Starting phenix.real_space_refine on Wed Nov 20 05:12:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bew_16011/11_2024/8bew_16011.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bew_16011/11_2024/8bew_16011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bew_16011/11_2024/8bew_16011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bew_16011/11_2024/8bew_16011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bew_16011/11_2024/8bew_16011.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bew_16011/11_2024/8bew_16011.cif" } resolution = 3.49 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= 0.002 sd= 0.029 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 Fe 68 7.16 5 Zn 2 6.06 5 P 2 5.49 5 S 238 5.16 5 C 13208 2.51 5 N 3556 2.21 5 O 3930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21004 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4464 Classifications: {'peptide': 571} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 544} Chain: "B" Number of atoms: 4764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4764 Classifications: {'peptide': 630} Link IDs: {'PCIS': 4, 'PTRANS': 25, 'TRANS': 600} Chain: "C" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1174 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "D" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4464 Classifications: {'peptide': 571} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 544} Chain: "E" Number of atoms: 4764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4764 Classifications: {'peptide': 630} Link IDs: {'PCIS': 4, 'PTRANS': 25, 'TRANS': 600} Chain: "F" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1174 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 60 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {'FES': 1, 'SF4': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 60 Unusual residues: {' ZN': 1, 'FES': 1, 'FMN': 1, 'SF4': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2322 SG CYS A 299 81.983 63.629 111.265 1.00 23.99 S ATOM 2757 SG CYS A 354 79.258 64.692 105.873 1.00 18.61 S ATOM 3836 SG CYS A 496 76.126 61.372 109.724 1.00 19.25 S ATOM 3857 SG CYS A 500 81.607 58.563 107.275 1.00 24.87 S ATOM 374 SG CYS A 50 49.001 56.395 113.447 1.00 21.12 S ATOM 465 SG CYS A 63 51.293 56.902 116.309 1.00 19.14 S ATOM 267 SG CYS A 36 52.924 60.358 113.755 1.00 18.84 S ATOM 349 SG CYS A 47 50.229 59.952 111.341 1.00 28.19 S ATOM 770 SG CYS A 102 59.489 67.695 95.906 1.00 20.16 S ATOM 744 SG CYS A 99 53.961 66.105 93.102 1.00 30.37 S ATOM 819 SG CYS A 108 56.555 63.384 99.035 1.00 18.78 S ATOM 1150 SG CYS A 146 57.280 71.329 107.413 1.00 42.95 S ATOM 1560 SG CYS A 199 61.368 66.668 104.904 1.00 11.02 S ATOM 1172 SG CYS A 149 57.509 65.127 109.372 1.00 42.95 S ATOM 1191 SG CYS A 152 61.902 69.184 110.970 1.00 42.95 S ATOM 1485 SG CYS A 189 72.929 72.396 111.119 1.00 21.45 S ATOM 1510 SG CYS A 192 73.082 66.228 112.105 1.00 15.16 S ATOM 1529 SG CYS A 195 68.321 68.571 108.823 1.00 12.01 S ATOM 1223 SG CYS A 156 68.882 69.646 115.398 1.00 12.03 S ATOM 8201 SG CYS B 491 45.486 67.413 115.905 1.00 42.95 S ATOM 8529 SG CYS B 534 43.456 69.591 121.758 1.00 22.53 S ATOM 8222 SG CYS B 494 42.356 72.187 115.863 1.00 29.71 S ATOM 8182 SG CYS B 488 48.156 72.531 119.187 1.00 15.49 S ATOM 8041 SG CYS B 471 21.956 84.437 109.065 1.00 42.57 S ATOM 8769 SG CYS B 564 20.520 87.450 107.252 1.00 47.44 S ATOM 8796 SG CYS B 569 24.288 86.802 107.091 1.00 48.58 S ATOM 5093 SG CYS B 82 30.344 90.765 140.913 1.00 52.01 S ATOM 5123 SG CYS B 86 28.969 91.942 137.698 1.00 54.99 S ATOM 4723 SG CYS B 31 30.281 95.011 143.934 1.00 58.01 S ATOM 4748 SG CYS B 36 30.595 96.363 141.085 1.00 53.67 S ATOM 9142 SG CYS B 618 21.394 102.998 98.172 1.00 80.41 S ATOM 9104 SG CYS B 612 22.971 97.405 95.137 1.00 83.14 S ATOM 8957 SG CYS B 592 26.332 102.253 93.336 1.00 74.41 S ATOM 8891 SG CYS B 582 12.484 109.167 94.165 1.00 77.65 S ATOM 8909 SG CYS B 585 17.779 112.347 96.056 1.00 81.43 S ATOM 9170 SG CYS B 622 18.196 111.608 97.738 1.00 79.80 S ATOM 10155 SG CYS C 128 35.037 87.649 128.867 1.00 54.77 S ATOM 10178 SG CYS C 132 31.872 89.975 129.445 1.00 65.42 S ATOM 9850 SG CYS C 87 35.352 92.125 125.803 1.00 57.42 S ATOM 9880 SG CYS C 92 31.976 92.644 124.887 1.00 49.26 S ATOM 13159 SG CYS D 354 36.876 43.924 77.586 1.00 18.96 S ATOM 12724 SG CYS D 299 36.204 40.740 72.342 1.00 23.66 S ATOM 14259 SG CYS D 500 39.867 37.858 76.691 1.00 23.01 S ATOM 14238 SG CYS D 496 41.646 43.545 73.850 1.00 20.78 S ATOM 10776 SG CYS D 50 63.795 59.806 69.305 1.00 14.43 S ATOM 10867 SG CYS D 63 62.002 58.358 66.918 1.00 17.57 S ATOM 10669 SG CYS D 36 58.581 59.636 68.888 1.00 16.26 S ATOM 10751 SG CYS D 47 60.409 61.328 70.714 1.00 19.44 S ATOM 11146 SG CYS D 99 52.206 65.150 88.602 1.00 29.01 S ATOM 11221 SG CYS D 108 52.982 60.667 83.171 1.00 24.61 S ATOM 11172 SG CYS D 102 47.785 61.459 86.017 1.00 24.54 S ATOM 11552 SG CYS D 146 47.018 64.397 73.985 1.00 42.95 S ATOM 11574 SG CYS D 149 51.305 59.905 72.776 1.00 42.95 S ATOM 11593 SG CYS D 152 45.338 58.948 70.901 1.00 42.95 S ATOM 11962 SG CYS D 199 47.575 58.565 77.137 1.00 42.95 S ATOM 11931 SG CYS D 195 41.707 54.187 73.401 1.00 18.49 S ATOM 11912 SG CYS D 192 40.200 48.732 70.677 1.00 16.94 S ATOM 11625 SG CYS D 156 40.816 53.645 66.662 1.00 19.50 S ATOM 11887 SG CYS D 189 36.015 53.184 70.985 1.00 16.04 S ATOM 18603 SG CYS E 491 58.225 69.453 65.371 1.00 25.62 S ATOM 18584 SG CYS E 488 52.872 70.527 61.705 1.00 11.40 S ATOM 18931 SG CYS E 534 58.352 71.517 59.212 1.00 16.06 S ATOM 18624 SG CYS E 494 56.708 74.951 64.733 1.00 30.20 S ATOM 18443 SG CYS E 471 61.157 98.834 68.677 1.00 44.93 S ATOM 19171 SG CYS E 564 59.794 102.156 70.064 1.00 52.17 S ATOM 19198 SG CYS E 569 57.588 99.015 70.153 1.00 48.46 S ATOM 15525 SG CYS E 86 52.582 95.047 38.291 1.00 55.94 S ATOM 15125 SG CYS E 31 49.539 94.829 34.331 1.00 64.90 S ATOM 15150 SG CYS E 36 47.440 97.155 35.508 1.00 61.52 S ATOM 19544 SG CYS E 618 47.522 112.824 76.981 1.00 79.88 S ATOM 19506 SG CYS E 612 50.066 108.304 81.283 1.00 78.06 S ATOM 19359 SG CYS E 592 44.129 109.411 82.015 1.00 72.86 S ATOM 19293 SG CYS E 582 48.521 123.867 79.853 1.00 73.37 S ATOM 19311 SG CYS E 585 42.671 122.021 78.105 1.00 74.68 S ATOM 19572 SG CYS E 622 43.047 120.767 76.323 1.00 75.85 S ATOM 20557 SG CYS F 128 51.176 90.118 49.666 1.00 55.52 S ATOM 20580 SG CYS F 132 52.401 93.722 48.640 1.00 64.21 S ATOM 20252 SG CYS F 87 47.401 92.708 52.813 1.00 54.79 S ATOM 20282 SG CYS F 92 49.752 95.600 51.791 1.00 58.52 S Time building chain proxies: 12.63, per 1000 atoms: 0.60 Number of scatterers: 21004 At special positions: 0 Unit cell: (120.06, 140.07, 180.09, 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 2 29.99 Fe 68 26.01 S 238 16.00 P 2 15.00 O 3930 8.00 N 3556 7.00 C 13208 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.39 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 602 " pdb="FE2 FES A 602 " - pdb=" SG CYS A 47 " pdb="FE1 FES A 602 " - pdb=" SG CYS A 50 " pdb="FE1 FES A 602 " - pdb=" SG CYS A 63 " pdb="FE2 FES A 602 " - pdb=" SG CYS A 36 " pdb=" FES B 704 " pdb="FE2 FES B 704 " - pdb=" SG CYS B 31 " pdb="FE2 FES B 704 " - pdb=" SG CYS B 36 " pdb="FE1 FES B 704 " - pdb=" SG CYS B 86 " pdb="FE1 FES B 704 " - pdb=" SG CYS B 82 " pdb=" FES C 201 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 92 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 87 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 132 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 128 " pdb=" FES D 602 " pdb="FE1 FES D 602 " - pdb=" SG CYS D 50 " pdb="FE2 FES D 602 " - pdb=" SG CYS D 47 " pdb="FE2 FES D 602 " - pdb=" SG CYS D 36 " pdb="FE1 FES D 602 " - pdb=" SG CYS D 63 " pdb=" FES E 704 " pdb="FE2 FES E 704 " - pdb=" SG CYS E 36 " pdb="FE2 FES E 704 " - pdb=" SG CYS E 31 " pdb="FE1 FES E 704 " - pdb=" SG CYS E 86 " pdb=" FES F 201 " pdb="FE2 FES F 201 " - pdb=" SG CYS F 92 " pdb="FE2 FES F 201 " - pdb=" SG CYS F 87 " pdb="FE1 FES F 201 " - pdb=" SG CYS F 132 " pdb="FE1 FES F 201 " - pdb=" SG CYS F 128 " pdb=" SF4 A 601 " pdb="FE2 SF4 A 601 " - pdb=" SG CYS A 354 " pdb="FE1 SF4 A 601 " - pdb=" SG CYS A 299 " pdb="FE3 SF4 A 601 " - pdb=" SG CYS A 496 " pdb="FE4 SF4 A 601 " - pdb=" SG CYS A 500 " pdb=" SF4 A 603 " pdb="FE1 SF4 A 603 " - pdb=" NE2 HIS A 95 " pdb="FE3 SF4 A 603 " - pdb=" SG CYS A 99 " pdb="FE2 SF4 A 603 " - pdb=" SG CYS A 102 " pdb="FE4 SF4 A 603 " - pdb=" SG CYS A 108 " pdb=" SF4 A 604 " pdb="FE3 SF4 A 604 " - pdb=" SG CYS A 149 " pdb="FE1 SF4 A 604 " - pdb=" SG CYS A 146 " pdb="FE2 SF4 A 604 " - pdb=" SG CYS A 199 " pdb="FE4 SF4 A 604 " - pdb=" SG CYS A 152 " pdb=" SF4 A 605 " pdb="FE1 SF4 A 605 " - pdb=" SG CYS A 189 " pdb="FE2 SF4 A 605 " - pdb=" SG CYS A 192 " pdb="FE4 SF4 A 605 " - pdb=" SG CYS A 156 " pdb="FE3 SF4 A 605 " - pdb=" SG CYS A 195 " pdb=" SF4 B 702 " pdb="FE1 SF4 B 702 " - pdb=" SG CYS B 491 " pdb="FE2 SF4 B 702 " - pdb=" SG CYS B 534 " pdb="FE4 SF4 B 702 " - pdb=" SG CYS B 488 " pdb="FE3 SF4 B 702 " - pdb=" SG CYS B 494 " pdb=" SF4 B 705 " pdb="FE4 SF4 B 705 " - pdb=" SG CYS B 592 " pdb="FE3 SF4 B 705 " - pdb=" SG CYS B 612 " pdb="FE1 SF4 B 705 " - pdb=" SG CYS B 618 " pdb=" SF4 B 706 " pdb="FE2 SF4 B 706 " - pdb=" SG CYS B 622 " pdb="FE1 SF4 B 706 " - pdb=" SG CYS B 582 " pdb="FE2 SF4 B 706 " - pdb=" SG CYS B 585 " pdb=" SF4 D 601 " pdb="FE2 SF4 D 601 " - pdb=" SG CYS D 299 " pdb="FE4 SF4 D 601 " - pdb=" SG CYS D 496 " pdb="FE1 SF4 D 601 " - pdb=" SG CYS D 354 " pdb="FE3 SF4 D 601 " - pdb=" SG CYS D 500 " pdb=" SF4 D 603 " pdb="FE3 SF4 D 603 " - pdb=" NE2 HIS D 95 " pdb="FE4 SF4 D 603 " - pdb=" SG CYS D 102 " pdb="FE2 SF4 D 603 " - pdb=" SG CYS D 108 " pdb="FE1 SF4 D 603 " - pdb=" SG CYS D 99 " pdb=" SF4 D 604 " pdb="FE1 SF4 D 604 " - pdb=" SG CYS D 146 " pdb="FE2 SF4 D 604 " - pdb=" SG CYS D 149 " pdb="FE4 SF4 D 604 " - pdb=" SG CYS D 199 " pdb="FE3 SF4 D 604 " - pdb=" SG CYS D 152 " pdb=" SF4 D 605 " pdb="FE4 SF4 D 605 " - pdb=" SG CYS D 189 " pdb="FE2 SF4 D 605 " - pdb=" SG CYS D 192 " pdb="FE1 SF4 D 605 " - pdb=" SG CYS D 195 " pdb="FE3 SF4 D 605 " - pdb=" SG CYS D 156 " pdb=" SF4 E 702 " pdb="FE1 SF4 E 702 " - pdb=" SG CYS E 491 " pdb="FE2 SF4 E 702 " - pdb=" SG CYS E 488 " pdb="FE3 SF4 E 702 " - pdb=" SG CYS E 534 " pdb="FE4 SF4 E 702 " - pdb=" SG CYS E 494 " pdb=" SF4 E 705 " pdb="FE3 SF4 E 705 " - pdb=" SG CYS E 612 " pdb="FE4 SF4 E 705 " - pdb=" SG CYS E 592 " pdb="FE1 SF4 E 705 " - pdb=" SG CYS E 618 " pdb=" SF4 E 706 " pdb="FE4 SF4 E 706 " - pdb=" SG CYS E 585 " pdb="FE2 SF4 E 706 " - pdb=" SG CYS E 582 " pdb="FE4 SF4 E 706 " - pdb=" SG CYS E 622 " Number of angles added : 191 Zn2+ tetrahedral coordination pdb=" ZN B 703 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 558 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 564 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 471 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 569 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 558 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 564 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 569 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 471 " Number of angles added : 6 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4888 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 24 sheets defined 47.7% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 77 through 93 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 150 through 158 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.895A pdb=" N LYS A 173 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.538A pdb=" N GLU A 181 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 193 through 199 removed outlier: 3.656A pdb=" N ARG A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS A 199 " --> pdb=" O CYS A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 193 through 199' Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.509A pdb=" N GLU A 238 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 239 " --> pdb=" O LEU A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 239' Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'A' and resid 267 through 289 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 310 through 317 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 322 through 334 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 355 through 361 removed outlier: 3.755A pdb=" N PHE A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 6.100A pdb=" N GLU A 365 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN A 367 " --> pdb=" O PRO A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 387 removed outlier: 3.562A pdb=" N LYS A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 432 removed outlier: 3.759A pdb=" N SER A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 440 removed outlier: 4.044A pdb=" N LYS A 439 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 446 removed outlier: 3.557A pdb=" N VAL A 445 " --> pdb=" O PHE A 442 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 446 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 442 through 446' Processing helix chain 'A' and resid 470 through 484 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 513 through 527 removed outlier: 3.637A pdb=" N LYS A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 548 removed outlier: 4.202A pdb=" N LYS A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 560 Processing helix chain 'B' and resid 6 through 23 removed outlier: 3.756A pdb=" N LEU B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 39 Processing helix chain 'B' and resid 40 through 55 removed outlier: 3.666A pdb=" N VAL B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 removed outlier: 4.011A pdb=" N GLU B 70 " --> pdb=" O ASP B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.560A pdb=" N ILE B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.885A pdb=" N LYS B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 removed outlier: 3.534A pdb=" N LYS B 155 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N HIS B 156 " --> pdb=" O VAL B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 152 through 156' Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 184 through 196 removed outlier: 3.606A pdb=" N ILE B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.869A pdb=" N LYS B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 removed outlier: 4.169A pdb=" N MET B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 261 removed outlier: 4.263A pdb=" N VAL B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 291 removed outlier: 3.596A pdb=" N VAL B 277 " --> pdb=" O TYR B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 300 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 345 through 349 removed outlier: 3.580A pdb=" N GLU B 348 " --> pdb=" O GLY B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'B' and resid 361 through 369 Processing helix chain 'B' and resid 369 through 375 removed outlier: 3.799A pdb=" N PHE B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 382 removed outlier: 4.164A pdb=" N THR B 382 " --> pdb=" O PRO B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 removed outlier: 3.594A pdb=" N LEU B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 422 removed outlier: 3.578A pdb=" N ASN B 421 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 Processing helix chain 'B' and resid 440 through 442 No H-bonds generated for 'chain 'B' and resid 440 through 442' Processing helix chain 'B' and resid 447 through 455 removed outlier: 3.737A pdb=" N LEU B 451 " --> pdb=" O ASP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 487 removed outlier: 3.514A pdb=" N PHE B 475 " --> pdb=" O CYS B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 510 removed outlier: 4.090A pdb=" N LYS B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B 500 " --> pdb=" O GLU B 496 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 503 " --> pdb=" O LYS B 499 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 532 removed outlier: 3.522A pdb=" N LEU B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 551 removed outlier: 3.868A pdb=" N THR B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 560 removed outlier: 3.789A pdb=" N TYR B 555 " --> pdb=" O PHE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.580A pdb=" N ALA B 573 " --> pdb=" O GLN B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 592 Processing helix chain 'B' and resid 616 through 622 removed outlier: 3.849A pdb=" N GLU B 620 " --> pdb=" O GLY B 616 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 24 removed outlier: 3.982A pdb=" N ILE C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 24 " --> pdb=" O ILE C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 47 through 58 removed outlier: 3.598A pdb=" N GLY C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.514A pdb=" N ILE C 64 " --> pdb=" O PRO C 60 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 71 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 removed outlier: 3.818A pdb=" N ILE C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 152 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.802A pdb=" N GLY D 29 " --> pdb=" O GLU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 Processing helix chain 'D' and resid 108 through 117 Processing helix chain 'D' and resid 150 through 158 Processing helix chain 'D' and resid 170 through 174 removed outlier: 3.604A pdb=" N LYS D 173 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 193 through 199 removed outlier: 3.501A pdb=" N VAL D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS D 199 " --> pdb=" O CYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 219 removed outlier: 3.575A pdb=" N ILE D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 233 removed outlier: 3.640A pdb=" N ARG D 233 " --> pdb=" O PRO D 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 230 through 233' Processing helix chain 'D' and resid 235 through 241 removed outlier: 3.555A pdb=" N GLU D 238 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 241 " --> pdb=" O GLU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 259 Processing helix chain 'D' and resid 267 through 289 Processing helix chain 'D' and resid 299 through 310 Processing helix chain 'D' and resid 311 through 317 removed outlier: 3.690A pdb=" N ILE D 314 " --> pdb=" O PRO D 311 " (cutoff:3.500A) Proline residue: D 315 - end of helix No H-bonds generated for 'chain 'D' and resid 311 through 317' Processing helix chain 'D' and resid 322 through 334 Processing helix chain 'D' and resid 334 through 340 Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 355 through 361 removed outlier: 3.868A pdb=" N PHE D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 367 removed outlier: 6.139A pdb=" N GLU D 365 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN D 367 " --> pdb=" O PRO D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 387 Processing helix chain 'D' and resid 406 through 410 removed outlier: 3.716A pdb=" N ALA D 409 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 410 " --> pdb=" O GLY D 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 406 through 410' Processing helix chain 'D' and resid 419 through 432 removed outlier: 4.168A pdb=" N ARG D 424 " --> pdb=" O GLU D 420 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 441 removed outlier: 3.603A pdb=" N LYS D 439 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE D 440 " --> pdb=" O GLY D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 446 removed outlier: 3.756A pdb=" N VAL D 445 " --> pdb=" O PHE D 442 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG D 446 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 442 through 446' Processing helix chain 'D' and resid 470 through 484 Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 513 through 528 removed outlier: 3.802A pdb=" N LYS D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 548 removed outlier: 4.189A pdb=" N LYS D 541 " --> pdb=" O ASN D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 560 Processing helix chain 'E' and resid 6 through 23 removed outlier: 3.713A pdb=" N ALA E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 21 " --> pdb=" O ILE E 17 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS E 22 " --> pdb=" O LYS E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 53 removed outlier: 3.780A pdb=" N LYS E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL E 51 " --> pdb=" O GLU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 116 removed outlier: 4.002A pdb=" N ILE E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL E 113 " --> pdb=" O VAL E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 170 removed outlier: 3.882A pdb=" N TYR E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.741A pdb=" N THR E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 195 Processing helix chain 'E' and resid 206 through 217 removed outlier: 3.837A pdb=" N LYS E 210 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 245 removed outlier: 3.879A pdb=" N MET E 242 " --> pdb=" O ASP E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 261 Processing helix chain 'E' and resid 273 through 291 removed outlier: 3.630A pdb=" N VAL E 277 " --> pdb=" O TYR E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 300 removed outlier: 3.513A pdb=" N GLY E 299 " --> pdb=" O ASN E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 329 removed outlier: 3.835A pdb=" N TYR E 325 " --> pdb=" O THR E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 349 Processing helix chain 'E' and resid 360 through 369 removed outlier: 4.636A pdb=" N GLU E 364 " --> pdb=" O ALA E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.572A pdb=" N PHE E 373 " --> pdb=" O GLY E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 412 removed outlier: 3.655A pdb=" N LEU E 410 " --> pdb=" O LYS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 422 removed outlier: 3.825A pdb=" N ASN E 421 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 434 Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 447 through 453 removed outlier: 3.817A pdb=" N LEU E 451 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 486 Processing helix chain 'E' and resid 491 through 510 removed outlier: 3.543A pdb=" N ARG E 495 " --> pdb=" O CYS E 491 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS E 499 " --> pdb=" O ARG E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 532 removed outlier: 3.510A pdb=" N LEU E 520 " --> pdb=" O GLY E 516 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER E 532 " --> pdb=" O ILE E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 540 Processing helix chain 'E' and resid 541 through 551 Processing helix chain 'E' and resid 551 through 560 removed outlier: 3.716A pdb=" N TYR E 555 " --> pdb=" O PHE E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 573 Processing helix chain 'E' and resid 586 through 592 Processing helix chain 'E' and resid 616 through 622 removed outlier: 3.906A pdb=" N GLU E 620 " --> pdb=" O GLY E 616 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS E 622 " --> pdb=" O CYS E 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 16 removed outlier: 3.606A pdb=" N GLU F 15 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS F 16 " --> pdb=" O ARG F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 24 removed outlier: 3.607A pdb=" N LYS F 23 " --> pdb=" O GLU F 19 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 24 " --> pdb=" O ILE F 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 19 through 24' Processing helix chain 'F' and resid 31 through 43 removed outlier: 4.064A pdb=" N GLN F 39 " --> pdb=" O LEU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 57 removed outlier: 3.684A pdb=" N TYR F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR F 57 " --> pdb=" O ILE F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 71 removed outlier: 3.762A pdb=" N ILE F 64 " --> pdb=" O PRO F 60 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 108 removed outlier: 4.249A pdb=" N LEU F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 160 removed outlier: 3.993A pdb=" N VAL F 156 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR F 160 " --> pdb=" O VAL F 156 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 16 removed outlier: 10.090A pdb=" N VAL A 73 " --> pdb=" O MET A 5 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR A 7 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA5, first strand: chain 'A' and resid 263 through 266 removed outlier: 6.633A pdb=" N VAL A 224 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE A 265 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL A 226 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL A 223 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL A 349 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 225 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL A 351 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN A 227 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ALA A 372 " --> pdb=" O MET A 346 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A 348 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU A 374 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER A 350 " --> pdb=" O LEU A 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 294 through 295 removed outlier: 6.285A pdb=" N MET A 294 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL A 493 " --> pdb=" O MET A 294 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N PHE A 490 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG A 464 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N GLU A 492 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 466 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N MET A 494 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA A 468 " --> pdb=" O MET A 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 61 removed outlier: 6.110A pdb=" N ASP B 61 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N MET B 79 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU B 91 " --> pdb=" O CYS B 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 305 through 311 removed outlier: 6.589A pdb=" N GLY B 265 " --> pdb=" O HIS B 307 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ARG B 309 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE B 267 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY B 311 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL B 269 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 224 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N TYR B 268 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYS B 226 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N ARG B 270 " --> pdb=" O CYS B 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 397 through 402 removed outlier: 3.508A pdb=" N GLY B 397 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL B 463 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA B 388 " --> pdb=" O VAL B 463 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL B 465 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER B 390 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N ASP B 467 " --> pdb=" O SER B 390 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 574 through 577 removed outlier: 4.155A pdb=" N ALA B 574 " --> pdb=" O GLY B 630 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.818A pdb=" N ILE C 84 " --> pdb=" O GLU C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 139 through 140 Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.582A pdb=" N VAL D 15 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 10.160A pdb=" N VAL D 73 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR D 7 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AB6, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AB7, first strand: chain 'D' and resid 166 through 168 Processing sheet with id=AB8, first strand: chain 'D' and resid 263 through 266 removed outlier: 6.533A pdb=" N VAL D 224 " --> pdb=" O LYS D 263 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHE D 265 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL D 226 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL D 223 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL D 349 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL D 225 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL D 351 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN D 227 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ALA D 372 " --> pdb=" O MET D 346 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL D 348 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU D 374 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER D 350 " --> pdb=" O LEU D 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 294 through 295 removed outlier: 6.300A pdb=" N MET D 294 " --> pdb=" O VAL D 491 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL D 493 " --> pdb=" O MET D 294 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE D 490 " --> pdb=" O ARG D 464 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 466 " --> pdb=" O PHE D 490 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 73 through 80 removed outlier: 7.765A pdb=" N GLU E 24 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N HIS E 76 " --> pdb=" O GLU E 24 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE E 26 " --> pdb=" O HIS E 76 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LYS E 78 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE E 28 " --> pdb=" O LYS E 78 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR E 80 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ILE E 30 " --> pdb=" O THR E 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 306 through 311 removed outlier: 6.572A pdb=" N GLY E 265 " --> pdb=" O HIS E 307 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ARG E 309 " --> pdb=" O GLY E 265 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE E 267 " --> pdb=" O ARG E 309 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLY E 311 " --> pdb=" O ILE E 267 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL E 269 " --> pdb=" O GLY E 311 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE E 224 " --> pdb=" O TYR E 266 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR E 268 " --> pdb=" O ILE E 224 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N CYS E 226 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ARG E 270 " --> pdb=" O CYS E 226 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN E 354 " --> pdb=" O ILE E 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 397 through 401 removed outlier: 3.727A pdb=" N VAL E 401 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS E 385 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL E 463 " --> pdb=" O ILE E 386 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA E 388 " --> pdb=" O VAL E 463 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL E 465 " --> pdb=" O ALA E 388 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER E 390 " --> pdb=" O VAL E 465 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ASP E 467 " --> pdb=" O SER E 390 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 574 through 577 removed outlier: 3.893A pdb=" N ALA E 574 " --> pdb=" O GLY E 630 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 597 through 598 removed outlier: 3.991A pdb=" N SER E 598 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL E 606 " --> pdb=" O SER E 598 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 82 through 85 765 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.58 Time building geometry restraints manager: 5.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 8568 1.44 - 1.65: 12430 1.65 - 1.86: 234 1.86 - 2.07: 0 2.07 - 2.28: 192 Bond restraints: 21424 Sorted by residual: bond pdb=" CA ARG C 125 " pdb=" CB ARG C 125 " ideal model delta sigma weight residual 1.528 1.567 -0.039 1.47e-02 4.63e+03 7.01e+00 bond pdb=" C ILE E 492 " pdb=" N PRO E 493 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.37e+00 bond pdb=" CA ILE B 362 " pdb=" C ILE B 362 " ideal model delta sigma weight residual 1.523 1.540 -0.016 9.20e-03 1.18e+04 3.21e+00 bond pdb=" C ILE B 492 " pdb=" N PRO B 493 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.73e+00 bond pdb=" CA PHE E 236 " pdb=" CB PHE E 236 " ideal model delta sigma weight residual 1.523 1.542 -0.019 1.35e-02 5.49e+03 2.00e+00 ... (remaining 21419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 28545 2.67 - 5.34: 342 5.34 - 8.01: 41 8.01 - 10.68: 8 10.68 - 13.35: 2 Bond angle restraints: 28938 Sorted by residual: angle pdb=" N GLU E 357 " pdb=" CA GLU E 357 " pdb=" C GLU E 357 " ideal model delta sigma weight residual 114.62 106.34 8.28 1.14e+00 7.69e-01 5.28e+01 angle pdb=" N VAL F 17 " pdb=" CA VAL F 17 " pdb=" C VAL F 17 " ideal model delta sigma weight residual 112.90 106.67 6.23 9.60e-01 1.09e+00 4.22e+01 angle pdb=" C GLY D 417 " pdb=" N VAL D 418 " pdb=" CA VAL D 418 " ideal model delta sigma weight residual 121.97 131.72 -9.75 1.80e+00 3.09e-01 2.94e+01 angle pdb=" N ILE A 355 " pdb=" CA ILE A 355 " pdb=" C ILE A 355 " ideal model delta sigma weight residual 113.42 107.76 5.66 1.17e+00 7.31e-01 2.34e+01 angle pdb=" N ALA E 314 " pdb=" CA ALA E 314 " pdb=" C ALA E 314 " ideal model delta sigma weight residual 110.35 116.78 -6.43 1.40e+00 5.10e-01 2.11e+01 ... (remaining 28933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 12751 35.28 - 70.55: 226 70.55 - 105.83: 31 105.83 - 141.11: 0 141.11 - 176.38: 2 Dihedral angle restraints: 13010 sinusoidal: 5338 harmonic: 7672 Sorted by residual: dihedral pdb=" C10 FMN B 701 " pdb=" C1' FMN B 701 " pdb=" N10 FMN B 701 " pdb=" C2' FMN B 701 " ideal model delta sinusoidal sigma weight residual 257.59 81.21 176.38 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C10 FMN E 701 " pdb=" C1' FMN E 701 " pdb=" N10 FMN E 701 " pdb=" C2' FMN E 701 " ideal model delta sinusoidal sigma weight residual -102.41 39.91 -142.32 1 2.00e+01 2.50e-03 4.30e+01 dihedral pdb=" CA GLY E 313 " pdb=" C GLY E 313 " pdb=" N ALA E 314 " pdb=" CA ALA E 314 " ideal model delta harmonic sigma weight residual -180.00 -152.58 -27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 13007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2420 0.052 - 0.105: 675 0.105 - 0.157: 106 0.157 - 0.209: 13 0.209 - 0.262: 4 Chirality restraints: 3218 Sorted by residual: chirality pdb=" CB THR F 57 " pdb=" CA THR F 57 " pdb=" OG1 THR F 57 " pdb=" CG2 THR F 57 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE B 446 " pdb=" CA ILE B 446 " pdb=" CG1 ILE B 446 " pdb=" CG2 ILE B 446 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE E 446 " pdb=" CA ILE E 446 " pdb=" CG1 ILE E 446 " pdb=" CG2 ILE E 446 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 3215 not shown) Planarity restraints: 3694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 135 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO C 136 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 136 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 136 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 149 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO C 150 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 150 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 150 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 149 " -0.041 5.00e-02 4.00e+02 6.26e-02 6.26e+00 pdb=" N PRO F 150 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO F 150 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 150 " -0.034 5.00e-02 4.00e+02 ... (remaining 3691 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 577 2.72 - 3.26: 20146 3.26 - 3.81: 31400 3.81 - 4.35: 39237 4.35 - 4.90: 66121 Nonbonded interactions: 157481 Sorted by model distance: nonbonded pdb=" OG1 THR D 375 " pdb=" OE1 GLU D 378 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASP E 447 " pdb=" OG SER E 450 " model vdw 2.177 3.040 nonbonded pdb=" OE2 GLU D 453 " pdb=" OH TYR D 488 " model vdw 2.238 3.040 nonbonded pdb=" OD1 ASP D 166 " pdb=" N PHE D 167 " model vdw 2.245 3.120 nonbonded pdb=" OD1 ASP A 166 " pdb=" N PHE A 167 " model vdw 2.247 3.120 ... (remaining 157476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 54.460 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 : 0.003 0.044 21424 Z= 0.218 Angle : 0.744 13.346 28938 Z= 0.414 Chirality : 0.048 0.262 3218 Planarity : 0.005 0.066 3694 Dihedral : 14.614 176.383 8122 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.09 % Favored : 95.73 % Rotamer: Outliers : 0.09 % Allowed : 0.22 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: -1.10 (0.16), residues: 2692 helix: -0.47 (0.16), residues: 1046 sheet: 0.25 (0.30), residues: 308 loop : -1.13 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 347 HIS 0.008 0.001 HIS E 76 PHE 0.038 0.002 PHE A 490 TYR 0.015 0.001 TYR D 544 ARG 0.004 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 2.432 Fit side-chains revert: symmetry clash REVERT: A 130 ASN cc_start: 0.7147 (p0) cc_final: 0.6877 (p0) REVERT: A 489 ASP cc_start: 0.7067 (t0) cc_final: 0.6429 (t0) REVERT: B 210 LYS cc_start: 0.8311 (mtmm) cc_final: 0.7990 (mttt) outliers start: 2 outliers final: 0 residues processed: 272 average time/residue: 0.3379 time to fit residues: 142.8972 Evaluate side-chains 189 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 3.9990 chunk 204 optimal weight: 0.0270 chunk 113 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 138 optimal weight: 0.0060 chunk 109 optimal weight: 6.9990 chunk 211 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 overall best weight: 1.1258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN D 325 GLN D 561 HIS E 342 ASN E 421 ASN E 428 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21424 Z= 0.167 Angle : 0.548 10.181 28938 Z= 0.288 Chirality : 0.043 0.171 3218 Planarity : 0.004 0.063 3694 Dihedral : 6.130 176.801 2940 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.05 % Favored : 95.80 % Rotamer: Outliers : 0.94 % Allowed : 7.17 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: -0.59 (0.16), residues: 2692 helix: 0.05 (0.16), residues: 1078 sheet: 0.65 (0.31), residues: 284 loop : -0.95 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 347 HIS 0.004 0.001 HIS F 37 PHE 0.017 0.001 PHE A 490 TYR 0.017 0.001 TYR C 52 ARG 0.005 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.7228 (p0) cc_final: 0.6965 (p0) REVERT: A 489 ASP cc_start: 0.7045 (t0) cc_final: 0.6683 (t0) REVERT: D 118 ASN cc_start: 0.7659 (t0) cc_final: 0.7241 (t0) outliers start: 21 outliers final: 12 residues processed: 231 average time/residue: 0.3145 time to fit residues: 116.5726 Evaluate side-chains 204 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain E residue 302 PHE Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 204 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 245 optimal weight: 0.6980 chunk 265 optimal weight: 50.0000 chunk 218 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 overall best weight: 7.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN A 194 GLN A 268 GLN B 421 ASN B 481 ASN ** B 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 HIS B 621 ASN E 12 ASN E 83 GLN E 227 ASN E 342 ASN E 558 HIS E 605 HIS E 621 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.111 21424 Z= 0.708 Angle : 0.840 11.384 28938 Z= 0.438 Chirality : 0.064 0.397 3218 Planarity : 0.006 0.064 3694 Dihedral : 6.882 174.990 2940 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.09 % Favored : 93.76 % Rotamer: Outliers : 2.01 % Allowed : 11.76 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.00 (0.16), residues: 2692 helix: -0.20 (0.16), residues: 1070 sheet: 0.27 (0.33), residues: 252 loop : -1.18 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 302 HIS 0.018 0.002 HIS D 95 PHE 0.036 0.003 PHE B 315 TYR 0.036 0.003 TYR A 113 ARG 0.006 0.001 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 2.341 Fit side-chains revert: symmetry clash REVERT: A 91 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8223 (tt) REVERT: A 100 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: A 118 ASN cc_start: 0.8178 (t0) cc_final: 0.7778 (t0) REVERT: A 130 ASN cc_start: 0.7477 (p0) cc_final: 0.7221 (p0) REVERT: A 489 ASP cc_start: 0.7133 (t0) cc_final: 0.6698 (t0) REVERT: B 279 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6897 (mtt) REVERT: C 140 VAL cc_start: 0.7881 (t) cc_final: 0.7596 (p) REVERT: D 214 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.6731 (m-10) REVERT: D 252 MET cc_start: 0.7683 (tmm) cc_final: 0.7203 (ttp) outliers start: 45 outliers final: 24 residues processed: 228 average time/residue: 0.3137 time to fit residues: 114.9474 Evaluate side-chains 200 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain E residue 302 PHE Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 132 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 117 optimal weight: 30.0000 chunk 164 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 260 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 70 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 557 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21424 Z= 0.278 Angle : 0.594 12.844 28938 Z= 0.311 Chirality : 0.047 0.169 3218 Planarity : 0.004 0.059 3694 Dihedral : 6.490 179.230 2940 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer: Outliers : 1.74 % Allowed : 14.35 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2692 helix: 0.21 (0.16), residues: 1058 sheet: 0.36 (0.31), residues: 272 loop : -1.09 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 302 HIS 0.009 0.001 HIS D 95 PHE 0.016 0.001 PHE B 315 TYR 0.014 0.001 TYR D 175 ARG 0.006 0.000 ARG B 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASN cc_start: 0.8049 (t0) cc_final: 0.7698 (t0) REVERT: A 130 ASN cc_start: 0.7358 (p0) cc_final: 0.7097 (p0) REVERT: A 186 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: A 489 ASP cc_start: 0.7112 (t0) cc_final: 0.6763 (t0) REVERT: C 140 VAL cc_start: 0.7911 (t) cc_final: 0.7706 (p) REVERT: D 214 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.6678 (m-10) REVERT: D 252 MET cc_start: 0.7460 (tmm) cc_final: 0.6987 (ttp) REVERT: D 273 MET cc_start: 0.8247 (tpt) cc_final: 0.7957 (tpt) REVERT: D 415 THR cc_start: 0.8693 (m) cc_final: 0.8445 (t) REVERT: E 205 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.6499 (t80) outliers start: 39 outliers final: 25 residues processed: 223 average time/residue: 0.3090 time to fit residues: 110.9474 Evaluate side-chains 209 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 205 PHE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 302 PHE Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 508 ILE Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 132 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS ** B 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 HIS E 550 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 21424 Z= 0.398 Angle : 0.642 10.105 28938 Z= 0.334 Chirality : 0.051 0.230 3218 Planarity : 0.005 0.058 3694 Dihedral : 6.578 178.198 2940 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.61 % Favored : 94.28 % Rotamer: Outliers : 2.41 % Allowed : 16.09 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.68 (0.16), residues: 2692 helix: 0.22 (0.16), residues: 1064 sheet: 0.22 (0.31), residues: 272 loop : -1.12 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 302 HIS 0.011 0.001 HIS D 95 PHE 0.023 0.002 PHE B 315 TYR 0.021 0.002 TYR A 113 ARG 0.003 0.000 ARG E 495 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: A 130 ASN cc_start: 0.7439 (p0) cc_final: 0.7195 (p0) REVERT: A 186 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7636 (tp30) REVERT: A 382 MET cc_start: 0.7735 (mmp) cc_final: 0.7335 (mtp) REVERT: A 489 ASP cc_start: 0.7136 (t0) cc_final: 0.6818 (t0) REVERT: D 214 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.6716 (m-10) REVERT: D 215 GLU cc_start: 0.7526 (pm20) cc_final: 0.6874 (pm20) REVERT: D 252 MET cc_start: 0.7525 (tmm) cc_final: 0.7048 (ttp) REVERT: D 273 MET cc_start: 0.8251 (tpt) cc_final: 0.7906 (tpt) REVERT: D 415 THR cc_start: 0.8756 (m) cc_final: 0.8555 (t) outliers start: 54 outliers final: 38 residues processed: 217 average time/residue: 0.2984 time to fit residues: 105.1733 Evaluate side-chains 210 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 302 PHE Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 508 ILE Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 132 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 153 optimal weight: 0.4980 chunk 64 optimal weight: 20.0000 chunk 261 optimal weight: 0.3980 chunk 216 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 137 optimal weight: 0.0970 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN B 129 HIS ** B 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 HIS F 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21424 Z= 0.191 Angle : 0.544 9.176 28938 Z= 0.282 Chirality : 0.044 0.188 3218 Planarity : 0.004 0.061 3694 Dihedral : 6.278 178.460 2940 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.94 % Favored : 95.95 % Rotamer: Outliers : 2.32 % Allowed : 16.44 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: -0.39 (0.16), residues: 2692 helix: 0.53 (0.17), residues: 1060 sheet: 0.38 (0.31), residues: 274 loop : -1.01 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 302 HIS 0.005 0.001 HIS D 95 PHE 0.013 0.001 PHE F 51 TYR 0.012 0.001 TYR A 140 ARG 0.004 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.7305 (p0) cc_final: 0.7067 (p0) REVERT: A 489 ASP cc_start: 0.7057 (t0) cc_final: 0.6740 (t0) REVERT: D 215 GLU cc_start: 0.7454 (pm20) cc_final: 0.7224 (pm20) REVERT: D 252 MET cc_start: 0.7421 (tmm) cc_final: 0.7070 (ttp) REVERT: D 273 MET cc_start: 0.8192 (tpt) cc_final: 0.7918 (tpt) REVERT: D 415 THR cc_start: 0.8669 (m) cc_final: 0.8413 (t) REVERT: E 472 MET cc_start: 0.7108 (mmm) cc_final: 0.6829 (mmm) outliers start: 52 outliers final: 31 residues processed: 233 average time/residue: 0.3048 time to fit residues: 114.8538 Evaluate side-chains 210 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 302 PHE Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 0.5980 chunk 29 optimal weight: 0.0170 chunk 148 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 260 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS ** B 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 HIS E 278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21424 Z= 0.185 Angle : 0.539 8.426 28938 Z= 0.279 Chirality : 0.044 0.168 3218 Planarity : 0.004 0.059 3694 Dihedral : 6.213 177.821 2940 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.64 % Favored : 95.25 % Rotamer: Outliers : 2.09 % Allowed : 17.47 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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 (0.17), residues: 2692 helix: 0.61 (0.17), residues: 1066 sheet: 0.50 (0.31), residues: 274 loop : -0.92 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 302 HIS 0.005 0.001 HIS D 95 PHE 0.013 0.001 PHE F 51 TYR 0.013 0.001 TYR A 140 ARG 0.004 0.000 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.6949 (m-80) REVERT: A 130 ASN cc_start: 0.7357 (p0) cc_final: 0.7105 (p0) REVERT: A 186 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7532 (tp30) REVERT: A 489 ASP cc_start: 0.7079 (t0) cc_final: 0.6715 (t0) REVERT: D 7 THR cc_start: 0.7363 (OUTLIER) cc_final: 0.6958 (p) REVERT: D 215 GLU cc_start: 0.7411 (pm20) cc_final: 0.7163 (pm20) REVERT: D 252 MET cc_start: 0.7407 (tmm) cc_final: 0.6992 (ttp) REVERT: D 273 MET cc_start: 0.8198 (tpt) cc_final: 0.7837 (tpt) REVERT: D 415 THR cc_start: 0.8647 (m) cc_final: 0.8392 (t) REVERT: E 245 ASP cc_start: 0.7349 (p0) cc_final: 0.6750 (p0) REVERT: E 472 MET cc_start: 0.7100 (mmm) cc_final: 0.6822 (mmm) REVERT: F 90 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8715 (t) outliers start: 47 outliers final: 33 residues processed: 232 average time/residue: 0.3012 time to fit residues: 113.8614 Evaluate side-chains 216 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 155 optimal weight: 0.4980 chunk 78 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 177 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 204 optimal weight: 20.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN ** B 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 129 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21424 Z= 0.172 Angle : 0.540 8.728 28938 Z= 0.279 Chirality : 0.043 0.180 3218 Planarity : 0.004 0.054 3694 Dihedral : 6.139 176.968 2940 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.35 % Favored : 95.54 % Rotamer: Outliers : 2.18 % Allowed : 17.56 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: -0.13 (0.17), residues: 2692 helix: 0.75 (0.17), residues: 1052 sheet: 0.57 (0.32), residues: 274 loop : -0.87 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 302 HIS 0.004 0.001 HIS D 95 PHE 0.011 0.001 PHE F 51 TYR 0.012 0.001 TYR A 140 ARG 0.003 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.6973 (m-80) REVERT: A 130 ASN cc_start: 0.7286 (p0) cc_final: 0.7035 (p0) REVERT: A 186 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7519 (tp30) REVERT: A 489 ASP cc_start: 0.7073 (t0) cc_final: 0.6751 (t0) REVERT: D 7 THR cc_start: 0.7413 (OUTLIER) cc_final: 0.7013 (p) REVERT: D 215 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7163 (pm20) REVERT: D 252 MET cc_start: 0.7358 (tmm) cc_final: 0.6966 (ttp) REVERT: D 273 MET cc_start: 0.8146 (tpt) cc_final: 0.7760 (tpt) REVERT: D 415 THR cc_start: 0.8623 (m) cc_final: 0.8366 (t) REVERT: E 245 ASP cc_start: 0.7328 (p0) cc_final: 0.6735 (p0) REVERT: E 472 MET cc_start: 0.7013 (mmm) cc_final: 0.6768 (mmm) outliers start: 49 outliers final: 37 residues processed: 223 average time/residue: 0.3001 time to fit residues: 108.6362 Evaluate side-chains 215 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 539 THR Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 138 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 9.9990 chunk 249 optimal weight: 20.0000 chunk 227 optimal weight: 4.9990 chunk 242 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 219 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 chunk 241 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS B 550 HIS ** B 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21424 Z= 0.323 Angle : 0.609 8.817 28938 Z= 0.315 Chirality : 0.047 0.179 3218 Planarity : 0.004 0.054 3694 Dihedral : 6.363 179.693 2940 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.53 % Favored : 94.35 % Rotamer: Outliers : 2.36 % Allowed : 17.87 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.24 (0.17), residues: 2692 helix: 0.69 (0.17), residues: 1050 sheet: 0.42 (0.32), residues: 274 loop : -0.94 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 302 HIS 0.009 0.001 HIS D 95 PHE 0.019 0.001 PHE B 315 TYR 0.017 0.001 TYR A 113 ARG 0.003 0.000 ARG E 495 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.7008 (m-80) REVERT: A 130 ASN cc_start: 0.7402 (p0) cc_final: 0.7163 (p0) REVERT: A 186 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: A 382 MET cc_start: 0.7348 (mtp) cc_final: 0.7136 (mtp) REVERT: A 489 ASP cc_start: 0.7094 (t0) cc_final: 0.6782 (t0) REVERT: D 7 THR cc_start: 0.7427 (OUTLIER) cc_final: 0.7012 (p) REVERT: D 215 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: D 252 MET cc_start: 0.7478 (tmm) cc_final: 0.7054 (ttp) REVERT: D 273 MET cc_start: 0.8179 (tpt) cc_final: 0.7949 (tpt) REVERT: E 245 ASP cc_start: 0.7392 (p0) cc_final: 0.6795 (p0) REVERT: E 472 MET cc_start: 0.7422 (mmm) cc_final: 0.7104 (mmt) outliers start: 53 outliers final: 44 residues processed: 216 average time/residue: 0.2961 time to fit residues: 106.0746 Evaluate side-chains 215 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 508 ILE Chi-restraints excluded: chain E residue 539 THR Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 10.0000 chunk 256 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 247 optimal weight: 0.0870 chunk 214 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS ** B 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21424 Z= 0.196 Angle : 0.567 12.109 28938 Z= 0.290 Chirality : 0.044 0.184 3218 Planarity : 0.004 0.053 3694 Dihedral : 6.210 177.696 2940 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.38 % Favored : 95.51 % Rotamer: Outliers : 1.92 % Allowed : 18.36 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: -0.10 (0.17), residues: 2692 helix: 0.80 (0.17), residues: 1052 sheet: 0.52 (0.32), residues: 274 loop : -0.87 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 347 HIS 0.005 0.001 HIS D 95 PHE 0.011 0.001 PHE F 51 TYR 0.012 0.001 TYR A 140 ARG 0.004 0.000 ARG C 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.6989 (m-80) REVERT: A 130 ASN cc_start: 0.7303 (p0) cc_final: 0.7047 (p0) REVERT: A 186 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7498 (tp30) REVERT: A 489 ASP cc_start: 0.7090 (t0) cc_final: 0.6720 (t0) REVERT: D 7 THR cc_start: 0.7432 (OUTLIER) cc_final: 0.7031 (p) REVERT: D 215 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7154 (pm20) REVERT: D 252 MET cc_start: 0.7391 (tmm) cc_final: 0.6981 (ttp) REVERT: E 245 ASP cc_start: 0.7370 (p0) cc_final: 0.6769 (p0) REVERT: E 472 MET cc_start: 0.7115 (mmm) cc_final: 0.6841 (mmm) outliers start: 43 outliers final: 39 residues processed: 214 average time/residue: 0.3105 time to fit residues: 108.5155 Evaluate side-chains 222 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 572 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 138 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 0.0170 chunk 228 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 197 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 220 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 0.0040 overall best weight: 0.4430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.169158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.113763 restraints weight = 29252.015| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.43 r_work: 0.3230 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21424 Z= 0.134 Angle : 0.536 11.595 28938 Z= 0.273 Chirality : 0.042 0.160 3218 Planarity : 0.004 0.057 3694 Dihedral : 6.046 174.589 2940 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.20 % Favored : 95.73 % Rotamer: Outliers : 1.20 % Allowed : 19.16 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.84 % 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: 0.08 (0.17), residues: 2692 helix: 0.95 (0.17), residues: 1052 sheet: 0.72 (0.32), residues: 274 loop : -0.79 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 347 HIS 0.004 0.000 HIS F 75 PHE 0.009 0.001 PHE B 482 TYR 0.015 0.001 TYR A 310 ARG 0.005 0.000 ARG C 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4005.82 seconds wall clock time: 74 minutes 9.52 seconds (4449.52 seconds total)