Starting phenix.real_space_refine on Wed May 21 04:50:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bew_16011/05_2025/8bew_16011.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bew_16011/05_2025/8bew_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/cci-nas-00/data/ceres_data/8bew_16011/05_2025/8bew_16011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bew_16011/05_2025/8bew_16011.map" model { file = "/net/cci-nas-00/data/ceres_data/8bew_16011/05_2025/8bew_16011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bew_16011/05_2025/8bew_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-5687/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: 12.72, per 1000 atoms: 0.61 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: 4.62 Conformation dependent library (CDL) restraints added in 2.8 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: 2.94 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: 7.29 Time building geometry restraints manager: 5.43 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=" C4 FMN B 701 " pdb=" C4A FMN B 701 " ideal model delta sigma weight residual 1.485 1.382 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C4 FMN E 701 " pdb=" C4A FMN E 701 " ideal model delta sigma weight residual 1.485 1.389 0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C4A FMN B 701 " pdb=" N5 FMN B 701 " ideal model delta sigma weight residual 1.300 1.375 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C4A FMN E 701 " pdb=" N5 FMN E 701 " ideal model delta sigma weight residual 1.300 1.368 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O5' FMN B 701 " pdb=" P FMN B 701 " ideal model delta sigma weight residual 1.676 1.609 0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 21419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 28269 2.17 - 4.33: 564 4.33 - 6.50: 76 6.50 - 8.66: 20 8.66 - 10.83: 9 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 - 17.98: 11695 17.98 - 35.96: 1083 35.96 - 53.93: 179 53.93 - 71.91: 28 71.91 - 89.89: 29 Dihedral angle restraints: 13014 sinusoidal: 5342 harmonic: 7672 Sorted by residual: 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 dihedral pdb=" CA GLY B 313 " pdb=" C GLY B 313 " pdb=" N ALA B 314 " pdb=" CA ALA B 314 " ideal model delta harmonic sigma weight residual -180.00 -155.19 -24.81 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA GLY F 58 " pdb=" C GLY F 58 " pdb=" N ILE F 59 " pdb=" CA ILE F 59 " ideal model delta harmonic sigma weight residual -180.00 -157.55 -22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 13011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2418 0.052 - 0.105: 678 0.105 - 0.157: 106 0.157 - 0.209: 12 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: 3696 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 3693 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: 0.05 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 54.380 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.910 ------------------------------------------------------------------------------- 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 : 0.004 0.103 21508 Z= 0.182 Angle : 1.168 38.036 29135 Z= 0.426 Chirality : 0.048 0.262 3218 Planarity : 0.005 0.066 3696 Dihedral : 14.403 89.889 8126 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 Details of bonding type rmsd hydrogen bonds : bond 0.18013 ( 765) hydrogen bonds : angle 6.37403 ( 2142) metal coordination : bond 0.01097 ( 83) metal coordination : angle 10.79099 ( 197) covalent geometry : bond 0.00377 (21424) covalent geometry : angle 0.76253 (28938) Misc. bond : bond 0.00534 ( 1) *********************** 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 : 2.368 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: 0.3138 time to fit residues: 131.9967 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 : 2.192 ------------------------------------------------------------------------------- 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: 0.8980 chunk 204 optimal weight: 0.0270 chunk 113 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 211 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.173724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.120013 restraints weight = 29297.137| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.86 r_work: 0.3264 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21508 Z= 0.103 Angle : 1.001 37.981 29135 Z= 0.293 Chirality : 0.043 0.171 3218 Planarity : 0.004 0.062 3696 Dihedral : 4.399 57.686 2944 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.86 % Favored : 95.99 % Rotamer: Outliers : 0.80 % Allowed : 7.49 % Favored : 91.71 % 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: -0.54 (0.16), residues: 2692 helix: 0.11 (0.16), residues: 1066 sheet: 0.59 (0.31), residues: 288 loop : -0.91 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 347 HIS 0.004 0.001 HIS F 37 PHE 0.019 0.001 PHE A 490 TYR 0.017 0.001 TYR C 52 ARG 0.005 0.000 ARG C 79 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 765) hydrogen bonds : angle 4.76389 ( 2142) metal coordination : bond 0.00936 ( 83) metal coordination : angle 10.28149 ( 197) covalent geometry : bond 0.00224 (21424) covalent geometry : angle 0.53693 (28938) Misc. bond : bond 0.00290 ( 1) *********************** 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 247 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 229 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8384 (p0) cc_final: 0.8147 (p0) REVERT: A 489 ASP cc_start: 0.8825 (t0) cc_final: 0.8494 (t0) REVERT: B 230 GLU cc_start: 0.7506 (pt0) cc_final: 0.7095 (pt0) REVERT: D 71 MET cc_start: 0.7480 (ptp) cc_final: 0.7260 (ptp) REVERT: D 89 GLU cc_start: 0.7428 (tt0) cc_final: 0.7161 (tt0) REVERT: D 118 ASN cc_start: 0.8775 (t0) cc_final: 0.8405 (t0) REVERT: D 360 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8619 (tm-30) REVERT: E 92 MET cc_start: 0.7729 (tpp) cc_final: 0.7446 (tpp) REVERT: E 190 ASP cc_start: 0.7516 (m-30) cc_final: 0.7144 (m-30) REVERT: E 285 GLU cc_start: 0.8766 (tp30) cc_final: 0.8376 (mt-10) REVERT: E 472 MET cc_start: 0.7217 (mmm) cc_final: 0.6694 (mmm) REVERT: F 134 LEU cc_start: 0.8414 (tp) cc_final: 0.8122 (tp) REVERT: F 139 MET cc_start: 0.6128 (ttp) cc_final: 0.5685 (tmm) outliers start: 18 outliers final: 11 residues processed: 237 average time/residue: 0.2953 time to fit residues: 111.3437 Evaluate side-chains 203 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 2.224 ------------------------------------------------------------------------------- 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 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 D residue 215 GLU Chi-restraints excluded: chain E residue 302 PHE Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain F residue 48 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 102 optimal weight: 0.0670 chunk 88 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 210 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 233 optimal weight: 10.0000 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 421 ASN B 621 ASN E 83 GLN E 227 ASN ** E 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 ASN E 605 HIS E 621 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.170485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116053 restraints weight = 29206.373| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.90 r_work: 0.3185 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21508 Z= 0.148 Angle : 1.045 37.213 29135 Z= 0.296 Chirality : 0.045 0.161 3218 Planarity : 0.004 0.064 3696 Dihedral : 4.278 50.631 2944 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.46 % Favored : 95.43 % Rotamer: Outliers : 1.34 % Allowed : 10.61 % Favored : 88.06 % 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: -0.29 (0.16), residues: 2692 helix: 0.41 (0.17), residues: 1054 sheet: 0.70 (0.32), residues: 284 loop : -0.84 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 302 HIS 0.006 0.001 HIS D 95 PHE 0.016 0.001 PHE D 44 TYR 0.013 0.001 TYR A 310 ARG 0.007 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 765) hydrogen bonds : angle 4.49143 ( 2142) metal coordination : bond 0.01202 ( 83) metal coordination : angle 10.91420 ( 197) covalent geometry : bond 0.00354 (21424) covalent geometry : angle 0.53762 (28938) Misc. bond : bond 0.00433 ( 1) *********************** 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: 30 poor density : 215 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.8357 (p0) cc_final: 0.8067 (p0) REVERT: A 166 ASP cc_start: 0.8034 (t0) cc_final: 0.7760 (t0) REVERT: A 489 ASP cc_start: 0.8827 (t0) cc_final: 0.8529 (t0) REVERT: B 230 GLU cc_start: 0.7466 (pt0) cc_final: 0.7164 (pt0) REVERT: B 237 MET cc_start: 0.9079 (pmm) cc_final: 0.8849 (pmm) REVERT: D 157 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8036 (mm-30) REVERT: D 158 GLU cc_start: 0.8424 (tp30) cc_final: 0.8058 (tm-30) REVERT: D 166 ASP cc_start: 0.7877 (t0) cc_final: 0.7542 (t0) REVERT: D 273 MET cc_start: 0.7484 (tpt) cc_final: 0.7088 (tpt) REVERT: E 157 CYS cc_start: 0.8256 (t) cc_final: 0.7466 (t) REVERT: E 472 MET cc_start: 0.7508 (mmm) cc_final: 0.7061 (mmt) REVERT: F 134 LEU cc_start: 0.8328 (tp) cc_final: 0.7973 (tp) outliers start: 30 outliers final: 19 residues processed: 231 average time/residue: 0.2916 time to fit residues: 108.9251 Evaluate side-chains 212 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 CYS 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 192 VAL 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 94 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 148 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 257 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 chunk 136 optimal weight: 0.1980 chunk 44 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 205 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN B 481 ASN B 550 HIS ** B 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 HIS E 83 GLN E 129 HIS E 278 GLN E 342 ASN E 558 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.165426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.109998 restraints weight = 29161.184| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.74 r_work: 0.3147 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 21508 Z= 0.252 Angle : 1.259 39.212 29135 Z= 0.346 Chirality : 0.051 0.238 3218 Planarity : 0.005 0.061 3696 Dihedral : 4.657 41.676 2944 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.57 % Favored : 94.32 % Rotamer: Outliers : 2.01 % Allowed : 13.41 % Favored : 84.58 % 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: -0.44 (0.16), residues: 2692 helix: 0.31 (0.16), residues: 1068 sheet: 0.62 (0.32), residues: 272 loop : -0.94 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 302 HIS 0.014 0.001 HIS D 95 PHE 0.025 0.002 PHE B 315 TYR 0.022 0.002 TYR A 113 ARG 0.005 0.001 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 765) hydrogen bonds : angle 4.57641 ( 2142) metal coordination : bond 0.02175 ( 83) metal coordination : angle 13.25630 ( 197) covalent geometry : bond 0.00615 (21424) covalent geometry : angle 0.63124 (28938) Misc. bond : bond 0.00683 ( 1) *********************** 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 247 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8220 (tt) REVERT: A 100 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: A 118 ASN cc_start: 0.8875 (t0) cc_final: 0.8543 (t0) REVERT: A 130 ASN cc_start: 0.8413 (p0) cc_final: 0.8156 (p0) REVERT: A 186 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8351 (tp30) REVERT: A 489 ASP cc_start: 0.8828 (t0) cc_final: 0.8470 (t0) REVERT: B 230 GLU cc_start: 0.7594 (pt0) cc_final: 0.7105 (pt0) REVERT: B 237 MET cc_start: 0.8990 (pmm) cc_final: 0.8413 (pmm) REVERT: C 75 HIS cc_start: 0.6729 (m90) cc_final: 0.6169 (m170) REVERT: D 11 LYS cc_start: 0.5570 (mtpp) cc_final: 0.5293 (mtpt) REVERT: D 158 GLU cc_start: 0.8326 (tp30) cc_final: 0.8037 (tm-30) REVERT: D 166 ASP cc_start: 0.8064 (t0) cc_final: 0.7822 (t0) REVERT: D 215 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: D 419 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8357 (ptm) REVERT: E 157 CYS cc_start: 0.8401 (t) cc_final: 0.8085 (t) REVERT: E 181 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7099 (mp) REVERT: E 245 ASP cc_start: 0.8161 (p0) cc_final: 0.7928 (p0) REVERT: E 275 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7711 (tp) REVERT: F 134 LEU cc_start: 0.8515 (tp) cc_final: 0.8056 (tp) outliers start: 45 outliers final: 26 residues processed: 227 average time/residue: 0.3012 time to fit residues: 110.2827 Evaluate side-chains 218 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 2.329 ------------------------------------------------------------------------------- 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 186 GLU Chi-restraints excluded: chain A residue 298 CYS 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 192 VAL Chi-restraints excluded: chain B residue 262 SER 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 215 GLU Chi-restraints excluded: chain D residue 275 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 181 LEU Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 156 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 212 optimal weight: 0.4980 chunk 204 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 116 optimal weight: 40.0000 chunk 154 optimal weight: 0.7980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS B 481 ASN ** B 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.165701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.110746 restraints weight = 28301.532| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.28 r_work: 0.3168 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21508 Z= 0.130 Angle : 1.068 37.238 29135 Z= 0.292 Chirality : 0.044 0.175 3218 Planarity : 0.004 0.060 3696 Dihedral : 4.292 37.058 2944 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.09 % Favored : 95.80 % Rotamer: Outliers : 1.43 % Allowed : 15.29 % Favored : 83.29 % 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 (0.16), residues: 2692 helix: 0.50 (0.17), residues: 1072 sheet: 0.67 (0.32), residues: 274 loop : -0.86 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 302 HIS 0.006 0.001 HIS D 95 PHE 0.014 0.001 PHE F 51 TYR 0.012 0.001 TYR F 82 ARG 0.004 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 765) hydrogen bonds : angle 4.33492 ( 2142) metal coordination : bond 0.01147 ( 83) metal coordination : angle 11.29120 ( 197) covalent geometry : bond 0.00311 (21424) covalent geometry : angle 0.53035 (28938) Misc. bond : bond 0.00365 ( 1) *********************** 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 231 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 MET cc_start: 0.8030 (tpt) cc_final: 0.7811 (tpt) REVERT: A 118 ASN cc_start: 0.8808 (t0) cc_final: 0.8428 (t0) REVERT: A 130 ASN cc_start: 0.8158 (p0) cc_final: 0.7872 (p0) REVERT: A 166 ASP cc_start: 0.7839 (t0) cc_final: 0.7605 (t0) REVERT: A 382 MET cc_start: 0.7686 (mmp) cc_final: 0.7442 (mtm) REVERT: A 489 ASP cc_start: 0.8754 (t0) cc_final: 0.8423 (t0) REVERT: B 230 GLU cc_start: 0.7516 (pt0) cc_final: 0.6908 (pt0) REVERT: B 237 MET cc_start: 0.9062 (pmm) cc_final: 0.8487 (pmm) REVERT: C 75 HIS cc_start: 0.6589 (m90) cc_final: 0.6074 (m170) REVERT: D 157 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7720 (mm-30) REVERT: D 158 GLU cc_start: 0.8318 (tp30) cc_final: 0.8040 (tm-30) REVERT: D 273 MET cc_start: 0.7815 (tpt) cc_final: 0.7364 (tpt) REVERT: D 275 ILE cc_start: 0.7277 (mm) cc_final: 0.7042 (tt) REVERT: E 54 ARG cc_start: 0.6717 (mtm110) cc_final: 0.6484 (mtm110) REVERT: E 92 MET cc_start: 0.7962 (tpp) cc_final: 0.7532 (tpp) REVERT: E 157 CYS cc_start: 0.8385 (t) cc_final: 0.8123 (t) REVERT: E 181 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6867 (mp) REVERT: E 190 ASP cc_start: 0.7364 (m-30) cc_final: 0.6988 (m-30) REVERT: E 245 ASP cc_start: 0.8119 (p0) cc_final: 0.7877 (p0) REVERT: E 279 MET cc_start: 0.8888 (mtp) cc_final: 0.8435 (mtt) REVERT: E 333 MET cc_start: 0.8711 (mmm) cc_final: 0.8366 (mtm) REVERT: E 472 MET cc_start: 0.7747 (mmm) cc_final: 0.7437 (mmm) REVERT: F 134 LEU cc_start: 0.8497 (tp) cc_final: 0.8084 (tp) REVERT: F 138 VAL cc_start: 0.7211 (t) cc_final: 0.6998 (p) REVERT: F 139 MET cc_start: 0.6725 (ttp) cc_final: 0.6000 (tmm) outliers start: 32 outliers final: 22 residues processed: 217 average time/residue: 0.3029 time to fit residues: 105.9865 Evaluate side-chains 212 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 12 ASN 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 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 279 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain F residue 15 GLU 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 169 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 114 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 93 optimal weight: 0.0040 chunk 70 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 overall best weight: 2.4596 ------------------------------------------------------------------------------- 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 ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.164879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109992 restraints weight = 28420.412| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.29 r_work: 0.3143 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21508 Z= 0.159 Angle : 1.086 37.060 29135 Z= 0.300 Chirality : 0.045 0.216 3218 Planarity : 0.004 0.055 3696 Dihedral : 4.277 34.473 2944 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.87 % Favored : 95.02 % Rotamer: Outliers : 2.01 % Allowed : 15.46 % Favored : 82.53 % 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: -0.20 (0.17), residues: 2692 helix: 0.59 (0.17), residues: 1060 sheet: 0.66 (0.32), residues: 274 loop : -0.86 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 302 HIS 0.008 0.001 HIS D 95 PHE 0.036 0.001 PHE E 302 TYR 0.014 0.001 TYR A 310 ARG 0.003 0.000 ARG C 79 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 765) hydrogen bonds : angle 4.27760 ( 2142) metal coordination : bond 0.01300 ( 83) metal coordination : angle 11.41828 ( 197) covalent geometry : bond 0.00383 (21424) covalent geometry : angle 0.54780 (28938) Misc. bond : bond 0.00435 ( 1) *********************** 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 240 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 MET cc_start: 0.8022 (tpt) cc_final: 0.7760 (tpt) REVERT: A 100 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: A 118 ASN cc_start: 0.8855 (t0) cc_final: 0.8459 (t0) REVERT: A 130 ASN cc_start: 0.8226 (p0) cc_final: 0.7952 (p0) REVERT: A 489 ASP cc_start: 0.8780 (t0) cc_final: 0.8458 (t0) REVERT: B 230 GLU cc_start: 0.7614 (pt0) cc_final: 0.7007 (pt0) REVERT: B 237 MET cc_start: 0.9066 (pmm) cc_final: 0.8460 (pmm) REVERT: B 279 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8327 (mtt) REVERT: C 75 HIS cc_start: 0.6787 (m90) cc_final: 0.6353 (m170) REVERT: D 7 THR cc_start: 0.7920 (OUTLIER) cc_final: 0.7665 (p) REVERT: D 11 LYS cc_start: 0.5634 (mtpp) cc_final: 0.5401 (mtpt) REVERT: D 49 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9152 (tt) REVERT: D 158 GLU cc_start: 0.8313 (tp30) cc_final: 0.8031 (tm-30) REVERT: D 214 TYR cc_start: 0.6703 (OUTLIER) cc_final: 0.5694 (m-10) REVERT: D 275 ILE cc_start: 0.7310 (mm) cc_final: 0.7083 (tt) REVERT: E 54 ARG cc_start: 0.6773 (mtm110) cc_final: 0.6537 (mtm110) REVERT: E 92 MET cc_start: 0.8126 (tpp) cc_final: 0.7810 (tpp) REVERT: E 157 CYS cc_start: 0.8391 (t) cc_final: 0.8122 (t) REVERT: E 190 ASP cc_start: 0.7378 (m-30) cc_final: 0.7016 (m-30) REVERT: E 205 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.6543 (t80) REVERT: E 245 ASP cc_start: 0.8105 (p0) cc_final: 0.7884 (p0) REVERT: E 333 MET cc_start: 0.8761 (mmm) cc_final: 0.8409 (mtm) REVERT: E 472 MET cc_start: 0.7862 (mmm) cc_final: 0.7575 (mmt) REVERT: F 134 LEU cc_start: 0.8512 (tp) cc_final: 0.8093 (tp) REVERT: F 138 VAL cc_start: 0.7194 (t) cc_final: 0.6981 (p) REVERT: F 139 MET cc_start: 0.6691 (ttp) cc_final: 0.5921 (tmm) outliers start: 45 outliers final: 29 residues processed: 223 average time/residue: 0.3050 time to fit residues: 109.1117 Evaluate side-chains 222 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 2.331 ------------------------------------------------------------------------------- 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 298 CYS 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 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 49 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 214 TYR 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 205 PHE Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 396 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 220 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 147 optimal weight: 0.5980 chunk 208 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS B 481 ASN ** B 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 HIS ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.163141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108373 restraints weight = 28249.054| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.26 r_work: 0.3143 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 21508 Z= 0.224 Angle : 1.227 39.500 29135 Z= 0.335 Chirality : 0.049 0.208 3218 Planarity : 0.004 0.056 3696 Dihedral : 4.515 34.624 2944 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.27 % Favored : 94.61 % Rotamer: Outliers : 2.76 % Allowed : 15.51 % Favored : 81.73 % 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: -0.33 (0.16), residues: 2692 helix: 0.51 (0.16), residues: 1064 sheet: 0.50 (0.31), residues: 274 loop : -0.94 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 302 HIS 0.012 0.001 HIS D 95 PHE 0.027 0.002 PHE F 42 TYR 0.020 0.002 TYR A 113 ARG 0.004 0.000 ARG C 79 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 765) hydrogen bonds : angle 4.43314 ( 2142) metal coordination : bond 0.01793 ( 83) metal coordination : angle 12.95013 ( 197) covalent geometry : bond 0.00545 (21424) covalent geometry : angle 0.61171 (28938) Misc. bond : bond 0.00596 ( 1) *********************** 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 249 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 187 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 MET cc_start: 0.8061 (tpt) cc_final: 0.7772 (tpt) REVERT: A 100 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: A 118 ASN cc_start: 0.8838 (t0) cc_final: 0.8415 (t0) REVERT: A 130 ASN cc_start: 0.8215 (p0) cc_final: 0.7950 (p0) REVERT: A 186 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8367 (tp30) REVERT: A 419 MET cc_start: 0.8308 (tpp) cc_final: 0.8003 (tpp) REVERT: A 489 ASP cc_start: 0.8765 (t0) cc_final: 0.8422 (t0) REVERT: A 544 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: B 230 GLU cc_start: 0.7643 (pt0) cc_final: 0.7301 (pt0) REVERT: B 237 MET cc_start: 0.8985 (pmm) cc_final: 0.8299 (pmm) REVERT: B 279 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8274 (mtt) REVERT: C 75 HIS cc_start: 0.6791 (m90) cc_final: 0.6316 (m170) REVERT: C 153 VAL cc_start: 0.6307 (t) cc_final: 0.6029 (t) REVERT: D 7 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7640 (p) REVERT: D 158 GLU cc_start: 0.8338 (tp30) cc_final: 0.8042 (tm-30) REVERT: D 214 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.5869 (m-10) REVERT: E 54 ARG cc_start: 0.6858 (mtm110) cc_final: 0.6612 (mtm110) REVERT: E 157 CYS cc_start: 0.8452 (t) cc_final: 0.8252 (t) REVERT: E 190 ASP cc_start: 0.7429 (m-30) cc_final: 0.7071 (m-30) REVERT: E 245 ASP cc_start: 0.8190 (p0) cc_final: 0.7971 (p0) REVERT: E 472 MET cc_start: 0.8068 (mmm) cc_final: 0.7761 (mmt) REVERT: F 134 LEU cc_start: 0.8561 (tp) cc_final: 0.8144 (tp) REVERT: F 139 MET cc_start: 0.6802 (ttp) cc_final: 0.5970 (tmm) outliers start: 62 outliers final: 39 residues processed: 234 average time/residue: 0.2845 time to fit residues: 108.2367 Evaluate side-chains 220 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 298 CYS 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 A residue 544 TYR 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 262 SER Chi-restraints excluded: chain B residue 279 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 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 352 MET Chi-restraints excluded: chain D residue 392 LYS 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 508 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 119 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 263 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 231 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 F 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.162001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.107179 restraints weight = 28582.329| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.81 r_work: 0.3093 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 21508 Z= 0.269 Angle : 1.316 41.934 29135 Z= 0.356 Chirality : 0.052 0.256 3218 Planarity : 0.005 0.058 3696 Dihedral : 4.662 36.585 2944 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.68 % Favored : 94.21 % Rotamer: Outliers : 2.54 % Allowed : 16.27 % Favored : 81.19 % 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: -0.48 (0.16), residues: 2692 helix: 0.40 (0.16), residues: 1064 sheet: 0.33 (0.31), residues: 274 loop : -1.01 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 302 HIS 0.014 0.001 HIS D 95 PHE 0.024 0.002 PHE B 315 TYR 0.023 0.002 TYR A 113 ARG 0.004 0.001 ARG C 85 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 765) hydrogen bonds : angle 4.54454 ( 2142) metal coordination : bond 0.02059 ( 83) metal coordination : angle 13.92095 ( 197) covalent geometry : bond 0.00656 (21424) covalent geometry : angle 0.65188 (28938) Misc. bond : bond 0.00589 ( 1) *********************** 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 239 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 182 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7727 (t70) cc_final: 0.7507 (t0) REVERT: A 100 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.7285 (m-80) REVERT: A 118 ASN cc_start: 0.8894 (t0) cc_final: 0.8483 (t0) REVERT: A 130 ASN cc_start: 0.8273 (p0) cc_final: 0.8014 (p0) REVERT: A 186 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8469 (tp30) REVERT: A 277 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7510 (tp30) REVERT: A 489 ASP cc_start: 0.8844 (t0) cc_final: 0.8466 (t0) REVERT: B 88 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6610 (tp40) REVERT: B 93 THR cc_start: 0.7571 (m) cc_final: 0.7205 (p) REVERT: B 230 GLU cc_start: 0.7613 (pt0) cc_final: 0.7343 (pt0) REVERT: B 237 MET cc_start: 0.8917 (pmm) cc_final: 0.8680 (pmm) REVERT: B 279 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8267 (mtt) REVERT: C 75 HIS cc_start: 0.6913 (m90) cc_final: 0.6447 (m170) REVERT: D 7 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7676 (p) REVERT: D 158 GLU cc_start: 0.8437 (tp30) cc_final: 0.8138 (tm-30) REVERT: D 214 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.5943 (m-10) REVERT: E 54 ARG cc_start: 0.6862 (mtm110) cc_final: 0.6620 (mtm110) REVERT: E 157 CYS cc_start: 0.8492 (t) cc_final: 0.8241 (t) REVERT: E 190 ASP cc_start: 0.7425 (m-30) cc_final: 0.7068 (m-30) REVERT: E 245 ASP cc_start: 0.8189 (p0) cc_final: 0.7975 (p0) REVERT: E 472 MET cc_start: 0.8136 (mmm) cc_final: 0.7854 (mmt) REVERT: F 134 LEU cc_start: 0.8551 (tp) cc_final: 0.8125 (tp) REVERT: F 139 MET cc_start: 0.6801 (ttp) cc_final: 0.5959 (tmm) outliers start: 57 outliers final: 43 residues processed: 227 average time/residue: 0.2856 time to fit residues: 104.9202 Evaluate side-chains 220 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 298 CYS 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 88 GLN Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 279 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 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 306 VAL Chi-restraints excluded: chain D residue 352 MET 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 181 LEU 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 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 115 THR Chi-restraints excluded: chain F residue 132 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 193 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 224 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 90 optimal weight: 0.2980 chunk 57 optimal weight: 20.0000 chunk 192 optimal weight: 30.0000 chunk 121 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.165452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.111157 restraints weight = 28211.946| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.23 r_work: 0.3185 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21508 Z= 0.111 Angle : 1.061 36.777 29135 Z= 0.295 Chirality : 0.044 0.181 3218 Planarity : 0.004 0.053 3696 Dihedral : 4.249 27.987 2944 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.20 % Favored : 95.73 % Rotamer: Outliers : 1.92 % Allowed : 16.93 % Favored : 81.15 % 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: -0.18 (0.16), residues: 2692 helix: 0.72 (0.17), residues: 1050 sheet: 0.52 (0.31), residues: 274 loop : -0.91 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 372 HIS 0.005 0.001 HIS F 75 PHE 0.023 0.001 PHE E 302 TYR 0.013 0.001 TYR D 427 ARG 0.003 0.000 ARG C 85 Details of bonding type rmsd hydrogen bonds : bond 0.03297 ( 765) hydrogen bonds : angle 4.28072 ( 2142) metal coordination : bond 0.01035 ( 83) metal coordination : angle 11.08302 ( 197) covalent geometry : bond 0.00260 (21424) covalent geometry : angle 0.54419 (28938) Misc. bond : bond 0.00325 ( 1) *********************** 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: 43 poor density : 186 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 MET cc_start: 0.8209 (tpt) cc_final: 0.7738 (tpp) REVERT: A 100 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7260 (m-80) REVERT: A 118 ASN cc_start: 0.8852 (t0) cc_final: 0.8437 (t0) REVERT: A 130 ASN cc_start: 0.8169 (p0) cc_final: 0.7914 (p0) REVERT: A 186 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8307 (tp30) REVERT: A 206 GLU cc_start: 0.8000 (mm-30) cc_final: 0.6387 (pt0) REVERT: A 489 ASP cc_start: 0.8756 (t0) cc_final: 0.8404 (t0) REVERT: B 93 THR cc_start: 0.7522 (m) cc_final: 0.7162 (p) REVERT: B 230 GLU cc_start: 0.7472 (pt0) cc_final: 0.7252 (pt0) REVERT: B 237 MET cc_start: 0.8961 (pmm) cc_final: 0.8748 (pmm) REVERT: B 279 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8275 (mtt) REVERT: C 75 HIS cc_start: 0.6865 (m90) cc_final: 0.6427 (m170) REVERT: D 158 GLU cc_start: 0.8286 (tp30) cc_final: 0.8066 (tm-30) REVERT: D 214 TYR cc_start: 0.6716 (OUTLIER) cc_final: 0.5802 (m-10) REVERT: D 275 ILE cc_start: 0.7340 (mm) cc_final: 0.7097 (tt) REVERT: E 54 ARG cc_start: 0.6905 (mtm110) cc_final: 0.6663 (mtm110) REVERT: E 100 PHE cc_start: 0.7088 (t80) cc_final: 0.6737 (t80) REVERT: E 157 CYS cc_start: 0.8450 (t) cc_final: 0.8129 (t) REVERT: E 190 ASP cc_start: 0.7428 (m-30) cc_final: 0.7079 (m-30) REVERT: E 333 MET cc_start: 0.8761 (mmm) cc_final: 0.8426 (mtm) REVERT: E 472 MET cc_start: 0.7770 (mmm) cc_final: 0.7533 (mmm) REVERT: F 134 LEU cc_start: 0.8570 (tp) cc_final: 0.8151 (tp) REVERT: F 139 MET cc_start: 0.6727 (ttp) cc_final: 0.6001 (tmm) outliers start: 43 outliers final: 36 residues processed: 217 average time/residue: 0.2852 time to fit residues: 100.0494 Evaluate side-chains 215 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 2.242 ------------------------------------------------------------------------------- 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 298 CYS 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 262 SER 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 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 13 VAL Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 214 TYR Chi-restraints excluded: chain D residue 352 MET 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 181 LEU Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 344 CYS 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 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 132 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 116 optimal weight: 7.9990 chunk 267 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 195 optimal weight: 20.0000 chunk 244 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 243 optimal weight: 8.9990 chunk 204 optimal weight: 20.0000 chunk 265 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.162722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108095 restraints weight = 28454.391| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.22 r_work: 0.3138 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 21508 Z= 0.235 Angle : 1.237 40.582 29135 Z= 0.340 Chirality : 0.049 0.219 3218 Planarity : 0.004 0.056 3696 Dihedral : 4.499 34.081 2944 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.09 % Rotamer: Outliers : 2.14 % Allowed : 16.93 % Favored : 80.93 % 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: -0.31 (0.16), residues: 2692 helix: 0.63 (0.16), residues: 1052 sheet: 0.36 (0.31), residues: 274 loop : -0.98 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 302 HIS 0.013 0.001 HIS D 95 PHE 0.021 0.002 PHE B 315 TYR 0.020 0.002 TYR A 113 ARG 0.004 0.000 ARG C 85 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 765) hydrogen bonds : angle 4.43667 ( 2142) metal coordination : bond 0.01828 ( 83) metal coordination : angle 12.99088 ( 197) covalent geometry : bond 0.00572 (21424) covalent geometry : angle 0.62625 (28938) Misc. bond : bond 0.00560 ( 1) ********************** 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 224 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 MET cc_start: 0.8119 (tpt) cc_final: 0.7657 (tpp) REVERT: A 38 ASP cc_start: 0.7704 (t70) cc_final: 0.7492 (t0) REVERT: A 100 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: A 130 ASN cc_start: 0.8207 (p0) cc_final: 0.7950 (p0) REVERT: A 186 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8397 (tp30) REVERT: A 277 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7484 (tp30) REVERT: A 489 ASP cc_start: 0.8756 (t0) cc_final: 0.8384 (t0) REVERT: B 93 THR cc_start: 0.7569 (m) cc_final: 0.7201 (p) REVERT: B 230 GLU cc_start: 0.7673 (pt0) cc_final: 0.7463 (pt0) REVERT: B 237 MET cc_start: 0.8915 (pmm) cc_final: 0.8711 (pmm) REVERT: B 279 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8331 (mtt) REVERT: C 75 HIS cc_start: 0.6903 (m90) cc_final: 0.6481 (m170) REVERT: D 7 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7677 (p) REVERT: D 158 GLU cc_start: 0.8323 (tp30) cc_final: 0.8009 (tm-30) REVERT: D 214 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.5971 (m-10) REVERT: D 275 ILE cc_start: 0.7442 (mm) cc_final: 0.7220 (tt) REVERT: E 54 ARG cc_start: 0.6905 (mtm110) cc_final: 0.6667 (mtm110) REVERT: E 157 CYS cc_start: 0.8507 (t) cc_final: 0.8294 (t) REVERT: E 190 ASP cc_start: 0.7411 (m-30) cc_final: 0.7050 (m-30) REVERT: E 245 ASP cc_start: 0.8288 (p0) cc_final: 0.8066 (p0) REVERT: E 472 MET cc_start: 0.8115 (mmm) cc_final: 0.7767 (mmm) REVERT: F 134 LEU cc_start: 0.8605 (tp) cc_final: 0.8181 (tp) REVERT: F 139 MET cc_start: 0.6587 (ttp) cc_final: 0.5977 (tmm) outliers start: 48 outliers final: 38 residues processed: 213 average time/residue: 0.3040 time to fit residues: 105.8052 Evaluate side-chains 211 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 2.549 ------------------------------------------------------------------------------- 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 298 CYS 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 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 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 352 MET 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 344 CYS 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 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 115 THR Chi-restraints excluded: chain F residue 132 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 12 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 154 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.165919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111741 restraints weight = 28400.781| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.27 r_work: 0.3188 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21508 Z= 0.114 Angle : 1.042 36.011 29135 Z= 0.294 Chirality : 0.043 0.176 3218 Planarity : 0.004 0.053 3696 Dihedral : 4.168 27.973 2944 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.05 % Favored : 95.88 % Rotamer: Outliers : 1.74 % Allowed : 17.42 % Favored : 80.84 % 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: 0.81 (0.17), residues: 1054 sheet: 0.52 (0.31), residues: 274 loop : -0.87 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 372 HIS 0.004 0.001 HIS D 95 PHE 0.022 0.001 PHE E 302 TYR 0.011 0.001 TYR A 140 ARG 0.004 0.000 ARG C 85 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 765) hydrogen bonds : angle 4.23351 ( 2142) metal coordination : bond 0.01099 ( 83) metal coordination : angle 10.81416 ( 197) covalent geometry : bond 0.00268 (21424) covalent geometry : angle 0.54427 (28938) Misc. bond : bond 0.00287 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10794.60 seconds wall clock time: 187 minutes 14.46 seconds (11234.46 seconds total)