluded: chain 7 residue 789 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 829 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 782 CYS Chi-restraints excluded: chain F residue 787 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 680 optimal weight: 0.9980 chunk 692 optimal weight: 2.9990 chunk 549 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 270 optimal weight: 7.9990 chunk 384 optimal weight: 7.9990 chunk 697 optimal weight: 4.9990 chunk 738 optimal weight: 1.9990 chunk 575 optimal weight: 6.9990 chunk 635 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 760 GLN D 49 GLN D 585 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.083845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.065522 restraints weight = 197891.042| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.98 r_work: 0.3213 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 65358 Z= 0.201 Angle : 0.537 14.296 88859 Z= 0.270 Chirality : 0.041 0.147 10314 Planarity : 0.004 0.056 11040 Dihedral : 12.661 177.230 9814 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.14 % Allowed : 12.10 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.10), residues: 7714 helix: 1.52 (0.10), residues: 3020 sheet: -0.13 (0.13), residues: 1508 loop : -0.82 (0.11), residues: 3186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 111 HIS 0.006 0.001 HIS 7 622 PHE 0.043 0.001 PHE 7 745 TYR 0.025 0.001 TYR 7 786 ARG 0.004 0.000 ARG A 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15428 Ramachandran restraints generated. 7714 Oldfield, 0 Emsley, 7714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 229 time to evaluate : 5.706 Fit side-chains REVERT: 2 258 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8299 (tt) REVERT: 3 261 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8335 (ptp) REVERT: 3 264 MET cc_start: 0.9019 (mtp) cc_final: 0.8562 (mtt) REVERT: 3 462 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8612 (mpp) REVERT: 4 272 MET cc_start: 0.7778 (mmm) cc_final: 0.7439 (mpt) REVERT: 4 780 MET cc_start: 0.8583 (tmm) cc_final: 0.8309 (tmm) REVERT: 4 811 MET cc_start: 0.7973 (ttp) cc_final: 0.7764 (ttm) REVERT: 5 197 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.6813 (m-80) REVERT: 5 404 MET cc_start: 0.7690 (mpm) cc_final: 0.7339 (mpm) REVERT: 6 313 MET cc_start: 0.8631 (mmt) cc_final: 0.8186 (mmt) REVERT: 7 95 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6703 (pp30) REVERT: B 462 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.8617 (mpp) REVERT: C 272 MET cc_start: 0.7781 (mmm) cc_final: 0.7443 (mpt) REVERT: C 811 MET cc_start: 0.7941 (ttp) cc_final: 0.7735 (ttm) REVERT: D 197 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.6623 (m-80) REVERT: D 552 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7332 (mtp) REVERT: F 64 MET cc_start: 0.7169 (mmm) cc_final: 0.6840 (mmm) REVERT: F 745 PHE cc_start: 0.8124 (t80) cc_final: 0.7903 (t80) REVERT: F 787 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8126 (p) outliers start: 79 outliers final: 59 residues processed: 286 average time/residue: 1.3148 time to fit residues: 502.1122 Evaluate side-chains 293 residues out of total 6920 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 225 time to evaluate : 5.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 473 VAL Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 206 THR Chi-restraints excluded: chain 3 residue 261 MET Chi-restraints excluded: chain 3 residue 359 ILE Chi-restraints excluded: chain 3 residue 462 MET Chi-restraints excluded: chain 3 residue 469 VAL Chi-restraints excluded: chain 3 residue 513 ILE Chi-restraints excluded: chain 3 residue 724 VAL Chi-restraints excluded: chain 4 residue 280 MET Chi-restraints excluded: chain 4 residue 435 VAL Chi-restraints excluded: chain 4 residue 501 ILE Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 724 LEU Chi-restraints excluded: chain 4 residue 829 ILE Chi-restraints excluded: chain 5 residue 35 ILE Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 5 residue 197 PHE Chi-restraints excluded: chain 5 residue 276 MET Chi-restraints excluded: chain 5 residue 277 THR Chi-restraints excluded: chain 5 residue 374 ILE Chi-restraints excluded: chain 5 residue 402 ASP Chi-restraints excluded: chain 5 residue 608 LEU Chi-restraints excluded: chain 6 residue 151 ILE Chi-restraints excluded: chain 6 residue 629 MET Chi-restraints excluded: chain 7 residue 95 GLN Chi-restraints excluded: chain 7 residue 122 ASP Chi-restraints excluded: chain 7 residue 222 SER Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 535 THR Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 651 VAL Chi-restraints excluded: chain 7 residue 660 VAL Chi-restraints excluded: chain 7 residue 685 THR Chi-restraints excluded: chain 7 residue 782 CYS Chi-restraints excluded: chain 7 residue 786 TYR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 829 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 651 VAL Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 685 THR Chi-restraints excluded: chain F residue 782 CYS Chi-restraints excluded: chain F residue 787 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 786 random chunks: chunk 488 optimal weight: 0.9990 chunk 325 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 495 optimal weight: 0.9980 chunk 299 optimal weight: 5.9990 chunk 295 optimal weight: 0.6980 chunk 726 optimal weight: 0.9990 chunk 363 optimal weight: 0.9980 chunk 461 optimal weight: 0.9990 chunk 698 optimal weight: 0.9980 chunk 758 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 585 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.084885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066815 restraints weight = 194097.789| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.94 r_work: 0.3241 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 65358 Z= 0.145 Angle : 0.520 14.091 88859 Z= 0.259 Chirality : 0.040 0.137 10314 Planarity : 0.003 0.058 11040 Dihedral : 12.536 177.207 9814 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.92 % Allowed : 12.41 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.10), residues: 7714 helix: 1.69 (0.10), residues: 3032 sheet: 0.00 (0.13), residues: 1518 loop : -0.73 (0.11), residues: 3164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 111 HIS 0.010 0.001 HIS 7 622 PHE 0.045 0.001 PHE 7 745 TYR 0.017 0.001 TYR 7 786 ARG 0.004 0.000 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28708.10 seconds wall clock time: 495 minutes 2.24 seconds (29702.24 seconds total)